feed.xml

<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="4.0.0">Jekyll</generator><link href="https://galaxyproject.eu/feed.xml" rel="self" type="application/atom+xml" /><link href="https://galaxyproject.eu/" rel="alternate" type="text/html" /><updated>2024-12-25T02:47:19+01:00</updated><id>https://galaxyproject.eu/feed.xml</id><title type="html">Galaxy Europe</title><subtitle>The European Galaxy Instance</subtitle><entry><title type="html">UseGalaxy.eu Tool Updates for 2024-12-22</title><link href="https://galaxyproject.eu/posts/2024/12/22/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2024-12-22" /><published>2024-12-22T00:00:00+01:00</published><updated>2024-12-22T00:00:00+01:00</updated><id>https://galaxyproject.eu/posts/2024/12/22/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2024/12/22/tool-update/">&lt;p&gt;On 2024-12-22, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in &lt;a href=&quot;https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#492/&quot;&gt;Jenkins Build #492&lt;/a&gt;&lt;/p&gt;

&lt;h2 id=&quot;annotation&quot;&gt;Annotation&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;augustus was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/augustus/0fc0f9cf035a&quot;&gt;0fc0f9cf035a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;augustus_training was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/augustus_training/aada0deea587&quot;&gt;aada0deea587&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;glimmer_build_icm was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/glimmer_build_icm/e903e26c014d&quot;&gt;e903e26c014d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;glimmer_knowledge_based was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/glimmer_knowledge_based/21d0af260f11&quot;&gt;21d0af260f11&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;glimmer_not_knowledge_based was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/glimmer_not_knowledge_based/75cedbd8cf1b&quot;&gt;75cedbd8cf1b&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;tetyper was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/tetyper/2b21643ce8d7&quot;&gt;2b21643ce8d7&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ectyper was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/nml/ectyper/daba54cd25ca&quot;&gt;daba54cd25ca&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;sistr_cmd was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/nml/sistr_cmd/cf767360ede1&quot;&gt;cf767360ede1&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;compute-indicators-for-turnover-boulders-fields&quot;&gt;Compute indicators for turnover boulders fields&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;cb_dissim was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/cb_dissim/ffaa9a71b2d2&quot;&gt;ffaa9a71b2d2&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;metagenomic-analysis&quot;&gt;Metagenomic Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;phyloseq_plot_bar was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_plot_bar/ad81e112f4d9&quot;&gt;ad81e112f4d9&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;staramr was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/nml/staramr/3548a93b39c1&quot;&gt;3548a93b39c1&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;checkv_build_database was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ufz/checkv_build_database/7e80c69020f7&quot;&gt;7e80c69020f7&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;data-managers&quot;&gt;Data Managers&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;genomad_build_database was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ufz/genomad_build_database/75abfb03b635&quot;&gt;75abfb03b635&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;vibrant_build_database was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ufz/vibrant_build_database/e0faddfd9cf9&quot;&gt;e0faddfd9cf9&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;virsorter_build_database was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ufz/virsorter_build_database/c456ae8354f2&quot;&gt;c456ae8354f2&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;qiime-2&quot;&gt;QIIME 2&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2&quot;&gt;2572fc0f88f2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623&quot;&gt;b883cbea5623&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;convert-formats&quot;&gt;Convert Formats&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;glimmer_glimmer_to_gff was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/glimmer_glimmer_to_gff/3d71ab1562d7&quot;&gt;3d71ab1562d7&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;graphdisplay-data&quot;&gt;Graph/Display Data&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;jbrowse2 was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/fubar/jbrowse2/21bb464c1d53&quot;&gt;21bb464c1d53&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;metabolomics&quot;&gt;Metabolomics&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;xcms_xcmsset was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/lecorguille/xcms_xcmsset/3bd53dcfa438&quot;&gt;3bd53dcfa438&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;genome-diversity&quot;&gt;Genome Diversity&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;fasttree was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fasttree/bc939965ce41&quot;&gt;bc939965ce41&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;variant-calling&quot;&gt;Variant Calling&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;bcftools_csq was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_csq/33df4e68959b&quot;&gt;33df4e68959b&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;none&quot;&gt;None&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;data_manager_diamond_database_builder was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78&quot;&gt;4a08b7b76b78&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</content><author><name></name></author><category term="tools" /><summary type="html">On 2024-12-22, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #492</summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2024-12-15</title><link href="https://galaxyproject.eu/posts/2024/12/15/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2024-12-15" /><published>2024-12-15T00:00:00+01:00</published><updated>2024-12-15T00:00:00+01:00</updated><id>https://galaxyproject.eu/posts/2024/12/15/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2024/12/15/tool-update/">&lt;p&gt;On 2024-12-15, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in &lt;a href=&quot;https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#491/&quot;&gt;Jenkins Build #491&lt;/a&gt;&lt;/p&gt;

&lt;h2 id=&quot;graphdisplay-data&quot;&gt;Graph/Display Data&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;pygenometracks was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/pygenometracks/59fd173ac850&quot;&gt;59fd173ac850&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;volcanoplot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/volcanoplot/99ace6c1ff57&quot;&gt;99ace6c1ff57&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;qiime-2&quot;&gt;QIIME 2&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2&quot;&gt;2572fc0f88f2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623&quot;&gt;b883cbea5623&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;proteomics&quot;&gt;Proteomics&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;fragpipe was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/galaxyp/fragpipe/e969a182e3cb&quot;&gt;e969a182e3cb&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;proteinortho was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/proteinortho/6140163233a5&quot;&gt;6140163233a5&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;proteinortho_grab_proteins was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/proteinortho_grab_proteins/36dffb2bc194&quot;&gt;36dffb2bc194&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;proteinortho_summary was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/proteinortho_summary/387d3633cade&quot;&gt;387d3633cade&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;get-data&quot;&gt;Get Data&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;uniprotxml_downloader was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/galaxyp/uniprotxml_downloader/4ddc8da62671&quot;&gt;4ddc8da62671&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;fastafastq&quot;&gt;FASTA/FASTQ&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;gfastats was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/gfastats/764f2516d837&quot;&gt;764f2516d837&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;text-manipulation&quot;&gt;Text Manipulation&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;diff was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/diff/10ef1bf99074&quot;&gt;10ef1bf99074&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;none&quot;&gt;None&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;data_manager_build_kraken2_database was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_build_kraken2_database/8c533e19b697&quot;&gt;8c533e19b697&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;data_manager_diamond_database_builder was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78&quot;&gt;4a08b7b76b78&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;data_manager_ncbi_fcs_gx_database_downloader was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_ncbi_fcs_gx_database_downloader/6be6e6198ac3&quot;&gt;6be6e6198ac3&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;genome-diversity&quot;&gt;Genome Diversity&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;fasttree was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fasttree/ef46a404db96&quot;&gt;ef46a404db96&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;metagenomic-analysis&quot;&gt;Metagenomic Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;decontam was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/decontam/3f238ab9d200&quot;&gt;3f238ab9d200&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;mothur&quot;&gt;Mothur&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;mothur_get_lineage was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/mothur_get_lineage/d1abc038d4bd&quot;&gt;d1abc038d4bd&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;variant-calling&quot;&gt;Variant Calling&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;cnvkit_access was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_access/25bba7640b06&quot;&gt;25bba7640b06&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_antitarget was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_antitarget/dd54b5c36317&quot;&gt;dd54b5c36317&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_autobin was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_autobin/505e6bbaee59&quot;&gt;505e6bbaee59&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_batch was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_batch/97d2b6742760&quot;&gt;97d2b6742760&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_breaks was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_breaks/384fa596e5d9&quot;&gt;384fa596e5d9&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_call was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_call/978ddcbedd60&quot;&gt;978ddcbedd60&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_coverage was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_coverage/5699301a3bd1&quot;&gt;5699301a3bd1&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_diagram was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_diagram/27ecb3477d34&quot;&gt;27ecb3477d34&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_fix was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_fix/49ecf6b6f9f4&quot;&gt;49ecf6b6f9f4&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_genemetrics was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_genemetrics/3e1d74c9e715&quot;&gt;3e1d74c9e715&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_heatmap was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_heatmap/26554a14f841&quot;&gt;26554a14f841&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_reference was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_reference/b45fa373a972&quot;&gt;b45fa373a972&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_scatter was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_scatter/02446206f574&quot;&gt;02446206f574&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_segment was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_segment/33be231ce128&quot;&gt;33be231ce128&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_segmetrics was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_segmetrics/86392285203a&quot;&gt;86392285203a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_sex was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_sex/0b34f56003dc&quot;&gt;0b34f56003dc&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_target was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_target/428b93a3acb4&quot;&gt;428b93a3acb4&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</content><author><name></name></author><category term="tools" /><summary type="html">On 2024-12-15, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #491</summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2024-12-08</title><link href="https://galaxyproject.eu/posts/2024/12/08/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2024-12-08" /><published>2024-12-08T00:00:00+01:00</published><updated>2024-12-08T00:00:00+01:00</updated><id>https://galaxyproject.eu/posts/2024/12/08/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2024/12/08/tool-update/">&lt;p&gt;On 2024-12-08, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in &lt;a href=&quot;https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#490/&quot;&gt;Jenkins Build #490&lt;/a&gt;&lt;/p&gt;

&lt;h2 id=&quot;climate-analysis&quot;&gt;Climate Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;harmonize_insitu_to_netcdf was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/harmonize_insitu_to_netcdf/15260949227d&quot;&gt;15260949227d&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;qiime-2&quot;&gt;QIIME 2&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2&quot;&gt;2572fc0f88f2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623&quot;&gt;b883cbea5623&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;mapping&quot;&gt;Mapping&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;rgrnastar was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/rgrnastar/53255f6eecfc&quot;&gt;53255f6eecfc&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;rna_starsolo was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/rna_starsolo/381a32c51141&quot;&gt;381a32c51141&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;convert-formats&quot;&gt;Convert Formats&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;msconvert was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/galaxyp/msconvert/ab6c14374bc0&quot;&gt;ab6c14374bc0&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;assembly&quot;&gt;Assembly&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;flye was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/flye/cd11366d92cf&quot;&gt;cd11366d92cf&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;fastk_fastk was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fastk_fastk/8049cb5537b7&quot;&gt;8049cb5537b7&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;machine-learning&quot;&gt;Machine Learning&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;black_forest_labs_flux was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/black_forest_labs_flux/7939ae8c5fd5&quot;&gt;7939ae8c5fd5&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;evolution&quot;&gt;Evolution&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;quicktree was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/quicktree/1e89a460d1bd&quot;&gt;1e89a460d1bd&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;genome-diversity&quot;&gt;Genome Diversity&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;fasttree was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fasttree/ef46a404db96&quot;&gt;ef46a404db96&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;hicexplorer&quot;&gt;HiCExplorer&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;hicexplorer_chicaggregatestatistic was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicaggregatestatistic/c3ffb2c1e314&quot;&gt;c3ffb2c1e314&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_chicdifferentialtest was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicdifferentialtest/45828071edc3&quot;&gt;45828071edc3&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_chicexportdata was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicexportdata/1a31e75e979e&quot;&gt;1a31e75e979e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_chicplotviewpoint was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicplotviewpoint/920526260066&quot;&gt;920526260066&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_chicqualitycontrol was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicqualitycontrol/f6a169b5e43b&quot;&gt;f6a169b5e43b&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_chicsignificantinteractions was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicsignificantinteractions/ff1af7bac1cb&quot;&gt;ff1af7bac1cb&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_chicviewpoint was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicviewpoint/37125838e360&quot;&gt;37125838e360&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_chicviewpointbackgroundmodel was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicviewpointbackgroundmodel/6f8debcf2ac9&quot;&gt;6f8debcf2ac9&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicadjustmatrix was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicadjustmatrix/e8760fc0e29b&quot;&gt;e8760fc0e29b&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicaggregatecontacts was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicaggregatecontacts/30677e95bc89&quot;&gt;30677e95bc89&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicaverageregions was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicaverageregions/3240e8a7c54f&quot;&gt;3240e8a7c54f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicbuildmatrix was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicbuildmatrix/d9967770de96&quot;&gt;d9967770de96&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hiccomparematrices was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hiccomparematrices/5dd1aae12f03&quot;&gt;5dd1aae12f03&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hiccompartmentspolarization was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hiccompartmentspolarization/87eb9c58cd19&quot;&gt;87eb9c58cd19&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicconvertformat was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicconvertformat/574f295b5ba4&quot;&gt;574f295b5ba4&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hiccorrectmatrix was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hiccorrectmatrix/937b7b9832d0&quot;&gt;937b7b9832d0&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hiccorrelate was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hiccorrelate/0f5786ffa10d&quot;&gt;0f5786ffa10d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicdetectloops was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicdetectloops/4375e25de06a&quot;&gt;4375e25de06a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicdifferentialtad was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicdifferentialtad/4977f65da0ff&quot;&gt;4977f65da0ff&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicfindrestrictionsites was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicfindrestrictionsites/f0b1bd38745a&quot;&gt;f0b1bd38745a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicfindtads was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicfindtads/478aacfbaa37&quot;&gt;478aacfbaa37&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hichyperoptdetectloops was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hichyperoptdetectloops/3e5c86c2f80d&quot;&gt;3e5c86c2f80d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicinfo was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicinfo/7fbd6feba1ca&quot;&gt;7fbd6feba1ca&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicinterintratad was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicinterintratad/908fa330b93b&quot;&gt;908fa330b93b&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicmergedomains was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicmergedomains/febfddb0b3e8&quot;&gt;febfddb0b3e8&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicmergeloops was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicmergeloops/1d9799f4b854&quot;&gt;1d9799f4b854&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicmergematrixbins was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicmergematrixbins/9d93c8fbe0a6&quot;&gt;9d93c8fbe0a6&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicnormalize was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicnormalize/5e83c077e31d&quot;&gt;5e83c077e31d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicpca was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicpca/f86ca478c6af&quot;&gt;f86ca478c6af&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicplotaverageregions was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotaverageregions/3f1b286a5c34&quot;&gt;3f1b286a5c34&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicplotdistvscounts was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotdistvscounts/89cfe7de541b&quot;&gt;89cfe7de541b&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicplotmatrix was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotmatrix/025a128652dc&quot;&gt;025a128652dc&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicplotsvl was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotsvl/1602cc5b673c&quot;&gt;1602cc5b673c&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicplotviewpoint was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotviewpoint/a10fce08c2dc&quot;&gt;a10fce08c2dc&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicquickqc was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicquickqc/b13e7a200525&quot;&gt;b13e7a200525&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicsummatrices was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicsummatrices/d74cf4a61d65&quot;&gt;d74cf4a61d65&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hictransform was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hictransform/df64cc4dfb4d&quot;&gt;df64cc4dfb4d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicvalidatelocations was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicvalidatelocations/d890828ab02a&quot;&gt;d890828ab02a&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;metagenomic-analysis&quot;&gt;Metagenomic Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;concoct_merge_cut_up_clustering was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/concoct_merge_cut_up_clustering/713189575b8b&quot;&gt;713189575b8b&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;dada2_assigntaxonomyaddspecies was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/dada2_assigntaxonomyaddspecies/3a89c3f99f3d&quot;&gt;3a89c3f99f3d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;dada2_primercheck was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/dada2_primercheck/74ec28dbdf17&quot;&gt;74ec28dbdf17&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;dada2_removebimeradenovo was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/dada2_removebimeradenovo/1770d188f72d&quot;&gt;1770d188f72d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;phyloseq_from_biom was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_from_biom/1feea247d08a&quot;&gt;1feea247d08a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;phyloseq_from_dada2 was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_from_dada2/40ebae5bbe51&quot;&gt;40ebae5bbe51&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;phyloseq_plot_ordination was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_plot_ordination/c35e0075c7a2&quot;&gt;c35e0075c7a2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;phyloseq_plot_richness was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_plot_richness/1a6c2cc92c6e&quot;&gt;1a6c2cc92c6e&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;variant-calling&quot;&gt;Variant Calling&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;ucsc_fatovcf was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ucsc_fatovcf/a40dd4fd3096&quot;&gt;a40dd4fd3096&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;none&quot;&gt;None&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;data_manager_diamond_database_builder was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78&quot;&gt;4a08b7b76b78&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;data_manager_mapseq was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_mapseq/19ef193d1316&quot;&gt;19ef193d1316&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;hca_sc_scanpy_tools&quot;&gt;hca_sc_scanpy_tools&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;scanpy_find_variable_genes was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_find_variable_genes/d88a29e2eba6&quot;&gt;d88a29e2eba6&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</content><author><name></name></author><category term="tools" /><summary type="html">On 2024-12-08, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #490</summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2024-12-01</title><link href="https://galaxyproject.eu/posts/2024/12/01/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2024-12-01" /><published>2024-12-01T00:00:00+01:00</published><updated>2024-12-01T00:00:00+01:00</updated><id>https://galaxyproject.eu/posts/2024/12/01/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2024/12/01/tool-update/">&lt;p&gt;On 2024-12-01, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in &lt;a href=&quot;https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#489/&quot;&gt;Jenkins Build #489&lt;/a&gt;&lt;/p&gt;

&lt;h2 id=&quot;qiime-2&quot;&gt;QIIME 2&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2&quot;&gt;2572fc0f88f2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623&quot;&gt;b883cbea5623&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;gemini&quot;&gt;Gemini&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;gemini_fusions was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/gemini_fusions/8a68d9a33023&quot;&gt;8a68d9a33023&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;annotation&quot;&gt;Annotation&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;groot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/groot/c15e34e39e09&quot;&gt;c15e34e39e09&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;genome-diversity&quot;&gt;Genome Diversity&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;fasttree was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fasttree/ef46a404db96&quot;&gt;ef46a404db96&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;rna-analysis&quot;&gt;RNA Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;sfold was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/sfold/6cce721f568c&quot;&gt;6cce721f568c&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;variant-calling&quot;&gt;Variant Calling&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;bcftools_consensus was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_consensus/147de996e34f&quot;&gt;147de996e34f&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;none&quot;&gt;None&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;data_manager_diamond_database_builder was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78&quot;&gt;4a08b7b76b78&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;hca_sc_label_analysis_tools&quot;&gt;hca_sc_label_analysis_tools&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;decoupler_pseudobulk was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ebi-gxa/decoupler_pseudobulk/09c833d9b03b&quot;&gt;09c833d9b03b&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</content><author><name></name></author><category term="tools" /><summary type="html">On 2024-12-01, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #489</summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2024-11-24</title><link href="https://galaxyproject.eu/posts/2024/11/24/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2024-11-24" /><published>2024-11-24T00:00:00+01:00</published><updated>2024-11-24T00:00:00+01:00</updated><id>https://galaxyproject.eu/posts/2024/11/24/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2024/11/24/tool-update/">&lt;p&gt;On 2024-11-24, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in &lt;a href=&quot;https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#488/&quot;&gt;Jenkins Build #488&lt;/a&gt;&lt;/p&gt;

&lt;h2 id=&quot;get-data&quot;&gt;Get Data&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;copernicusmarine was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/copernicusmarine/c07f11d8e49a&quot;&gt;c07f11d8e49a&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;metagenomic-analysis&quot;&gt;Metagenomic Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;krakentools_alpha_diversity was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/krakentools_alpha_diversity/78b69342c280&quot;&gt;78b69342c280&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;krakentools_beta_diversity was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/krakentools_beta_diversity/4505d7643673&quot;&gt;4505d7643673&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;krakentools_combine_kreports was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/krakentools_combine_kreports/3d2cffa2c4ab&quot;&gt;3d2cffa2c4ab&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;krakentools_extract_kraken_reads was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/krakentools_extract_kraken_reads/4bf1e2701504&quot;&gt;4bf1e2701504&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;krakentools_kreport2krona was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/krakentools_kreport2krona/02bbace216f2&quot;&gt;02bbace216f2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;krakentools_kreport2mpa was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/krakentools_kreport2mpa/d33cf727ed94&quot;&gt;d33cf727ed94&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;checkv_build_database was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ufz/checkv_build_database/88042a5ead89&quot;&gt;88042a5ead89&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;data-managers&quot;&gt;Data Managers&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;genomad_build_database was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ufz/genomad_build_database/c4ec3d81eeee&quot;&gt;c4ec3d81eeee&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;vibrant_build_database was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ufz/vibrant_build_database/3f68072f2da6&quot;&gt;3f68072f2da6&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;virsorter_build_database was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ufz/virsorter_build_database/863ba94fb6e4&quot;&gt;863ba94fb6e4&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;qiime-2&quot;&gt;QIIME 2&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2&quot;&gt;2572fc0f88f2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623&quot;&gt;b883cbea5623&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;fetch_sequences___alignments&quot;&gt;fetch_sequences___alignments&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;extract_genomic_dna was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/extract_genomic_dna/80414c33a59a&quot;&gt;80414c33a59a&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;assembly&quot;&gt;Assembly&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;blobtoolkit was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/blobtoolkit/392811378515&quot;&gt;392811378515&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;abyss was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/abyss/db9b10824c61&quot;&gt;db9b10824c61&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;machine-learning&quot;&gt;Machine Learning&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;black_forest_labs_flux was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/black_forest_labs_flux/21ee409e6cde&quot;&gt;21ee409e6cde&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;imaging&quot;&gt;Imaging&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;cp_cellprofiler4 was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/cp_cellprofiler4/9799fc53433e&quot;&gt;9799fc53433e&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;fastafastq&quot;&gt;FASTA/FASTQ&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;bbtools_bbduk was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bbtools_bbduk/d58c27d2c5a7&quot;&gt;d58c27d2c5a7&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;bbtools_bbmerge was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bbtools_bbmerge/1bb2b5b52030&quot;&gt;1bb2b5b52030&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;bbtools_tadpole was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bbtools_tadpole/ce13b4678f18&quot;&gt;ce13b4678f18&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ncbi_fcs_gx was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ncbi_fcs_gx/32d058f3462a&quot;&gt;32d058f3462a&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;gemini&quot;&gt;Gemini&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;gemini_annotate was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/gemini_annotate/8da05bf2b1d1&quot;&gt;8da05bf2b1d1&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;genome-diversity&quot;&gt;Genome Diversity&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;fasttree was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fasttree/ef46a404db96&quot;&gt;ef46a404db96&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;mapping&quot;&gt;Mapping&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;bbtools_bbmap was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bbtools_bbmap/8015d7ab8357&quot;&gt;8015d7ab8357&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;multiple-alignments&quot;&gt;Multiple Alignments&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;trimal was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/trimal/e379c0202766&quot;&gt;e379c0202766&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;variant-calling&quot;&gt;Variant Calling&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;bbtools_callvariants was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bbtools_callvariants/3854db061e6e&quot;&gt;3854db061e6e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ensembl_vep was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ensembl_vep/c91e09b60325&quot;&gt;c91e09b60325&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;none&quot;&gt;None&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;data_manager_diamond_database_builder was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78&quot;&gt;4a08b7b76b78&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;rna-analysis&quot;&gt;RNA Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;infernal was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/infernal/3711f654044e&quot;&gt;3711f654044e&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</content><author><name></name></author><category term="tools" /><summary type="html">On 2024-11-24, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #488</summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2024-11-17</title><link href="https://galaxyproject.eu/posts/2024/11/17/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2024-11-17" /><published>2024-11-17T00:00:00+01:00</published><updated>2024-11-17T00:00:00+01:00</updated><id>https://galaxyproject.eu/posts/2024/11/17/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2024/11/17/tool-update/">&lt;p&gt;On 2024-11-17, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in &lt;a href=&quot;https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#487/&quot;&gt;Jenkins Build #487&lt;/a&gt;&lt;/p&gt;

&lt;h2 id=&quot;metabolomics&quot;&gt;Metabolomics&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;matchms_add_key was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/matchms_add_key/a5d41764722d&quot;&gt;a5d41764722d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;matchms_convert was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/matchms_convert/9e83636da9d3&quot;&gt;9e83636da9d3&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;matchms_filtering was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/matchms_filtering/83c4b4359ac4&quot;&gt;83c4b4359ac4&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;matchms_fingerprint_similarity was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/matchms_fingerprint_similarity/fd890f162ce6&quot;&gt;fd890f162ce6&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;matchms_formatter was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/matchms_formatter/a5a5b147da70&quot;&gt;a5a5b147da70&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;matchms_metadata_export was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/matchms_metadata_export/8832425b1ff6&quot;&gt;8832425b1ff6&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;matchms_metadata_match was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/matchms_metadata_match/330b0dfae8da&quot;&gt;330b0dfae8da&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;matchms_metadata_merge was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/matchms_metadata_merge/1fd950c5586a&quot;&gt;1fd950c5586a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;matchms_networking was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/matchms_networking/f04b378325e5&quot;&gt;f04b378325e5&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;matchms_remove_key was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/matchms_remove_key/fbdb2ae524df&quot;&gt;fbdb2ae524df&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;matchms_remove_spectra was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/matchms_remove_spectra/d50ce2f51fc0&quot;&gt;d50ce2f51fc0&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;matchms_spectral_similarity was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/matchms_spectral_similarity/7ba589b01dbc&quot;&gt;7ba589b01dbc&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;matchms_split was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/matchms_split/ea6c5636c0cf&quot;&gt;ea6c5636c0cf&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;matchms_subsetting was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/matchms_subsetting/5bbd1a8404f5&quot;&gt;5bbd1a8404f5&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;qiime-2&quot;&gt;QIIME 2&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2&quot;&gt;2572fc0f88f2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623&quot;&gt;b883cbea5623&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;machine-learning&quot;&gt;Machine Learning&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;sklearn_clf_metrics was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/sklearn_clf_metrics/15bcf1a7543b&quot;&gt;15bcf1a7543b&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;assembly&quot;&gt;Assembly&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;pretext_graph was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/pretext_graph/408ece2e4647&quot;&gt;408ece2e4647&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;pretext_map was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/pretext_map/511e5e3cd55e&quot;&gt;511e5e3cd55e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;pretext_map was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/pretext_map/c6cec5ab35c1&quot;&gt;c6cec5ab35c1&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;quast was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/quast/a3b35edea53a&quot;&gt;a3b35edea53a&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;annotation&quot;&gt;Annotation&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;tbprofiler was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/tbprofiler/8cb134b8c1a5&quot;&gt;8cb134b8c1a5&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;fastafastq&quot;&gt;FASTA/FASTQ&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;fastp was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fastp/a626e8c0e1ba&quot;&gt;a626e8c0e1ba&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;filter-and-sort&quot;&gt;Filter and Sort&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;bigwig_outlier_bed was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bigwig_outlier_bed/bae6cba73e32&quot;&gt;bae6cba73e32&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;genome-diversity&quot;&gt;Genome Diversity&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;fasttree was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fasttree/ef46a404db96&quot;&gt;ef46a404db96&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;get-data&quot;&gt;Get Data&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;fastq_dl was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fastq_dl/5e7401777990&quot;&gt;5e7401777990&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;graphdisplay-data&quot;&gt;Graph/Display Data&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;pretext_snapshot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/pretext_snapshot/26f2fe7e53a1&quot;&gt;26f2fe7e53a1&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;metagenomic-analysis&quot;&gt;Metagenomic Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;ampvis2_alpha_diversity was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_alpha_diversity/bd518ee51da5&quot;&gt;bd518ee51da5&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_boxplot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_boxplot/5e4e2b612a4f&quot;&gt;5e4e2b612a4f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_core was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_core/2bbf288d6334&quot;&gt;2bbf288d6334&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_core was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_core/e595eafb5ecf&quot;&gt;e595eafb5ecf&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_export_fasta was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_export_fasta/0cce683798d3&quot;&gt;0cce683798d3&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_export_fasta was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_export_fasta/3fd332f614f3&quot;&gt;3fd332f614f3&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_frequency was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_frequency/ac3774320d28&quot;&gt;ac3774320d28&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_heatmap was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_heatmap/c980e4bd48f2&quot;&gt;c980e4bd48f2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_load was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_load/576dd33588bf&quot;&gt;576dd33588bf&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_load was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_load/738474880da8&quot;&gt;738474880da8&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_merge_ampvis2 was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_merge_ampvis2/2f9731cc4c87&quot;&gt;2f9731cc4c87&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_merge_ampvis2 was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_merge_ampvis2/378ce300fb3d&quot;&gt;378ce300fb3d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_mergereplicates was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_mergereplicates/1f6f3bc6edd1&quot;&gt;1f6f3bc6edd1&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_mergereplicates was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_mergereplicates/f34ea612eecf&quot;&gt;f34ea612eecf&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_octave was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_octave/33087ecbd8f4&quot;&gt;33087ecbd8f4&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_ordinate was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_ordinate/7825694588d6&quot;&gt;7825694588d6&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_otu_network was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_otu_network/454bfdfa6de5&quot;&gt;454bfdfa6de5&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_otu_network was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_otu_network/bb054c50a96c&quot;&gt;bb054c50a96c&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_rankabundance was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_rankabundance/18de61c5527c&quot;&gt;18de61c5527c&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_rankabundance was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_rankabundance/cf0944377d87&quot;&gt;cf0944377d87&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_rarecurve was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_rarecurve/094d0b97f92c&quot;&gt;094d0b97f92c&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_setmetadata was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_setmetadata/a9dacd650ad5&quot;&gt;a9dacd650ad5&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_subset_samples was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_subset_samples/f9fa155c191f&quot;&gt;f9fa155c191f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_subset_samples was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_subset_samples/ff07f41b8e54&quot;&gt;ff07f41b8e54&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_subset_taxa was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_subset_taxa/76cb398e9110&quot;&gt;76cb398e9110&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_timeseries was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_timeseries/bd41251e42ec&quot;&gt;bd41251e42ec&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_venn was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_venn/bbb4a531d80b&quot;&gt;bbb4a531d80b&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_venn was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_venn/f28f2faad83b&quot;&gt;f28f2faad83b&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;polypolish was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/polypolish/915637bd1d1a&quot;&gt;915637bd1d1a&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;multiple-alignments&quot;&gt;Multiple Alignments&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;trimal was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/trimal/ebe28cac8d8b&quot;&gt;ebe28cac8d8b&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;phylogenetics&quot;&gt;Phylogenetics&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;hyphy_bgm was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/hyphy_bgm/a54340ea0866&quot;&gt;a54340ea0866&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;variant-calling&quot;&gt;Variant Calling&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;sniffles was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/sniffles/ceff2f6a5368&quot;&gt;ceff2f6a5368&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;virology&quot;&gt;Virology&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;freyja_aggregate_plot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/freyja_aggregate_plot/54acd5139cab&quot;&gt;54acd5139cab&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;freyja_boot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/freyja_boot/16331f8cff98&quot;&gt;16331f8cff98&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;freyja_demix was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/freyja_demix/c5f2ce99da69&quot;&gt;c5f2ce99da69&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;freyja_variants was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/freyja_variants/d17f930148a5&quot;&gt;d17f930148a5&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;snipit was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/snipit/877e80114d25&quot;&gt;877e80114d25&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;none&quot;&gt;None&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;data_manager_build_kraken2_database was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_build_kraken2_database/e9ee4d074d5d&quot;&gt;e9ee4d074d5d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;data_manager_diamond_database_builder was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78&quot;&gt;4a08b7b76b78&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;rna-analysis&quot;&gt;RNA Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;infernal was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/infernal/1d74ed49cf41&quot;&gt;1d74ed49cf41&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;xas-x-ray-absorption-spectroscopy&quot;&gt;XAS (X-ray Absorption Spectroscopy)&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;larch_artemis was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/muon-spectroscopy-computational-project/larch_artemis/e0407f36fcea&quot;&gt;e0407f36fcea&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;larch_athena was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/muon-spectroscopy-computational-project/larch_athena/6e94ae7d1ca1&quot;&gt;6e94ae7d1ca1&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;larch_criteria_report was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/muon-spectroscopy-computational-project/larch_criteria_report/aa9cb2b42741&quot;&gt;aa9cb2b42741&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;larch_feff was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/muon-spectroscopy-computational-project/larch_feff/8ee492af5586&quot;&gt;8ee492af5586&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;larch_lcf was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/muon-spectroscopy-computational-project/larch_lcf/90a69f15ab92&quot;&gt;90a69f15ab92&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;larch_plot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/muon-spectroscopy-computational-project/larch_plot/0339eb694129&quot;&gt;0339eb694129&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;larch_select_paths was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/muon-spectroscopy-computational-project/larch_select_paths/204c4afe2f1e&quot;&gt;204c4afe2f1e&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</content><author><name></name></author><category term="tools" /><summary type="html">On 2024-11-17, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #487</summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2024-11-10</title><link href="https://galaxyproject.eu/posts/2024/11/10/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2024-11-10" /><published>2024-11-10T00:00:00+01:00</published><updated>2024-11-10T00:00:00+01:00</updated><id>https://galaxyproject.eu/posts/2024/11/10/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2024/11/10/tool-update/">&lt;p&gt;On 2024-11-10, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in &lt;a href=&quot;https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#486/&quot;&gt;Jenkins Build #486&lt;/a&gt;&lt;/p&gt;

&lt;h2 id=&quot;get-data&quot;&gt;Get Data&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;obis_data was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/obis_data/5bae75c49f2e&quot;&gt;5bae75c49f2e&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;biodiversity-data-exploration&quot;&gt;Biodiversity data exploration&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;obisindicators was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/obisindicators/4e7c1fb5e894&quot;&gt;4e7c1fb5e894&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;obisindicators was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/obisindicators/dc187fe78055&quot;&gt;dc187fe78055&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;qiime-2&quot;&gt;QIIME 2&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2&quot;&gt;2572fc0f88f2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623&quot;&gt;b883cbea5623&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2_core__tools__import_fastq was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2_core__tools__import_fastq/1c3937219d27&quot;&gt;1c3937219d27&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;fastafastq&quot;&gt;FASTA/FASTQ&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;gfastats was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/gfastats/f4a3eff8ab85&quot;&gt;f4a3eff8ab85&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;seqkit_fx2tab was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/seqkit_fx2tab/2e60cd811bd2&quot;&gt;2e60cd811bd2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;seqkit_locate was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/seqkit_locate/95ef41cc06f7&quot;&gt;95ef41cc06f7&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;seqkit_sort was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/seqkit_sort/29ef2c5ec205&quot;&gt;29ef2c5ec205&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;seqkit_stats was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/seqkit_stats/795cd16de38f&quot;&gt;795cd16de38f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;seqkit_translate was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/seqkit_translate/1936d097808a&quot;&gt;1936d097808a&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;single-cell&quot;&gt;Single-cell&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;music_compare was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/music_compare/4447ed460308&quot;&gt;4447ed460308&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;music_compare was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/music_compare/d817b3807562&quot;&gt;d817b3807562&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;music_construct_eset was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/music_construct_eset/282819d09a4f&quot;&gt;282819d09a4f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;music_construct_eset was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/music_construct_eset/48f0fb3061b1&quot;&gt;48f0fb3061b1&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;music_deconvolution was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/music_deconvolution/2ba99a52bd44&quot;&gt;2ba99a52bd44&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;music_deconvolution was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/music_deconvolution/8cd2ecfa2e61&quot;&gt;8cd2ecfa2e61&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;music_inspect_eset was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/music_inspect_eset/7705cc75ac18&quot;&gt;7705cc75ac18&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;music_inspect_eset was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/music_inspect_eset/fde4c972e7c5&quot;&gt;fde4c972e7c5&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;music_manipulate_eset was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/music_manipulate_eset/22232092be53&quot;&gt;22232092be53&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;music_manipulate_eset was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/music_manipulate_eset/b5185a4f5209&quot;&gt;b5185a4f5209&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;anndata_export was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/anndata_export/7a6655aa6eb2&quot;&gt;7a6655aa6eb2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;anndata_import was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/anndata_import/6f143dfe902a&quot;&gt;6f143dfe902a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;anndata_inspect was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/anndata_inspect/14c576ea6148&quot;&gt;14c576ea6148&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;anndata_manipulate was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/anndata_manipulate/c4209ea387d4&quot;&gt;c4209ea387d4&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cosg was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cosg/fe5996e87b41&quot;&gt;fe5996e87b41&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;modify_loom was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/modify_loom/db575b4c8b22&quot;&gt;db575b4c8b22&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;raceid_clustering was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/raceid_clustering/49776718ae90&quot;&gt;49776718ae90&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;raceid_filtnormconf was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/raceid_filtnormconf/8b917923f7d4&quot;&gt;8b917923f7d4&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;raceid_inspectclusters was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/raceid_inspectclusters/c7ddb719554d&quot;&gt;c7ddb719554d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;raceid_inspecttrajectory was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/raceid_inspecttrajectory/6e90c8adf84f&quot;&gt;6e90c8adf84f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;raceid_trajectory was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/raceid_trajectory/2bfd55b87af3&quot;&gt;2bfd55b87af3&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;sceasy_convert was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/sceasy_convert/5c9b16bdbd5e&quot;&gt;5c9b16bdbd5e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;sinto_barcode was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/sinto_barcode/fb61eb03e313&quot;&gt;fb61eb03e313&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;sinto_fragments was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/sinto_fragments/6f66f523a9b7&quot;&gt;6f66f523a9b7&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;snapatac2_clustering was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/snapatac2_clustering/d3ea0ba3d066&quot;&gt;d3ea0ba3d066&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;snapatac2_peaks_and_motif was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/snapatac2_peaks_and_motif/64fa083411f1&quot;&gt;64fa083411f1&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;snapatac2_plotting was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/snapatac2_plotting/05bd4db20227&quot;&gt;05bd4db20227&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;snapatac2_preprocessing was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/snapatac2_preprocessing/c5c94e01a1b5&quot;&gt;c5c94e01a1b5&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;metabolomics&quot;&gt;Metabolomics&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;dimspy_hdf5_to_txt was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/computational-metabolomics/dimspy_hdf5_to_txt/ea439d85b6c5&quot;&gt;ea439d85b6c5&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;assembly&quot;&gt;Assembly&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;fastk_fastk was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fastk_fastk/9f8c786bd424&quot;&gt;9f8c786bd424&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;trycycler_cluster was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/trycycler_cluster/0368ac680e70&quot;&gt;0368ac680e70&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;trycycler_consensus was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/trycycler_consensus/a7ed21de23fe&quot;&gt;a7ed21de23fe&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;trycycler_partition was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/trycycler_partition/7673a6c920b2&quot;&gt;7673a6c920b2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;trycycler_reconcile_msa was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/trycycler_reconcile_msa/ed312479d9eb&quot;&gt;ed312479d9eb&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;trycycler_subsample was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/trycycler_subsample/b9b0246a2be3&quot;&gt;b9b0246a2be3&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;convert-formats&quot;&gt;Convert Formats&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;bam2fastx was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bam2fastx/0bfdf46e5e31&quot;&gt;0bfdf46e5e31&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ucsc_wigtobigwig was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ucsc_wigtobigwig/fa49730d1d4b&quot;&gt;fa49730d1d4b&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;genome-diversity&quot;&gt;Genome Diversity&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;fasttree was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fasttree/ef46a404db96&quot;&gt;ef46a404db96&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;hicexplorer&quot;&gt;HiCExplorer&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;hicexplorer_chicaggregatestatistic was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicaggregatestatistic/952abbc4b1de&quot;&gt;952abbc4b1de&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_chicdifferentialtest was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicdifferentialtest/f1c35f3f310d&quot;&gt;f1c35f3f310d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_chicexportdata was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicexportdata/cab616fe7e64&quot;&gt;cab616fe7e64&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_chicplotviewpoint was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicplotviewpoint/b9ab56aecd18&quot;&gt;b9ab56aecd18&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_chicqualitycontrol was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicqualitycontrol/9ea228a9afc8&quot;&gt;9ea228a9afc8&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_chicsignificantinteractions was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicsignificantinteractions/f8320df1866b&quot;&gt;f8320df1866b&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_chicviewpoint was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicviewpoint/c4ed35f4f77f&quot;&gt;c4ed35f4f77f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_chicviewpointbackgroundmodel was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicviewpointbackgroundmodel/c354255ff705&quot;&gt;c354255ff705&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicadjustmatrix was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicadjustmatrix/782bdcb775fb&quot;&gt;782bdcb775fb&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicaggregatecontacts was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicaggregatecontacts/63c8377c58b3&quot;&gt;63c8377c58b3&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicaverageregions was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicaverageregions/fe3aa71590d5&quot;&gt;fe3aa71590d5&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicbuildmatrix was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicbuildmatrix/0f611e7d7858&quot;&gt;0f611e7d7858&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hiccomparematrices was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hiccomparematrices/4f9305d3bb34&quot;&gt;4f9305d3bb34&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hiccompartmentspolarization was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hiccompartmentspolarization/a315574104c6&quot;&gt;a315574104c6&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicconvertformat was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicconvertformat/a83732c79949&quot;&gt;a83732c79949&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hiccorrectmatrix was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hiccorrectmatrix/30d7390bc918&quot;&gt;30d7390bc918&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hiccorrelate was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hiccorrelate/cd40ca76865a&quot;&gt;cd40ca76865a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicdetectloops was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicdetectloops/bf9379529c3e&quot;&gt;bf9379529c3e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicdifferentialtad was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicdifferentialtad/07dd436ea686&quot;&gt;07dd436ea686&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicfindrestrictionsites was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicfindrestrictionsites/f1b3902f8baf&quot;&gt;f1b3902f8baf&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicfindtads was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicfindtads/11de0d28ab30&quot;&gt;11de0d28ab30&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hichyperoptdetectloops was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hichyperoptdetectloops/bb8849fca57c&quot;&gt;bb8849fca57c&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicinfo was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicinfo/b0f33533181d&quot;&gt;b0f33533181d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicinterintratad was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicinterintratad/32173084d53f&quot;&gt;32173084d53f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicmergedomains was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicmergedomains/4b194e675916&quot;&gt;4b194e675916&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicmergeloops was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicmergeloops/910c6a1c3a27&quot;&gt;910c6a1c3a27&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicmergematrixbins was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicmergematrixbins/f72063d9426b&quot;&gt;f72063d9426b&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicnormalize was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicnormalize/2aa5b6b65197&quot;&gt;2aa5b6b65197&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicpca was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicpca/1da5f169b491&quot;&gt;1da5f169b491&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicplotaverageregions was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotaverageregions/9b383d429659&quot;&gt;9b383d429659&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicplotdistvscounts was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotdistvscounts/06ced663d24f&quot;&gt;06ced663d24f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicplotmatrix was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotmatrix/f741330d4a71&quot;&gt;f741330d4a71&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicplotsvl was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotsvl/beb5b5917d2f&quot;&gt;beb5b5917d2f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicplotviewpoint was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotviewpoint/e285920f8585&quot;&gt;e285920f8585&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicquickqc was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicquickqc/5cbd7a902a8d&quot;&gt;5cbd7a902a8d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicsummatrices was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicsummatrices/f81750434d70&quot;&gt;f81750434d70&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hictransform was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hictransform/1de2276f633f&quot;&gt;1de2276f633f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicvalidatelocations was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicvalidatelocations/cef9fb4ece1c&quot;&gt;cef9fb4ece1c&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;mapping&quot;&gt;Mapping&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;pbmm2 was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/pbmm2/7100ed4a31a2&quot;&gt;7100ed4a31a2&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;metagenomic-analysis&quot;&gt;Metagenomic Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;name2taxid was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/name2taxid/b83613ee99ad&quot;&gt;b83613ee99ad&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;profile2cami was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/profile2cami/d38b9fdf04e0&quot;&gt;d38b9fdf04e0&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;mothur&quot;&gt;Mothur&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;mothur_chimera_perseus was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/mothur_chimera_perseus/0f3baac24045&quot;&gt;0f3baac24045&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;rna-analysis&quot;&gt;RNA Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;seurat_clustering was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/seurat_clustering/51eb02d9b17a&quot;&gt;51eb02d9b17a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;seurat_create was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/seurat_create/af8bdeb89691&quot;&gt;af8bdeb89691&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;seurat_data was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/seurat_data/4ec52a83ec82&quot;&gt;4ec52a83ec82&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;seurat_integrate was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/seurat_integrate/74fa68f4e579&quot;&gt;74fa68f4e579&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;seurat_plot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/seurat_plot/fee4b4eb0ef5&quot;&gt;fee4b4eb0ef5&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;seurat_preprocessing was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/seurat_preprocessing/6bccf5f85f92&quot;&gt;6bccf5f85f92&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;seurat_reduce_dimension was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/seurat_reduce_dimension/46ed93e8da30&quot;&gt;46ed93e8da30&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;variant-calling&quot;&gt;Variant Calling&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;bcftools_convert_from_vcf was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_convert_from_vcf/b8e9da766b0f&quot;&gt;b8e9da766b0f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;bcftools_convert_from_vcf was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_convert_from_vcf/cacc9970727a&quot;&gt;cacc9970727a&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;virology&quot;&gt;Virology&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;irma was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/irma/a9a78a68d6c8&quot;&gt;a9a78a68d6c8&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;none&quot;&gt;None&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;data_manager_diamond_database_builder was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78&quot;&gt;4a08b7b76b78&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</content><author><name></name></author><category term="tools" /><summary type="html">On 2024-11-10, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #486</summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2024-11-03</title><link href="https://galaxyproject.eu/posts/2024/11/03/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2024-11-03" /><published>2024-11-03T00:00:00+01:00</published><updated>2024-11-03T00:00:00+01:00</updated><id>https://galaxyproject.eu/posts/2024/11/03/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2024/11/03/tool-update/">&lt;p&gt;On 2024-11-03, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in &lt;a href=&quot;https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#485/&quot;&gt;Jenkins Build #485&lt;/a&gt;&lt;/p&gt;

&lt;h2 id=&quot;get-data&quot;&gt;Get Data&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;copernicusmarine was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/copernicusmarine/4edd010161e9&quot;&gt;4edd010161e9&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;metabolomics&quot;&gt;Metabolomics&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;isolib was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/isolib/2b1118bce0b1&quot;&gt;2b1118bce0b1&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mfassignr_findrecalseries was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/mfassignr_findrecalseries/1b4881c150cc&quot;&gt;1b4881c150cc&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mfassignr_histnoise was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/mfassignr_histnoise/9654573e6889&quot;&gt;9654573e6889&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mfassignr_isofiltr was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/mfassignr_isofiltr/1c199c3d5993&quot;&gt;1c199c3d5993&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mfassignr_kmdnoise was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/mfassignr_kmdnoise/a7a823839ae3&quot;&gt;a7a823839ae3&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mfassignr_mfassign was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/mfassignr_mfassign/22c80f584bb1&quot;&gt;22c80f584bb1&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mfassignr_mfassigncho was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/mfassignr_mfassigncho/da64d663694b&quot;&gt;da64d663694b&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mfassignr_recal was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/mfassignr_recal/cfcf45ba58be&quot;&gt;cfcf45ba58be&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mfassignr_recallist was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/mfassignr_recallist/6c7b17d38a1d&quot;&gt;6c7b17d38a1d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mfassignr_snplot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/mfassignr_snplot/f19c0631b9e5&quot;&gt;f19c0631b9e5&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;recetox_aplcms_align_features was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_align_features/ec196e27a61a&quot;&gt;ec196e27a61a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;recetox_aplcms_compute_clusters was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_compute_clusters/59c393d35e0e&quot;&gt;59c393d35e0e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;recetox_aplcms_compute_template was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_compute_template/50b9918aeff2&quot;&gt;50b9918aeff2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;recetox_aplcms_correct_time was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_correct_time/a82db010c53e&quot;&gt;a82db010c53e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;recetox_aplcms_generate_feature_table was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_generate_feature_table/89178a72388a&quot;&gt;89178a72388a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;recetox_aplcms_merge_known_table was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_merge_known_table/b7c8a44b9cc1&quot;&gt;b7c8a44b9cc1&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;recetox_aplcms_recover_weaker_signals was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_recover_weaker_signals/f92b1b64da93&quot;&gt;f92b1b64da93&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;recetox_aplcms_remove_noise was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_remove_noise/7acd11ddc061&quot;&gt;7acd11ddc061&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;qiime-2&quot;&gt;QIIME 2&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;qiime2__alignment__mafft was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__alignment__mafft/da8c194c5dc5&quot;&gt;da8c194c5dc5&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__alignment__mafft_add was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__alignment__mafft_add/793348b25298&quot;&gt;793348b25298&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__alignment__mask was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__alignment__mask/d71423249631&quot;&gt;d71423249631&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__composition__add_pseudocount was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__composition__add_pseudocount/e2822b9553cb&quot;&gt;e2822b9553cb&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__composition__ancom was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__composition__ancom/c59b1d501ecf&quot;&gt;c59b1d501ecf&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__composition__ancombc was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__composition__ancombc/952686c734e9&quot;&gt;952686c734e9&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__composition__tabulate was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__composition__tabulate/cb1a60431256&quot;&gt;cb1a60431256&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__cutadapt__demux_paired was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__cutadapt__demux_paired/12dfb163a004&quot;&gt;12dfb163a004&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__cutadapt__demux_single was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__cutadapt__demux_single/47652cda9695&quot;&gt;47652cda9695&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__cutadapt__trim_paired was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__cutadapt__trim_paired/e82bd0e0c7ad&quot;&gt;e82bd0e0c7ad&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__cutadapt__trim_single was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__cutadapt__trim_single/f8d5e0d4dfec&quot;&gt;f8d5e0d4dfec&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__dada2__denoise_ccs was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__dada2__denoise_ccs/e73ff752eb45&quot;&gt;e73ff752eb45&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__dada2__denoise_paired was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__dada2__denoise_paired/933b92011b91&quot;&gt;933b92011b91&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__dada2__denoise_pyro was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__dada2__denoise_pyro/d9e75c4f54b9&quot;&gt;d9e75c4f54b9&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__dada2__denoise_single was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__dada2__denoise_single/354f63459d37&quot;&gt;354f63459d37&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2&quot;&gt;2572fc0f88f2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623&quot;&gt;b883cbea5623&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__deblur__denoise_other was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_other/816ca3000a39&quot;&gt;816ca3000a39&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__deblur__visualize_stats was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__visualize_stats/2e4eafd6f1f6&quot;&gt;2e4eafd6f1f6&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__demux__emp_paired was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__demux__emp_paired/8edb4dc16d6e&quot;&gt;8edb4dc16d6e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__demux__emp_single was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__demux__emp_single/8e01d149bcdb&quot;&gt;8e01d149bcdb&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__demux__filter_samples was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__demux__filter_samples/7595f1cbe5b7&quot;&gt;7595f1cbe5b7&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__demux__subsample_paired was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__demux__subsample_paired/669e59a2a229&quot;&gt;669e59a2a229&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__demux__subsample_single was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__demux__subsample_single/76384b6b3d90&quot;&gt;76384b6b3d90&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__demux__summarize was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__demux__summarize/1a13e87462a0&quot;&gt;1a13e87462a0&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity__adonis was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity__adonis/4701a5b2b60d&quot;&gt;4701a5b2b60d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity__alpha was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity__alpha/324ab5e710fa&quot;&gt;324ab5e710fa&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity__alpha_correlation was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity__alpha_correlation/356a07706de8&quot;&gt;356a07706de8&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity__alpha_group_significance was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity__alpha_group_significance/96988c25ca01&quot;&gt;96988c25ca01&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity__alpha_phylogenetic was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity__alpha_phylogenetic/5c0e7186a169&quot;&gt;5c0e7186a169&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity__alpha_rarefaction was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity__alpha_rarefaction/22bfda174157&quot;&gt;22bfda174157&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity__beta was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity__beta/97a8f4d7b51d&quot;&gt;97a8f4d7b51d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity__beta_correlation was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity__beta_correlation/93d88cdf089a&quot;&gt;93d88cdf089a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity__beta_group_significance was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity__beta_group_significance/a0d20b8b681e&quot;&gt;a0d20b8b681e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity__beta_phylogenetic was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity__beta_phylogenetic/394712a51004&quot;&gt;394712a51004&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity__beta_rarefaction was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity__beta_rarefaction/1506cdb7caad&quot;&gt;1506cdb7caad&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity__bioenv was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity__bioenv/21ca3e4d0f06&quot;&gt;21ca3e4d0f06&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity__core_metrics was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity__core_metrics/703db464b072&quot;&gt;703db464b072&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity__core_metrics_phylogenetic was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity__core_metrics_phylogenetic/7fc930fc43cf&quot;&gt;7fc930fc43cf&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity__filter_alpha_diversity was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity__filter_alpha_diversity/35e7602594d8&quot;&gt;35e7602594d8&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity__filter_distance_matrix was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity__filter_distance_matrix/6d85ed80f077&quot;&gt;6d85ed80f077&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity__mantel was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity__mantel/39109e3921ee&quot;&gt;39109e3921ee&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity__pcoa was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity__pcoa/0a6baa36f13c&quot;&gt;0a6baa36f13c&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity__pcoa_biplot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity__pcoa_biplot/41a52cf11f2d&quot;&gt;41a52cf11f2d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity__procrustes_analysis was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity__procrustes_analysis/db458dd840c2&quot;&gt;db458dd840c2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity__tsne was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity__tsne/eccbb594cd17&quot;&gt;eccbb594cd17&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity__umap was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity__umap/9c7d4870e7c2&quot;&gt;9c7d4870e7c2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity_lib__alpha_passthrough was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity_lib__alpha_passthrough/71a10fd28964&quot;&gt;71a10fd28964&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity_lib__beta_passthrough was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity_lib__beta_passthrough/7bc5ff8456ff&quot;&gt;7bc5ff8456ff&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity_lib__beta_phylogenetic_meta_passthrough was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity_lib__beta_phylogenetic_meta_passthrough/a6205ca8caec&quot;&gt;a6205ca8caec&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity_lib__beta_phylogenetic_passthrough was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity_lib__beta_phylogenetic_passthrough/5ab19b2ef7d8&quot;&gt;5ab19b2ef7d8&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity_lib__bray_curtis was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity_lib__bray_curtis/84b38b24a50e&quot;&gt;84b38b24a50e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity_lib__faith_pd was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity_lib__faith_pd/f3e3dfe874f0&quot;&gt;f3e3dfe874f0&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity_lib__jaccard was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity_lib__jaccard/df2902af58c1&quot;&gt;df2902af58c1&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity_lib__observed_features was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity_lib__observed_features/89d7fabc1120&quot;&gt;89d7fabc1120&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity_lib__pielou_evenness was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity_lib__pielou_evenness/3fff9475b959&quot;&gt;3fff9475b959&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity_lib__shannon_entropy was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity_lib__shannon_entropy/b2ccb5709bed&quot;&gt;b2ccb5709bed&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity_lib__unweighted_unifrac was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity_lib__unweighted_unifrac/16f6f1bb70df&quot;&gt;16f6f1bb70df&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__diversity_lib__weighted_unifrac was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__diversity_lib__weighted_unifrac/a166647c366a&quot;&gt;a166647c366a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__emperor__biplot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__emperor__biplot/500d81d6d22d&quot;&gt;500d81d6d22d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__emperor__plot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__emperor__plot/64a9ebc05ae4&quot;&gt;64a9ebc05ae4&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__emperor__procrustes_plot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__emperor__procrustes_plot/e2e3685e9ead&quot;&gt;e2e3685e9ead&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_classifier__blast was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_classifier__blast/24b72d60805e&quot;&gt;24b72d60805e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_classifier__classify_consensus_blast was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_classifier__classify_consensus_blast/0024a2733c77&quot;&gt;0024a2733c77&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_classifier__classify_consensus_vsearch was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_classifier__classify_consensus_vsearch/f965e6e951e7&quot;&gt;f965e6e951e7&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_classifier__classify_hybrid_vsearch_sklearn was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_classifier__classify_hybrid_vsearch_sklearn/6f3e4b4cd85f&quot;&gt;6f3e4b4cd85f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_classifier__classify_sklearn was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_classifier__classify_sklearn/771d8be25d7a&quot;&gt;771d8be25d7a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_classifier__extract_reads was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_classifier__extract_reads/9db411be36ba&quot;&gt;9db411be36ba&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_classifier__find_consensus_annotation was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_classifier__find_consensus_annotation/b6121b90c568&quot;&gt;b6121b90c568&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_classifier__fit_classifier_naive_bayes was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_classifier__fit_classifier_naive_bayes/1088a30ad72f&quot;&gt;1088a30ad72f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_classifier__fit_classifier_sklearn was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_classifier__fit_classifier_sklearn/b58536f29139&quot;&gt;b58536f29139&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_classifier__vsearch_global was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_classifier__vsearch_global/7ca8ce947d06&quot;&gt;7ca8ce947d06&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_table__core_features was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_table__core_features/0b1424ea3495&quot;&gt;0b1424ea3495&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_table__filter_features was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_table__filter_features/10954feb4893&quot;&gt;10954feb4893&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_table__filter_features_conditionally was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_table__filter_features_conditionally/46bc11016e31&quot;&gt;46bc11016e31&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_table__filter_samples was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_table__filter_samples/0597a61cb4b5&quot;&gt;0597a61cb4b5&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_table__filter_seqs was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_table__filter_seqs/8aec6a03bd3f&quot;&gt;8aec6a03bd3f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_table__group was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_table__group/4acd06f54adc&quot;&gt;4acd06f54adc&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_table__heatmap was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_table__heatmap/1579e3bbdc11&quot;&gt;1579e3bbdc11&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_table__merge was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_table__merge/b5eb47c65e65&quot;&gt;b5eb47c65e65&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_table__merge_seqs was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_table__merge_seqs/6d3775f3a859&quot;&gt;6d3775f3a859&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_table__merge_taxa was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_table__merge_taxa/a96e86eac4e3&quot;&gt;a96e86eac4e3&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_table__presence_absence was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_table__presence_absence/d853b44a37b5&quot;&gt;d853b44a37b5&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_table__rarefy was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_table__rarefy/adf22a045073&quot;&gt;adf22a045073&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_table__relative_frequency was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_table__relative_frequency/eaada56f497a&quot;&gt;eaada56f497a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_table__rename_ids was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_table__rename_ids/8ae8ef4804fa&quot;&gt;8ae8ef4804fa&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_table__summarize was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_table__summarize/d0f2249afe30&quot;&gt;d0f2249afe30&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_table__tabulate_seqs was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_table__tabulate_seqs/c4570ced1d88&quot;&gt;c4570ced1d88&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__feature_table__transpose was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__feature_table__transpose/8a3e71857c0a&quot;&gt;8a3e71857c0a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__fragment_insertion__classify_otus_experimental was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__fragment_insertion__classify_otus_experimental/62764fe71186&quot;&gt;62764fe71186&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__fragment_insertion__filter_features was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__fragment_insertion__filter_features/b27d577c13e0&quot;&gt;b27d577c13e0&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__fragment_insertion__sepp was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__fragment_insertion__sepp/a74f06287b8c&quot;&gt;a74f06287b8c&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__longitudinal__anova was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__longitudinal__anova/649a6f5a7ff8&quot;&gt;649a6f5a7ff8&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__longitudinal__feature_volatility was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__longitudinal__feature_volatility/ecc06a63663d&quot;&gt;ecc06a63663d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__longitudinal__first_differences was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__longitudinal__first_differences/2cb105e00a71&quot;&gt;2cb105e00a71&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__longitudinal__first_distances was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__longitudinal__first_distances/2c445317c0c1&quot;&gt;2c445317c0c1&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__longitudinal__linear_mixed_effects was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__longitudinal__linear_mixed_effects/d10f755328ea&quot;&gt;d10f755328ea&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__longitudinal__maturity_index was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__longitudinal__maturity_index/1945315814fc&quot;&gt;1945315814fc&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__longitudinal__nmit was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__longitudinal__nmit/4facf6ad69be&quot;&gt;4facf6ad69be&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__longitudinal__pairwise_differences was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__longitudinal__pairwise_differences/82847cdbf7fd&quot;&gt;82847cdbf7fd&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__longitudinal__pairwise_distances was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__longitudinal__pairwise_distances/c02040f48a72&quot;&gt;c02040f48a72&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__longitudinal__plot_feature_volatility was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__longitudinal__plot_feature_volatility/2b93f7a91399&quot;&gt;2b93f7a91399&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__longitudinal__volatility was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__longitudinal__volatility/646d4929b1ea&quot;&gt;646d4929b1ea&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__metadata__distance_matrix was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__metadata__distance_matrix/855d0a9bc79c&quot;&gt;855d0a9bc79c&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__metadata__shuffle_groups was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__metadata__shuffle_groups/d310fdba1caf&quot;&gt;d310fdba1caf&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__metadata__tabulate was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__metadata__tabulate/9857be21dcaf&quot;&gt;9857be21dcaf&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__phylogeny__align_to_tree_mafft_fasttree was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__phylogeny__align_to_tree_mafft_fasttree/b552bc376487&quot;&gt;b552bc376487&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__phylogeny__align_to_tree_mafft_iqtree was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__phylogeny__align_to_tree_mafft_iqtree/ec98b720efc9&quot;&gt;ec98b720efc9&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__phylogeny__align_to_tree_mafft_raxml was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__phylogeny__align_to_tree_mafft_raxml/5d20cf180904&quot;&gt;5d20cf180904&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__phylogeny__fasttree was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__phylogeny__fasttree/139fe749b0e5&quot;&gt;139fe749b0e5&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__phylogeny__filter_table was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__phylogeny__filter_table/fa11896bafbb&quot;&gt;fa11896bafbb&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__phylogeny__filter_tree was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__phylogeny__filter_tree/d24d147a225d&quot;&gt;d24d147a225d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__phylogeny__iqtree was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__phylogeny__iqtree/77c94392c3e8&quot;&gt;77c94392c3e8&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__phylogeny__iqtree_ultrafast_bootstrap was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__phylogeny__iqtree_ultrafast_bootstrap/e682a7a080a0&quot;&gt;e682a7a080a0&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__phylogeny__midpoint_root was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__phylogeny__midpoint_root/0a0e30476122&quot;&gt;0a0e30476122&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__phylogeny__raxml was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__phylogeny__raxml/a40eb1afbd0f&quot;&gt;a40eb1afbd0f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__phylogeny__raxml_rapid_bootstrap was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__phylogeny__raxml_rapid_bootstrap/9d523344e9fb&quot;&gt;9d523344e9fb&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__phylogeny__robinson_foulds was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__phylogeny__robinson_foulds/48893627c8f9&quot;&gt;48893627c8f9&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__quality_control__bowtie2_build was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__quality_control__bowtie2_build/3a464de609d5&quot;&gt;3a464de609d5&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__quality_control__evaluate_composition was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__quality_control__evaluate_composition/d9c71e139c9b&quot;&gt;d9c71e139c9b&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__quality_control__evaluate_seqs was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__quality_control__evaluate_seqs/f45d42427237&quot;&gt;f45d42427237&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__quality_control__evaluate_taxonomy was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__quality_control__evaluate_taxonomy/8e6a404fb338&quot;&gt;8e6a404fb338&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__quality_control__exclude_seqs was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__quality_control__exclude_seqs/505d6f366518&quot;&gt;505d6f366518&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__quality_control__filter_reads was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__quality_control__filter_reads/8ea205bf4e7b&quot;&gt;8ea205bf4e7b&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__quality_filter__q_score was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__quality_filter__q_score/d786401d6619&quot;&gt;d786401d6619&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__rescript__get_bv_brc_genome_features was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__rescript__get_bv_brc_genome_features/c735738cecca&quot;&gt;c735738cecca&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__rescript__get_bv_brc_genomes was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__rescript__get_bv_brc_genomes/9dd05f5c60b9&quot;&gt;9dd05f5c60b9&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__rescript__get_bv_brc_metadata was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__rescript__get_bv_brc_metadata/f3cd42768927&quot;&gt;f3cd42768927&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__sample_classifier__classify_samples was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__sample_classifier__classify_samples/6c18cbbf0f5b&quot;&gt;6c18cbbf0f5b&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__sample_classifier__classify_samples_from_dist was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__sample_classifier__classify_samples_from_dist/5f37765a9e5e&quot;&gt;5f37765a9e5e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__sample_classifier__classify_samples_ncv was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__sample_classifier__classify_samples_ncv/ab96421e61c5&quot;&gt;ab96421e61c5&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__sample_classifier__confusion_matrix was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__sample_classifier__confusion_matrix/3164358cd72f&quot;&gt;3164358cd72f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__sample_classifier__fit_classifier was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__sample_classifier__fit_classifier/2116b939ff07&quot;&gt;2116b939ff07&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__sample_classifier__fit_regressor was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__sample_classifier__fit_regressor/e44450046a90&quot;&gt;e44450046a90&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__sample_classifier__heatmap was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__sample_classifier__heatmap/e2c3a69905fe&quot;&gt;e2c3a69905fe&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__sample_classifier__metatable was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__sample_classifier__metatable/905113a20ca7&quot;&gt;905113a20ca7&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__sample_classifier__predict_classification was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__sample_classifier__predict_classification/555cb8da4688&quot;&gt;555cb8da4688&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__sample_classifier__predict_regression was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__sample_classifier__predict_regression/e0913981ccc4&quot;&gt;e0913981ccc4&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__sample_classifier__regress_samples was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__sample_classifier__regress_samples/a400ec06bae3&quot;&gt;a400ec06bae3&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__sample_classifier__regress_samples_ncv was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__sample_classifier__regress_samples_ncv/c468c032ee23&quot;&gt;c468c032ee23&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__sample_classifier__scatterplot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__sample_classifier__scatterplot/22e510854bb2&quot;&gt;22e510854bb2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__sample_classifier__split_table was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__sample_classifier__split_table/b0af6d277910&quot;&gt;b0af6d277910&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__sample_classifier__summarize was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__sample_classifier__summarize/e56a7f3e8b05&quot;&gt;e56a7f3e8b05&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__stats__alpha_group_significance was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__stats__alpha_group_significance/d6f4c80a29a2&quot;&gt;d6f4c80a29a2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__stats__collate_stats was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__stats__collate_stats/10e19418eedb&quot;&gt;10e19418eedb&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__stats__facet_across was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__stats__facet_across/caf764ebca30&quot;&gt;caf764ebca30&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__stats__facet_within was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__stats__facet_within/5349488971e9&quot;&gt;5349488971e9&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__stats__mann_whitney_u_facet was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__stats__mann_whitney_u_facet/3860c369685d&quot;&gt;3860c369685d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__stats__plot_rainclouds was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__stats__plot_rainclouds/0699c24331f4&quot;&gt;0699c24331f4&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__stats__prep_alpha_distribution was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__stats__prep_alpha_distribution/c7ae38450ff9&quot;&gt;c7ae38450ff9&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__stats__wilcoxon_srt was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__stats__wilcoxon_srt/3cbec5fc30ad&quot;&gt;3cbec5fc30ad&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__stats__wilcoxon_srt_facet was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__stats__wilcoxon_srt_facet/181c3cf66bd8&quot;&gt;181c3cf66bd8&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__taxa__barplot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__taxa__barplot/3da2f87501ee&quot;&gt;3da2f87501ee&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__taxa__collapse was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__taxa__collapse/e8ab6eff4cf8&quot;&gt;e8ab6eff4cf8&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__taxa__filter_seqs was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__taxa__filter_seqs/526b35d5a4cd&quot;&gt;526b35d5a4cd&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__taxa__filter_table was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__taxa__filter_table/ca4a6aa29205&quot;&gt;ca4a6aa29205&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__vizard__boxplot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__vizard__boxplot/765052908e52&quot;&gt;765052908e52&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__vizard__heatmap was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__vizard__heatmap/45c348a09fa0&quot;&gt;45c348a09fa0&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__vizard__lineplot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__vizard__lineplot/df9f1ff48c29&quot;&gt;df9f1ff48c29&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__vizard__scatterplot_2d was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__vizard__scatterplot_2d/acada7129b61&quot;&gt;acada7129b61&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__vsearch__cluster_features_closed_reference was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__vsearch__cluster_features_closed_reference/89648217a7ef&quot;&gt;89648217a7ef&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__vsearch__cluster_features_de_novo was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__vsearch__cluster_features_de_novo/31b630d08cda&quot;&gt;31b630d08cda&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__vsearch__cluster_features_open_reference was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__vsearch__cluster_features_open_reference/576b090ccd63&quot;&gt;576b090ccd63&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__vsearch__dereplicate_sequences was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__vsearch__dereplicate_sequences/d33fbe0e2c37&quot;&gt;d33fbe0e2c37&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__vsearch__fastq_stats was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__vsearch__fastq_stats/b770f74843a4&quot;&gt;b770f74843a4&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__vsearch__merge_pairs was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__vsearch__merge_pairs/421396209ac3&quot;&gt;421396209ac3&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__vsearch__uchime_denovo was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__vsearch__uchime_denovo/c328a49a8ebf&quot;&gt;c328a49a8ebf&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__vsearch__uchime_ref was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__vsearch__uchime_ref/74b478765f80&quot;&gt;74b478765f80&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2_core__tools__export was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2_core__tools__export/40bcc0e139fa&quot;&gt;40bcc0e139fa&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2_core__tools__import was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2_core__tools__import/8a0db69428c7&quot;&gt;8a0db69428c7&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;chemicaltoolbox&quot;&gt;ChemicalToolBox&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;alphafold2 was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/galaxy-australia/alphafold2/3f188450ca4f&quot;&gt;3f188450ca4f&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;convert-formats&quot;&gt;Convert Formats&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;hictk was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hictk/af0d9df0641e&quot;&gt;af0d9df0641e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ucsc_twobittofa was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ucsc_twobittofa/e9bbe2f71784&quot;&gt;e9bbe2f71784&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;machine-learning&quot;&gt;Machine Learning&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;black_forest_labs_flux was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/black_forest_labs_flux/3e22bda128be&quot;&gt;3e22bda128be&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;keras_model_config was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/keras_model_config/e474e701d58b&quot;&gt;e474e701d58b&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;single-cell&quot;&gt;Single-cell&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;alevin was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/alevin/b0fe3e482cb7&quot;&gt;b0fe3e482cb7&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;music_compare was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/music_compare/7009462b958f&quot;&gt;7009462b958f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;music_construct_eset was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/music_construct_eset/7022ce682d2f&quot;&gt;7022ce682d2f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;music_deconvolution was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/music_deconvolution/e7b79fd6b595&quot;&gt;e7b79fd6b595&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;music_inspect_eset was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/music_inspect_eset/94c0b3baf8fd&quot;&gt;94c0b3baf8fd&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;music_manipulate_eset was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/music_manipulate_eset/192355cd1641&quot;&gt;192355cd1641&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;scanpy_remove_confounders was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_remove_confounders/c5541bfb8feb&quot;&gt;c5541bfb8feb&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;annotation&quot;&gt;Annotation&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;busco was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/busco/e5c372c91e46&quot;&gt;e5c372c91e46&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;genome-diversity&quot;&gt;Genome Diversity&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;fasttree was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fasttree/ef46a404db96&quot;&gt;ef46a404db96&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;graphdisplay-data&quot;&gt;Graph/Display Data&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;ggplot2_histogram was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ggplot2_histogram/536078949ae4&quot;&gt;536078949ae4&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;pretext_snapshot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/pretext_snapshot/326098bc19cc&quot;&gt;326098bc19cc&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;metagenomic-analysis&quot;&gt;Metagenomic Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;ampvis2_alpha_diversity was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_alpha_diversity/77000428c613&quot;&gt;77000428c613&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;srst2 was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/srst2/f995ba9f1caa&quot;&gt;f995ba9f1caa&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;send-data&quot;&gt;Send Data&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;ena_upload was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ena_upload/e1b3b37aa69f&quot;&gt;e1b3b37aa69f&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;none&quot;&gt;None&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;data_manager_diamond_database_builder was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78&quot;&gt;4a08b7b76b78&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;hca_sc_label_analysis_tools&quot;&gt;hca_sc_label_analysis_tools&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;decoupler_pseudobulk was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ebi-gxa/decoupler_pseudobulk/ef054892d47f&quot;&gt;ef054892d47f&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;imaging&quot;&gt;Imaging&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;squidpy_scatter was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/goeckslab/squidpy_scatter/b84c324b58bd&quot;&gt;b84c324b58bd&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;squidpy_spatial was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/goeckslab/squidpy_spatial/2a5036c29889&quot;&gt;2a5036c29889&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</content><author><name></name></author><category term="tools" /><summary type="html">On 2024-11-03, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #485</summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2024-10-27</title><link href="https://galaxyproject.eu/posts/2024/10/27/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2024-10-27" /><published>2024-10-27T00:00:00+02:00</published><updated>2024-10-27T00:00:00+02:00</updated><id>https://galaxyproject.eu/posts/2024/10/27/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2024/10/27/tool-update/">&lt;p&gt;On 2024-10-27, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in &lt;a href=&quot;https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#484/&quot;&gt;Jenkins Build #484&lt;/a&gt;&lt;/p&gt;

&lt;h2 id=&quot;climate-analysis&quot;&gt;Climate Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;divand_full_analysis was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/divand_full_analysis/77787acbd793&quot;&gt;77787acbd793&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;landcover_subindicator was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/landcover_subindicator/828c02027180&quot;&gt;828c02027180&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;get-data&quot;&gt;Get Data&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;argo_getdata was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/argo_getdata/055a934a380f&quot;&gt;055a934a380f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;argo_getdata was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/argo_getdata/f3c64a15ee7e&quot;&gt;f3c64a15ee7e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;copernicusmarine was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/copernicusmarine/4de886e6300d&quot;&gt;4de886e6300d&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;gis-data-handling&quot;&gt;GIS Data Handling&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;aquainfra_ogc_api_processes was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/aquainfra_ogc_api_processes/1ff618d89af4&quot;&gt;1ff618d89af4&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;metabolomics&quot;&gt;Metabolomics&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;mfassignr_findrecalseries was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/mfassignr_findrecalseries/18e13043167d&quot;&gt;18e13043167d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mfassignr_histnoise was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/mfassignr_histnoise/12b63108d645&quot;&gt;12b63108d645&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mfassignr_histnoise was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/mfassignr_histnoise/5dd25cf1ac0a&quot;&gt;5dd25cf1ac0a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mfassignr_isofiltr was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/mfassignr_isofiltr/b880fcae60ea&quot;&gt;b880fcae60ea&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mfassignr_kmdnoise was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/mfassignr_kmdnoise/39a642fc9638&quot;&gt;39a642fc9638&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mfassignr_kmdnoise was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/mfassignr_kmdnoise/634ae07958a2&quot;&gt;634ae07958a2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mfassignr_mfassign was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/mfassignr_mfassign/0492fff60960&quot;&gt;0492fff60960&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mfassignr_mfassign was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/mfassignr_mfassign/d5745e78fcfe&quot;&gt;d5745e78fcfe&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mfassignr_mfassigncho was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/mfassignr_mfassigncho/59326d3b9c52&quot;&gt;59326d3b9c52&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mfassignr_mfassigncho was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/mfassignr_mfassigncho/b96a462d9c3f&quot;&gt;b96a462d9c3f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mfassignr_recal was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/mfassignr_recal/861917f1a211&quot;&gt;861917f1a211&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mfassignr_recallist was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/mfassignr_recallist/4f671baab2fd&quot;&gt;4f671baab2fd&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mfassignr_snplot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/mfassignr_snplot/7279d7a37c43&quot;&gt;7279d7a37c43&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;recetox_aplcms_correct_time was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_correct_time/501a232f3cd5&quot;&gt;501a232f3cd5&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;qiime-2&quot;&gt;QIIME 2&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2&quot;&gt;2572fc0f88f2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623&quot;&gt;b883cbea5623&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;rna-analysis&quot;&gt;RNA Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;cuffmerge was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/devteam/cuffmerge/04adc9db1581&quot;&gt;04adc9db1581&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;featurecounts was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/featurecounts/1b851f87fbe0&quot;&gt;1b851f87fbe0&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;trinity_abundance_estimates_to_matrix was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/trinity_abundance_estimates_to_matrix/81a4697677e7&quot;&gt;81a4697677e7&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;variant-calling&quot;&gt;Variant Calling&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;ensembl_vep was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ensembl_vep/c47ecf0e932d&quot;&gt;c47ecf0e932d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;snpeff was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/snpeff/ca2b512e8d7c&quot;&gt;ca2b512e8d7c&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;text-manipulation&quot;&gt;Text Manipulation&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;concatenate_multiple_datasets was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/artbio/concatenate_multiple_datasets/5b1b635232ed&quot;&gt;5b1b635232ed&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;concatenate_multiple_datasets was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/artbio/concatenate_multiple_datasets/5b2cc63d7a21&quot;&gt;5b2cc63d7a21&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;assembly&quot;&gt;Assembly&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;hifiasm was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hifiasm/5161f204ba63&quot;&gt;5161f204ba63&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;genome-diversity&quot;&gt;Genome Diversity&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;fasttree was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fasttree/ef46a404db96&quot;&gt;ef46a404db96&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;metagenomic-analysis&quot;&gt;Metagenomic Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;ampvis2_alpha_diversity was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_alpha_diversity/c14c7fd4d1be&quot;&gt;c14c7fd4d1be&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_boxplot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_boxplot/61db741e4614&quot;&gt;61db741e4614&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_core was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_core/4b023017896a&quot;&gt;4b023017896a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_export_fasta was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_export_fasta/5939a607c306&quot;&gt;5939a607c306&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_frequency was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_frequency/467da4453127&quot;&gt;467da4453127&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_heatmap was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_heatmap/9dab85e62cf2&quot;&gt;9dab85e62cf2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_load was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_load/7db90993aa92&quot;&gt;7db90993aa92&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_merge_ampvis2 was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_merge_ampvis2/5c6edb00ef4a&quot;&gt;5c6edb00ef4a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_mergereplicates was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_mergereplicates/21a8b4e5e300&quot;&gt;21a8b4e5e300&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_octave was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_octave/79ea913636fe&quot;&gt;79ea913636fe&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_ordinate was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_ordinate/520dd44283ea&quot;&gt;520dd44283ea&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_otu_network was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_otu_network/4122ff5882e0&quot;&gt;4122ff5882e0&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_rankabundance was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_rankabundance/17b44753a1df&quot;&gt;17b44753a1df&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_rarecurve was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_rarecurve/30ac301ba3d6&quot;&gt;30ac301ba3d6&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_setmetadata was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_setmetadata/7c9c6448b57c&quot;&gt;7c9c6448b57c&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_subset_samples was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_subset_samples/1db7e3d33871&quot;&gt;1db7e3d33871&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_subset_taxa was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_subset_taxa/20a62b3a3038&quot;&gt;20a62b3a3038&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_timeseries was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_timeseries/9c6dbd8a875b&quot;&gt;9c6dbd8a875b&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ampvis2_venn was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_venn/e85ff12bc025&quot;&gt;e85ff12bc025&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;decontam was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/decontam/33cb918da8d7&quot;&gt;33cb918da8d7&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;phylogenetics&quot;&gt;Phylogenetics&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;hyphy_annotate was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/hyphy_annotate/68cd2d8e3840&quot;&gt;68cd2d8e3840&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;virology&quot;&gt;Virology&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;varvamp was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/varvamp/d6d746d0d1d0&quot;&gt;d6d746d0d1d0&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;none&quot;&gt;None&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;data_manager_diamond_database_builder was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78&quot;&gt;4a08b7b76b78&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;data_manager_gtdbtk_database_installer was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_gtdbtk_database_installer/e7b39a7e0024&quot;&gt;e7b39a7e0024&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;data_manager_mapseq was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_mapseq/23511530b8fd&quot;&gt;23511530b8fd&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;hca_sc_label_analysis_tools&quot;&gt;hca_sc_label_analysis_tools&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;decoupler_pseudobulk was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ebi-gxa/decoupler_pseudobulk/70a5c6f2408d&quot;&gt;70a5c6f2408d&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</content><author><name></name></author><category term="tools" /><summary type="html">On 2024-10-27, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #484</summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2024-10-21</title><link href="https://galaxyproject.eu/posts/2024/10/21/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2024-10-21" /><published>2024-10-21T00:00:00+02:00</published><updated>2024-10-21T00:00:00+02:00</updated><id>https://galaxyproject.eu/posts/2024/10/21/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2024/10/21/tool-update/">&lt;p&gt;On 2024-10-21, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in &lt;a href=&quot;https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#483/&quot;&gt;Jenkins Build #483&lt;/a&gt;&lt;/p&gt;

&lt;h2 id=&quot;data-and-metadata-management&quot;&gt;Data and Metadata Management&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;data_paper_from_eml was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/data_paper_from_eml/cfe884e53600&quot;&gt;cfe884e53600&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;chemicaltoolbox&quot;&gt;ChemicalToolBox&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;qcxms_getres was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/qcxms_getres/89b026d67e9f&quot;&gt;89b026d67e9f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qcxms_neutral_run was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/qcxms_neutral_run/33b7a99b6de3&quot;&gt;33b7a99b6de3&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qcxms_production_run was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/qcxms_production_run/356f7916ac07&quot;&gt;356f7916ac07&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;qiime-2&quot;&gt;QIIME 2&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2&quot;&gt;2572fc0f88f2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623&quot;&gt;b883cbea5623&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;get-data&quot;&gt;Get Data&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;unipept was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/galaxyp/unipept/917fd3ebc223&quot;&gt;917fd3ebc223&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;annotation&quot;&gt;Annotation&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;agat was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/agat/d6ede73082da&quot;&gt;d6ede73082da&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;abritamr was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/abritamr/468fd92deaaa&quot;&gt;468fd92deaaa&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;assembly&quot;&gt;Assembly&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;erga_ear was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/erga_ear/3dd6be0cd8dd&quot;&gt;3dd6be0cd8dd&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;graphdisplay-data&quot;&gt;Graph/Display Data&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;jbrowse2 was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/fubar/jbrowse2/cec274db51c0&quot;&gt;cec274db51c0&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;imaging&quot;&gt;Imaging&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;bioimage_inference was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/bioimage_inference/9b8fc55cb9eb&quot;&gt;9b8fc55cb9eb&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;scale_image was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/imgteam/scale_image/72b8a6b7661b&quot;&gt;72b8a6b7661b&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;machine-learning&quot;&gt;Machine Learning&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;black_forest_labs_flux was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/black_forest_labs_flux/0d0561746128&quot;&gt;0d0561746128&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;none&quot;&gt;None&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;data_manager_motus was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/data_manager_motus/0370fe3cf518&quot;&gt;0370fe3cf518&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;data_manager_build_kraken2_database was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_build_kraken2_database/13851aefa67a&quot;&gt;13851aefa67a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;data_manager_build_kraken2_database was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_build_kraken2_database/1e34d2e3d285&quot;&gt;1e34d2e3d285&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;data_manager_build_kraken2_database was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_build_kraken2_database/539b008cfe1c&quot;&gt;539b008cfe1c&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;data_manager_build_kraken2_database was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_build_kraken2_database/9002633b4737&quot;&gt;9002633b4737&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;data_manager_build_kraken2_database was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_build_kraken2_database/90b4d4f0a3a4&quot;&gt;90b4d4f0a3a4&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;data_manager_diamond_database_builder was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78&quot;&gt;4a08b7b76b78&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;data_manager_ncbi_fcs_gx_database_downloader was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_ncbi_fcs_gx_database_downloader/6be6e6198ac3&quot;&gt;6be6e6198ac3&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;metagenomic-analysis&quot;&gt;Metagenomic Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;tiara was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/tiara/66058890173e&quot;&gt;66058890173e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;decontam was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/decontam/6621beb8bf3e&quot;&gt;6621beb8bf3e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mapseq was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/mapseq/30e275ed0442&quot;&gt;30e275ed0442&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;profile2cami was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/profile2cami/6bc0c090133f&quot;&gt;6bc0c090133f&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;convert-formats&quot;&gt;Convert Formats&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;tooldistillator was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/tooldistillator/ea93df4b3df2&quot;&gt;ea93df4b3df2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;tooldistillator_summarize was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/tooldistillator_summarize/24eec94e6dfc&quot;&gt;24eec94e6dfc&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;evolution&quot;&gt;Evolution&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;iqtree was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/iqtree/f87ac61981f0&quot;&gt;f87ac61981f0&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;fastafastq&quot;&gt;FASTA/FASTQ&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;fastp was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fastp/dbfc505896e9&quot;&gt;dbfc505896e9&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;seqtk was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/seqtk/a019807f4e67&quot;&gt;a019807f4e67&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;genome-diversity&quot;&gt;Genome Diversity&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;fasttree was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fasttree/ef46a404db96&quot;&gt;ef46a404db96&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;single-cell&quot;&gt;Single-cell&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;scanpy_cluster_reduce_dimension was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_cluster_reduce_dimension/8983e7a04ba7&quot;&gt;8983e7a04ba7&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;scanpy_filter was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_filter/64388be6d510&quot;&gt;64388be6d510&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;scanpy_inspect was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_inspect/d1cd8c147809&quot;&gt;d1cd8c147809&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;scanpy_inspect was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_inspect/d86cb2ce311b&quot;&gt;d86cb2ce311b&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;scanpy_normalize was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_normalize/4bda4412b8c2&quot;&gt;4bda4412b8c2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;scanpy_plot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_plot/62acdd96d4a0&quot;&gt;62acdd96d4a0&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;scanpy_remove_confounders was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_remove_confounders/974bb00b2f43&quot;&gt;974bb00b2f43&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;variant-calling&quot;&gt;Variant Calling&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;freebayes was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/devteam/freebayes/3e954e7125bf&quot;&gt;3e954e7125bf&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;apollo&quot;&gt;Apollo&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;apollo_iframe was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/gga/apollo_iframe/29159d9ce6f0&quot;&gt;29159d9ce6f0&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</content><author><name></name></author><category term="tools" /><summary type="html">On 2024-10-21, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #483</summary></entry></feed>