From 3a32a2c8819961f58c27f7b8e26445d62473e8c5 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Tue, 3 Dec 2024 14:45:28 -0500 Subject: [PATCH 1/3] update meryl --- .../kmer-profiling-hifi-VGP1/CHANGELOG.md | 7 + .../kmer-profiling-hifi-VGP1.ga | 163 ++++---- .../CHANGELOG.md | 6 + .../kmer-profiling-hifi-trio-VGP2.ga | 349 ++++++++++-------- 4 files changed, 310 insertions(+), 215 deletions(-) diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md index 02da3755e..956a7742d 100644 --- a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md @@ -1,5 +1,12 @@ # Changelog + +## [0.1.8] 2024-12-03 + +- `https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6` was updated to `https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl_count_kmers/meryl_count_kmers/1.3+galaxy7` +- `https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6` was updated to `https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl_groups_kmers/meryl_groups_kmers/1.3+galaxy7` +- `https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6` was updated to `https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl_histogram_kmers/meryl_histogram_kmers/1.3+galaxy7` + ## [0.1.7] 2024-08-05 ### Automatic update diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga index 3e5142b9b..5c393fb3d 100644 --- a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga @@ -15,7 +15,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.1.7", + "release": "0.1.8", "name": "kmer-profiling-hifi-VGP1", "report": { "markdown": "\n# Workflow Execution Report\n\n\n```galaxy\ninvocation_time()\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope linear plot\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope log plot\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope transformed linear plot\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope transformed log plot\")\n```\n\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" @@ -37,8 +37,8 @@ "name": "Input dataset collection", "outputs": [], "position": { - "left": 0, - "top": 86.5078125 + "left": 0.0, + "top": 237.75781276855386 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}", @@ -64,8 +64,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 17.57421875, - "top": 226.734375 + "left": 68.13671875, + "top": 408.3515627685539 }, "tool_id": null, "tool_state": "{\"default\": 21, \"parameter_type\": \"integer\", \"optional\": true}", @@ -91,8 +91,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 50.12890625, - "top": 342.609375 + "left": 177.15234375, + "top": 569.6054690185539 }, "tool_id": null, "tool_state": "{\"default\": 2, \"parameter_type\": \"integer\", \"optional\": true}", @@ -104,17 +104,56 @@ }, "3": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, "id": 3, "input_connections": { - "operation_type|input_reads": { + "style_cond|type_cond|pick_from_0|value": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Pick parameter value", + "outputs": [ + { + "name": "integer_param", + "type": "expression.json" + } + ], + "position": { + "left": 329.0234375, + "top": 381.1640627685539 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "b19e21af9c52", + "name": "pick_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"style_cond\": {\"pick_style\": \"first_or_default\", \"__current_case__\": 1, \"type_cond\": {\"param_type\": \"integer\", \"__current_case__\": 1, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"ConnectedValue\"}}], \"default_value\": \"21\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.2.0", + "type": "tool", + "uuid": "9a2f7fb6-aaf7-4e81-9d9a-a198db3cd397", + "when": null, + "workflow_outputs": [] + }, + "4": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl_count_kmers/meryl_count_kmers/1.3+galaxy7", + "errors": null, + "id": 4, + "input_connections": { + "input_reads": { "id": 0, "output_name": "output" }, - "operation_type|options_kmer_size|input_kmer_size": { - "id": 1, - "output_name": "output" + "options_kmer_size|input_kmer_size": { + "id": 3, + "output_name": "integer_param" } }, "inputs": [], @@ -127,8 +166,8 @@ } ], "position": { - "left": 296.8668759977911, - "top": 27 + "left": 419.9140625, + "top": 102.30468776855386 }, "post_job_actions": { "HideDatasetActionread_db": { @@ -137,28 +176,28 @@ "output_name": "read_db" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl_count_kmers/meryl_count_kmers/1.3+galaxy7", "tool_shed_repository": { - "changeset_revision": "29dabd8db6f2", - "name": "meryl", + "changeset_revision": "bb6774c6aeaf", + "name": "meryl_count_kmers", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"operation_type\": {\"command_type\": \"count-kmers\", \"__current_case__\": 0, \"count_operations\": \"count\", \"input_reads\": {\"__class__\": \"ConnectedValue\"}, \"options_kmer_size\": {\"kmer_size\": \"provide\", \"__current_case__\": 0, \"input_kmer_size\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3+galaxy6", + "tool_state": "{\"count_operation\": \"count\", \"input_reads\": {\"__class__\": \"ConnectedValue\"}, \"options_kmer_size\": {\"kmer_size\": \"provide\", \"__current_case__\": 0, \"input_kmer_size\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.3+galaxy7", "type": "tool", - "uuid": "9f3718fe-c33a-43c1-b36e-964a929678f7", + "uuid": "fc4e77b0-4f5a-4679-9177-87b2a3cd71ed", "when": null, "workflow_outputs": [] }, - "4": { + "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl_groups_kmers/meryl_groups_kmers/1.3+galaxy7", "errors": null, - "id": 4, + "id": 5, "input_connections": { - "operation_type|input_meryldb_02": { - "id": 3, + "input_meryldb_02": { + "id": 4, "output_name": "read_db" } }, @@ -172,8 +211,8 @@ } ], "position": { - "left": 576.8668759977911, - "top": 0 + "left": 702.75390625, + "top": 0.0 }, "post_job_actions": { "TagDatasetActionread_db": { @@ -184,34 +223,34 @@ "output_name": "read_db" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl_groups_kmers/meryl_groups_kmers/1.3+galaxy7", "tool_shed_repository": { - "changeset_revision": "29dabd8db6f2", - "name": "meryl", + "changeset_revision": "c4758f3bf36e", + "name": "meryl_groups_kmers", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"operation_type\": {\"command_type\": \"groups-kmers\", \"__current_case__\": 3, \"groups_operations\": \"union-sum\", \"input_meryldb_02\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3+galaxy6", + "tool_state": "{\"groups_operations\": \"union-sum\", \"input_meryldb_02\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.3+galaxy7", "type": "tool", - "uuid": "6467a6da-23e0-4ee0-af0e-7f5fc8a636de", + "uuid": "2ea15dc0-a71e-48a6-8d41-d568120525b4", "when": null, "workflow_outputs": [ { "label": "Merged Meryl Database", "output_name": "read_db", - "uuid": "9055fdc0-d158-435e-b662-e5a4f2766b42" + "uuid": "72fcc42e-2c61-4e86-a2dc-6fe974f2a35d" } ] }, - "5": { + "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl_histogram_kmers/meryl_histogram_kmers/1.3+galaxy7", "errors": null, - "id": 5, + "id": 6, "input_connections": { - "operation_type|input_meryldb_02": { - "id": 4, + "input_meryldb_02": { + "id": 5, "output_name": "read_db" } }, @@ -225,8 +264,8 @@ } ], "position": { - "left": 856.8668759977911, - "top": 42 + "left": 992.953125, + "top": 83.94920349121094 }, "post_job_actions": { "HideDatasetActionread_db_hist": { @@ -235,33 +274,33 @@ "output_name": "read_db_hist" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl_histogram_kmers/meryl_histogram_kmers/1.3+galaxy7", "tool_shed_repository": { - "changeset_revision": "29dabd8db6f2", - "name": "meryl", + "changeset_revision": "9a0227fa7521", + "name": "meryl_histogram_kmers", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"operation_type\": {\"command_type\": \"histogram-kmers\", \"__current_case__\": 4, \"input_meryldb_02\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3+galaxy6", + "tool_state": "{\"input_meryldb_02\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.3+galaxy7", "type": "tool", - "uuid": "10eb771d-1437-4602-91b7-e7e6d806dc2e", + "uuid": "12353c6c-2b6c-400f-887d-41a5c3f3f277", "when": null, "workflow_outputs": [] }, - "6": { + "7": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0", "errors": null, - "id": 6, + "id": 7, "input_connections": { "input": { - "id": 5, + "id": 6, "output_name": "read_db_hist" }, "kmer_length": { - "id": 1, - "output_name": "output" + "id": 3, + "output_name": "integer_param" }, "ploidy": { "id": 2, @@ -302,8 +341,8 @@ } ], "position": { - "left": 1136.866875997791, - "top": 15 + "left": 1274.636407247791, + "top": 125.53515651855386 }, "post_job_actions": { "TagDatasetActionlinear_plot": { @@ -369,11 +408,6 @@ "uuid": "955de351-ef19-42dc-89d7-ca213994515a", "when": null, "workflow_outputs": [ - { - "label": "GenomeScope linear plot", - "output_name": "linear_plot", - "uuid": "57230be4-36d5-4307-b4b0-b8a73f6800ce" - }, { "label": "GenomeScope transformed linear plot", "output_name": "transformed_linear_plot", @@ -398,6 +432,11 @@ "label": "GenomeScope log plot", "output_name": "log_plot", "uuid": "988e2189-d5f2-4e9e-8fc2-4434e68e8501" + }, + { + "label": "GenomeScope linear plot", + "output_name": "linear_plot", + "uuid": "57230be4-36d5-4307-b4b0-b8a73f6800ce" } ] } @@ -406,6 +445,6 @@ "Reviewed", "VGP" ], - "uuid": "0808b15a-7e3e-4b06-b804-f3d2cc73981a", - "version": 2 -} + "uuid": "58adb6d9-0345-44ca-82fd-e394eda5a18b", + "version": 3 +} \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/CHANGELOG.md b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/CHANGELOG.md index 9fd63f4a8..4c2a5f64e 100644 --- a/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.1.5] 2024-12-03 + +- `https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6` was updated to `https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl_count_kmers/meryl_count_kmers/1.3+galaxy7` +- `https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6` was updated to `https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl_groups_kmers/meryl_groups_kmers/1.3+galaxy7` +- `https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6` was updated to `https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl_histogram_kmers/meryl_histogram_kmers/1.3+galaxy7` + ## [0.1.4] 2024-08-05 ### Automatic update diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2.ga b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2.ga index f374f3a93..6d9066094 100644 --- a/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2.ga +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2.ga @@ -1,6 +1,7 @@ { "a_galaxy_workflow": "true", "annotation": "Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury. Part of the VGP pipeline.", + "comments": [], "creator": [ { "class": "Organization", @@ -14,8 +15,11 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.1.4", + "release": "0.1.5", "name": "kmer-profiling-hifi-trio-VGP2", + "report": { + "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" + }, "steps": { "0": { "annotation": "", @@ -154,17 +158,105 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, "id": 5, "input_connections": { - "operation_type|input_reads": { + "style_cond|type_cond|pick_from_0|value": { + "id": 3, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Pick parameter value", + "outputs": [ + { + "name": "integer_param", + "type": "expression.json" + } + ], + "position": { + "left": 271.5784037973972, + "top": 632.6981223972093 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "b19e21af9c52", + "name": "pick_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"style_cond\": {\"pick_style\": \"first_or_default\", \"__current_case__\": 1, \"type_cond\": {\"param_type\": \"integer\", \"__current_case__\": 1, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"ConnectedValue\"}}], \"default_value\": \"21\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.2.0", + "type": "tool", + "uuid": "89acf50f-a411-4e93-adfd-f90f14306d52", + "when": null, + "workflow_outputs": [] + }, + "6": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl_count_kmers/meryl_count_kmers/1.3+galaxy7", + "errors": null, + "id": 6, + "input_connections": { + "input_reads": { "id": 1, "output_name": "output" }, - "operation_type|options_kmer_size|input_kmer_size": { - "id": 3, + "options_kmer_size|input_kmer_size": { + "id": 5, + "output_name": "integer_param" + } + }, + "inputs": [], + "label": null, + "name": "Meryl", + "outputs": [ + { + "name": "read_db", + "type": "meryldb" + } + ], + "position": { + "left": 939.3740103274155, + "top": 110.13449847651007 + }, + "post_job_actions": { + "HideDatasetActionread_db": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "read_db" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl_count_kmers/meryl_count_kmers/1.3+galaxy7", + "tool_shed_repository": { + "changeset_revision": "bb6774c6aeaf", + "name": "meryl_count_kmers", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"count_operation\": \"count\", \"input_reads\": {\"__class__\": \"ConnectedValue\"}, \"options_kmer_size\": {\"kmer_size\": \"provide\", \"__current_case__\": 0, \"input_kmer_size\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.3+galaxy7", + "type": "tool", + "uuid": "813fe35d-87e5-4948-8bf0-24f087d872f4", + "when": null, + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", + "errors": null, + "id": 7, + "input_connections": { + "operation_type|input_reads": { + "id": 2, "output_name": "output" + }, + "operation_type|options_kmer_size|input_kmer_size": { + "id": 5, + "output_name": "integer_param" } }, "inputs": [], @@ -177,8 +269,8 @@ } ], "position": { - "left": 977.19921875, - "top": 290.35629999997394 + "left": 908.7621267409064, + "top": 1144.9401063508444 }, "post_job_actions": { "HideDatasetActionread_db": { @@ -197,15 +289,15 @@ "tool_state": "{\"operation_type\": {\"command_type\": \"count-kmers\", \"__current_case__\": 0, \"count_operations\": \"count\", \"input_reads\": {\"__class__\": \"ConnectedValue\"}, \"options_kmer_size\": {\"kmer_size\": \"provide\", \"__current_case__\": 0, \"input_kmer_size\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.3+galaxy6", "type": "tool", - "uuid": "3cb010a0-5dcd-4fb2-b6b2-a66b95001f4e", + "uuid": "4d9b4be1-8f1a-4457-8955-0649971b6f63", "when": null, "workflow_outputs": [] }, - "6": { + "8": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", "errors": null, - "id": 6, + "id": 8, "input_connections": { "operation_type|child_reads": { "id": 0, @@ -216,8 +308,8 @@ "output_name": "output" }, "operation_type|options_kmer_size|input_kmer_size": { - "id": 3, - "output_name": "output" + "id": 5, + "output_name": "integer_param" }, "operation_type|paternal_reads": { "id": 1, @@ -254,8 +346,8 @@ } ], "position": { - "left": 1310.74609375, - "top": 425.69223858421145 + "left": 1448.4867361305037, + "top": 422.4463592843802 }, "post_job_actions": { "HideDatasetActionmat_db_hist": { @@ -346,19 +438,15 @@ } ] }, - "7": { + "9": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl_groups_kmers/meryl_groups_kmers/1.3+galaxy7", "errors": null, - "id": 7, + "id": 9, "input_connections": { - "operation_type|input_reads": { - "id": 2, - "output_name": "output" - }, - "operation_type|options_kmer_size|input_kmer_size": { - "id": 3, - "output_name": "output" + "input_meryldb_02": { + "id": 6, + "output_name": "read_db" } }, "inputs": [], @@ -371,8 +459,8 @@ } ], "position": { - "left": 1007.23046875, - "top": 1038.121924999974 + "left": 1301.3547331422744, + "top": 25.748345240269117 }, "post_job_actions": { "HideDatasetActionread_db": { @@ -381,28 +469,28 @@ "output_name": "read_db" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl_groups_kmers/meryl_groups_kmers/1.3+galaxy7", "tool_shed_repository": { - "changeset_revision": "29dabd8db6f2", - "name": "meryl", + "changeset_revision": "c4758f3bf36e", + "name": "meryl_groups_kmers", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"operation_type\": {\"command_type\": \"count-kmers\", \"__current_case__\": 0, \"count_operations\": \"count\", \"input_reads\": {\"__class__\": \"ConnectedValue\"}, \"options_kmer_size\": {\"kmer_size\": \"provide\", \"__current_case__\": 0, \"input_kmer_size\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3+galaxy6", + "tool_state": "{\"groups_operations\": \"union-sum\", \"input_meryldb_02\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.3+galaxy7", "type": "tool", - "uuid": "0ceeb463-4b8f-49dc-b7e3-66987628ac17", + "uuid": "d10ac58d-439d-4555-b911-f1d0fad69603", "when": null, "workflow_outputs": [] }, - "8": { + "10": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl_groups_kmers/meryl_groups_kmers/1.3+galaxy7", "errors": null, - "id": 8, + "id": 10, "input_connections": { - "operation_type|input_meryldb_02": { - "id": 5, + "input_meryldb_02": { + "id": 7, "output_name": "read_db" } }, @@ -416,8 +504,8 @@ } ], "position": { - "left": 1309.24609375, - "top": 306.91879999997394 + "left": 1297.8309419338123, + "top": 1231.0599821130284 }, "post_job_actions": { "HideDatasetActionread_db": { @@ -426,33 +514,33 @@ "output_name": "read_db" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl_groups_kmers/meryl_groups_kmers/1.3+galaxy7", "tool_shed_repository": { - "changeset_revision": "29dabd8db6f2", - "name": "meryl", + "changeset_revision": "c4758f3bf36e", + "name": "meryl_groups_kmers", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"operation_type\": {\"command_type\": \"groups-kmers\", \"__current_case__\": 3, \"groups_operations\": \"union-sum\", \"input_meryldb_02\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3+galaxy6", + "tool_state": "{\"groups_operations\": \"union-sum\", \"input_meryldb_02\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.3+galaxy7", "type": "tool", - "uuid": "cb7e3912-db9c-437c-ab5a-80844bd6ce2a", + "uuid": "645ecd54-ea5c-4382-a0a3-6b46edb979bc", "when": null, "workflow_outputs": [] }, - "9": { + "11": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0", "errors": null, - "id": 9, + "id": 11, "input_connections": { "input": { - "id": 6, + "id": 8, "output_name": "read_db_hist" }, "kmer_length": { - "id": 3, - "output_name": "output" + "id": 5, + "output_name": "integer_param" }, "ploidy": { "id": 4, @@ -560,6 +648,11 @@ "uuid": "12e75ec0-5722-4ad7-b333-636c3c9ad9c8", "when": null, "workflow_outputs": [ + { + "label": "GenomeScope transformed linear plot (child)", + "output_name": "transformed_linear_plot", + "uuid": "acebbb13-a1bd-4866-9e6f-b15708e7c78d" + }, { "label": "GenomeScope transformed log plot (child)", "output_name": "transformed_log_plot", @@ -570,11 +663,6 @@ "output_name": "summary", "uuid": "12268f46-c221-4417-884b-27cdad90ec05" }, - { - "label": "GenomeScope transformed linear plot (child)", - "output_name": "transformed_linear_plot", - "uuid": "acebbb13-a1bd-4866-9e6f-b15708e7c78d" - }, { "label": "GenomeScope linear plot (child)", "output_name": "linear_plot", @@ -592,59 +680,14 @@ } ] }, - "10": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", - "errors": null, - "id": 10, - "input_connections": { - "operation_type|input_meryldb_02": { - "id": 7, - "output_name": "read_db" - } - }, - "inputs": [], - "label": null, - "name": "Meryl", - "outputs": [ - { - "name": "read_db", - "type": "meryldb" - } - ], - "position": { - "left": 1303.27734375, - "top": 1097.121924999974 - }, - "post_job_actions": { - "HideDatasetActionread_db": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "read_db" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", - "tool_shed_repository": { - "changeset_revision": "29dabd8db6f2", - "name": "meryl", - "owner": "iuc", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"operation_type\": {\"command_type\": \"groups-kmers\", \"__current_case__\": 3, \"groups_operations\": \"union-sum\", \"input_meryldb_02\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3+galaxy6", - "type": "tool", - "uuid": "3453dbb5-08f9-4f34-a7d3-ab8498156b39", - "when": null, - "workflow_outputs": [] - }, - "11": { + "12": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl_histogram_kmers/meryl_histogram_kmers/1.3+galaxy7", "errors": null, - "id": 11, + "id": 12, "input_connections": { - "operation_type|input_meryldb_02": { - "id": 8, + "input_meryldb_02": { + "id": 9, "output_name": "read_db" } }, @@ -658,8 +701,8 @@ } ], "position": { - "left": 1565.08984375, - "top": 345.93442499997394 + "left": 1578.841276483822, + "top": 7.625007303688233 }, "post_job_actions": { "HideDatasetActionread_db_hist": { @@ -668,27 +711,27 @@ "output_name": "read_db_hist" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl_histogram_kmers/meryl_histogram_kmers/1.3+galaxy7", "tool_shed_repository": { - "changeset_revision": "29dabd8db6f2", - "name": "meryl", + "changeset_revision": "9a0227fa7521", + "name": "meryl_histogram_kmers", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"operation_type\": {\"command_type\": \"histogram-kmers\", \"__current_case__\": 4, \"input_meryldb_02\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3+galaxy6", + "tool_state": "{\"input_meryldb_02\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.3+galaxy7", "type": "tool", - "uuid": "fdbda877-8e7f-4b3b-862e-c71bf65ee35e", + "uuid": "eb911656-5d33-4381-a2fe-ba00465e9146", "when": null, "workflow_outputs": [] }, - "12": { + "13": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl_histogram_kmers/meryl_histogram_kmers/1.3+galaxy7", "errors": null, - "id": 12, + "id": 13, "input_connections": { - "operation_type|input_meryldb_02": { + "input_meryldb_02": { "id": 10, "output_name": "read_db" } @@ -703,8 +746,8 @@ } ], "position": { - "left": 1558.05859375, - "top": 1091.137549999974 + "left": 1560.0367016837042, + "top": 1140.0239514182024 }, "post_job_actions": { "HideDatasetActionread_db_hist": { @@ -713,33 +756,33 @@ "output_name": "read_db_hist" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl_histogram_kmers/meryl_histogram_kmers/1.3+galaxy7", "tool_shed_repository": { - "changeset_revision": "29dabd8db6f2", - "name": "meryl", + "changeset_revision": "9a0227fa7521", + "name": "meryl_histogram_kmers", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"operation_type\": {\"command_type\": \"histogram-kmers\", \"__current_case__\": 4, \"input_meryldb_02\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.3+galaxy6", + "tool_state": "{\"input_meryldb_02\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.3+galaxy7", "type": "tool", - "uuid": "76278c97-9522-4f03-b3a3-77c23c460bdc", + "uuid": "2d366d57-1781-4053-b1f5-a4abdeb7b508", "when": null, "workflow_outputs": [] }, - "13": { + "14": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0", "errors": null, - "id": 13, + "id": 14, "input_connections": { "input": { - "id": 11, + "id": 12, "output_name": "read_db_hist" }, "kmer_length": { - "id": 3, - "output_name": "output" + "id": 5, + "output_name": "integer_param" }, "ploidy": { "id": 4, @@ -846,16 +889,6 @@ "uuid": "c65bd0f5-d8d5-4d1d-81bf-6d05458bc160", "when": null, "workflow_outputs": [ - { - "label": "GenomeScope linear plot (paternal)", - "output_name": "linear_plot", - "uuid": "bba131ee-0c54-404a-87f8-067faebea46b" - }, - { - "label": "GenomeScope transformed log plot (paternal)", - "output_name": "transformed_log_plot", - "uuid": "eddc8909-df19-48c2-8406-d6bc784ceb8b" - }, { "label": "GenomeScope log plot (paternal)", "output_name": "log_plot", @@ -865,22 +898,32 @@ "label": "GenomeScope transformed linear plot (paternal)", "output_name": "transformed_linear_plot", "uuid": "2b73811b-e91e-49c6-a122-5065977f9f0e" + }, + { + "label": "GenomeScope linear plot (paternal)", + "output_name": "linear_plot", + "uuid": "bba131ee-0c54-404a-87f8-067faebea46b" + }, + { + "label": "GenomeScope transformed log plot (paternal)", + "output_name": "transformed_log_plot", + "uuid": "eddc8909-df19-48c2-8406-d6bc784ceb8b" } ] }, - "14": { + "15": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0", "errors": null, - "id": 14, + "id": 15, "input_connections": { "input": { - "id": 12, + "id": 13, "output_name": "read_db_hist" }, "kmer_length": { - "id": 3, - "output_name": "output" + "id": 5, + "output_name": "integer_param" }, "ploidy": { "id": 4, @@ -987,6 +1030,11 @@ "uuid": "87497ba1-5c23-4852-9e2f-0bd78dc86753", "when": null, "workflow_outputs": [ + { + "label": "GenomeScope linear plot (maternal)", + "output_name": "linear_plot", + "uuid": "ed208558-8a6f-4405-bd9c-7e6343e9f71d" + }, { "label": "GenomeScope log plot (maternal)", "output_name": "log_plot", @@ -1001,11 +1049,6 @@ "label": "GenomeScope transformed linear plot (maternal)", "output_name": "transformed_linear_plot", "uuid": "7ecb789d-57e3-40f2-81ff-f853b444609b" - }, - { - "label": "GenomeScope linear plot (maternal)", - "output_name": "linear_plot", - "uuid": "ed208558-8a6f-4405-bd9c-7e6343e9f71d" } ] } @@ -1014,6 +1057,6 @@ "Reviewed", "VGP" ], - "uuid": "af01815b-5b66-4578-ade7-6e2caed0c19a", - "version": 9 -} + "uuid": "d146054e-ba07-4d0f-b6af-fef24101d9bc", + "version": 5 +} \ No newline at end of file From 2da1ac74da829bc860bd50e358f3e6254c1f4f3a Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Wed, 11 Dec 2024 08:50:33 -0500 Subject: [PATCH 2/3] add optionnal connection fix --- workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md index 956a7742d..8d550d3e8 100644 --- a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md @@ -6,6 +6,8 @@ - `https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6` was updated to `https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl_count_kmers/meryl_count_kmers/1.3+galaxy7` - `https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6` was updated to `https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl_groups_kmers/meryl_groups_kmers/1.3+galaxy7` - `https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6` was updated to `https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl_histogram_kmers/meryl_histogram_kmers/1.3+galaxy7` +- Fix invalid connections using optional inputs to set default values for non-optional tool inputs. Now using the "pick parameter value" tool to set default value + ## [0.1.7] 2024-08-05 From a79b67b892a2eaba14d91e6a1c20791df710e1f4 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Wed, 11 Dec 2024 08:51:05 -0500 Subject: [PATCH 3/3] add optional connection fix --- .../VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/CHANGELOG.md b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/CHANGELOG.md index 4c2a5f64e..7dbafc92d 100644 --- a/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/CHANGELOG.md @@ -5,7 +5,8 @@ - `https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6` was updated to `https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl_count_kmers/meryl_count_kmers/1.3+galaxy7` - `https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6` was updated to `https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl_groups_kmers/meryl_groups_kmers/1.3+galaxy7` - `https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6` was updated to `https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl_histogram_kmers/meryl_histogram_kmers/1.3+galaxy7` - +- Fix invalid connections using optional inputs to set default values for non-optional tool inputs. Now using the "pick parameter value" tool to set default value +- ## [0.1.4] 2024-08-05 ### Automatic update