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VGP 1 and 2 - update meryl to the galaxy7 wrapper #622

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merged 3 commits into from
Dec 11, 2024
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VGP 1 and 2 - update meryl to the galaxy7 wrapper #622

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3a32a2c
update meryl
Delphine-L Dec 3, 2024
2da1ac7
add optionnal connection fix
Delphine-L Dec 11, 2024
a79b67b
add optional connection fix
Delphine-L Dec 11, 2024
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9 changes: 9 additions & 0 deletions workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md
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@@ -1,5 +1,14 @@
# 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`
- 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

### Automatic update
Expand Down
163 changes: 101 additions & 62 deletions workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga
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Expand Up @@ -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"
Expand All @@ -37,8 +37,8 @@
"name": "Input dataset collection",
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"tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}",
Expand All @@ -64,8 +64,8 @@
"name": "Input parameter",
"outputs": [],
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"left": 68.13671875,
"top": 408.3515627685539
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"tool_id": null,
"tool_state": "{\"default\": 21, \"parameter_type\": \"integer\", \"optional\": true}",
Expand All @@ -91,8 +91,8 @@
"name": "Input parameter",
"outputs": [],
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"top": 569.6054690185539
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"tool_id": null,
"tool_state": "{\"default\": 2, \"parameter_type\": \"integer\", \"optional\": true}",
Expand All @@ -104,17 +104,56 @@
},
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"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0",
"errors": null,
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"input_connections": {
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"id": 1,
"output_name": "output"
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"inputs": [],
"label": null,
"name": "Pick parameter value",
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{
"name": "integer_param",
"type": "expression.json"
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],
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"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",
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"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl_count_kmers/meryl_count_kmers/1.3+galaxy7",
"errors": null,
"id": 4,
"input_connections": {
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"operation_type|options_kmer_size|input_kmer_size": {
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"output_name": "output"
"options_kmer_size|input_kmer_size": {
"id": 3,
"output_name": "integer_param"
}
},
"inputs": [],
Expand All @@ -127,8 +166,8 @@
}
],
"position": {
"left": 296.8668759977911,
"top": 27
"left": 419.9140625,
"top": 102.30468776855386
},
"post_job_actions": {
"HideDatasetActionread_db": {
Expand All @@ -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",
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"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"
}
},
Expand All @@ -172,8 +211,8 @@
}
],
"position": {
"left": 576.8668759977911,
"top": 0
"left": 702.75390625,
"top": 0.0
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"post_job_actions": {
"TagDatasetActionread_db": {
Expand All @@ -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"
}
},
Expand All @@ -225,8 +264,8 @@
}
],
"position": {
"left": 856.8668759977911,
"top": 42
"left": 992.953125,
"top": 83.94920349121094
},
"post_job_actions": {
"HideDatasetActionread_db_hist": {
Expand All @@ -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,
Expand Down Expand Up @@ -302,8 +341,8 @@
}
],
"position": {
"left": 1136.866875997791,
"top": 15
"left": 1274.636407247791,
"top": 125.53515651855386
},
"post_job_actions": {
"TagDatasetActionlinear_plot": {
Expand Down Expand Up @@ -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",
Expand All @@ -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"
}
]
}
Expand All @@ -406,6 +445,6 @@
"Reviewed",
"VGP"
],
"uuid": "0808b15a-7e3e-4b06-b804-f3d2cc73981a",
"version": 2
}
"uuid": "58adb6d9-0345-44ca-82fd-e394eda5a18b",
"version": 3
}
7 changes: 7 additions & 0 deletions workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/CHANGELOG.md
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# 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`
- 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
Expand Down
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