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Split collections into 2 #593
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a8871e1
add workflows
lldelisle e2903b5
add tests
lldelisle a863ef3
add .dockstore
lldelisle 5733596
add README CHANGELOG release
lldelisle 86b19a6
relabel tests files and update dockstore
lldelisle f3dfa05
use - instead of _
lldelisle 2208649
do not get space in workflow names
lldelisle 0619a94
update workflows and tests
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29 changes: 29 additions & 0 deletions
29
workflows/data-manipulation/split-collection/.dockstore.yml
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| version: 1.2 | ||
| workflows: | ||
| - name: Split-collection-by-pattern-in-identifiers | ||
| subclass: Galaxy | ||
| publish: true | ||
| primaryDescriptorPath: /Split-collection-by-pattern-in-identifiers.ga | ||
| testParameterFiles: | ||
| - /Split-collection-by-pattern-in-identifiers-tests.yml | ||
| authors: | ||
| - name: Lucille Delisle | ||
| orcid: 0000-0002-1964-4960 | ||
| - name: Split-collection-using-tabular | ||
| subclass: Galaxy | ||
| publish: true | ||
| primaryDescriptorPath: /Split-collection-using-tabular.ga | ||
| testParameterFiles: | ||
| - /Split-collection-using-tabular-tests.yml | ||
| authors: | ||
| - name: Lucille Delisle | ||
| orcid: 0000-0002-1964-4960 | ||
| - name: Split-collection-using-comma-separated-list | ||
| subclass: Galaxy | ||
| publish: true | ||
| primaryDescriptorPath: /Split-collection-using-comma-separated-list.ga | ||
| testParameterFiles: | ||
| - /Split-collection-using-comma-separated-list-tests.yml | ||
| authors: | ||
| - name: Lucille Delisle | ||
| orcid: 0000-0002-1964-4960 |
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| # Changelog | ||
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| ## [0.1] 2024-11-12 | ||
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| First release |
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| # Split collection | ||
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| These workflows allow to split a collection into 2 using identifiers. | ||
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| The common input to all workflows is a collection of type 'list'. | ||
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| The way to split the collection differs with the workflow. | ||
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| - In the workflow "Split collection by pattern in identifiers", you need to specify a "pattern". This is a word that is present only in one part of your samples. This will split your collection into 2: one with the identifiers which have the 'pattern' and the other one with the identifiers which don't have. | ||
| - In the workflow "Split collection using tabular", you need to give a tabular where the first column is the identifier and the second column is the group (no header). All identifiers where the second column match the first item will be grouped into a collection. Others will be in another collection. | ||
| - In the workflow "Split collection using comma separated list", you need to give the group of each item of your collection separated by comma. For example, if you have 3 items in your collection, you can put "1,1,2" to put the first 2 together and the third one appart. | ||
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| Warnings: | ||
| - If you specify more than 2 groups in the second and third workflow, it will not create 3 collections. | ||
51 changes: 51 additions & 0 deletions
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...s/data-manipulation/split-collection/Split-collection-by-pattern-in-identifiers-tests.yml
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| - doc: Test outline for Split-collection-by-pattern-in-identifiers.ga | ||
| job: | ||
| Input Dataset Collection: | ||
| class: Collection | ||
| collection_type: list | ||
| elements: | ||
| - class: File | ||
| identifier: cat1_1 | ||
| path: test-data/file.txt | ||
| - class: File | ||
| identifier: cat1_2 | ||
| path: test-data/file.txt | ||
| - class: File | ||
| identifier: cat1_3 | ||
| path: test-data/file.txt | ||
| - class: File | ||
| identifier: cat2_1 | ||
| path: test-data/file.txt | ||
| - class: File | ||
| identifier: cat3_1 | ||
| path: test-data/file.txt | ||
| pattern: cat1 | ||
| outputs: | ||
| unselected_collection: | ||
| class: Collection | ||
| collection_type: list | ||
| element_tests: | ||
| cat2_1: | ||
| asserts: | ||
| has_text: | ||
| text: "whatever" | ||
| cat3_1: | ||
| asserts: | ||
| has_text: | ||
| text: "whatever" | ||
| selected_collection: | ||
| class: Collection | ||
| collection_type: list | ||
| element_tests: | ||
| cat1_1: | ||
| asserts: | ||
| has_text: | ||
| text: "whatever" | ||
| cat1_2: | ||
| asserts: | ||
| has_text: | ||
| text: "whatever" | ||
| cat1_3: | ||
| asserts: | ||
| has_text: | ||
| text: "whatever" |
244 changes: 244 additions & 0 deletions
244
workflows/data-manipulation/split-collection/Split-collection-by-pattern-in-identifiers.ga
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| { | ||
| "a_galaxy_workflow": "true", | ||
| "annotation": "This workflow takes a collection and returns 2 collections. One with the items which contains the pattern, one with the items which do not contains the pattern.", | ||
| "comments": [], | ||
| "creator": [ | ||
| { | ||
| "class": "Person", | ||
| "identifier": "https://orcid.org/0000-0002-1964-4960", | ||
| "name": "Lucille Delisle" | ||
| } | ||
| ], | ||
| "format-version": "0.1", | ||
| "license": "MIT", | ||
| "release": "0.1", | ||
| "name": "Split collection by pattern in identifiers", | ||
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|
||
| "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": "Collection you want to split into 2", | ||
| "content_id": null, | ||
| "errors": null, | ||
| "id": 0, | ||
| "input_connections": {}, | ||
| "inputs": [ | ||
| { | ||
| "description": "Collection you want to split into 2", | ||
| "name": "Input Dataset Collection" | ||
| } | ||
| ], | ||
| "label": "Input Dataset Collection", | ||
| "name": "Input dataset collection", | ||
| "outputs": [], | ||
| "position": { | ||
| "left": 0, | ||
| "top": 72 | ||
| }, | ||
| "tool_id": null, | ||
| "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", | ||
| "tool_version": null, | ||
| "type": "data_collection_input", | ||
| "uuid": "3065a6b3-a33e-4eb3-97d7-13681b2b4e40", | ||
| "when": null, | ||
| "workflow_outputs": [] | ||
| }, | ||
| "1": { | ||
| "annotation": "pattern used to select the items in the collection", | ||
| "content_id": null, | ||
| "errors": null, | ||
| "id": 1, | ||
| "input_connections": {}, | ||
| "inputs": [ | ||
| { | ||
| "description": "pattern used to select the items in the collection", | ||
| "name": "pattern" | ||
| } | ||
| ], | ||
| "label": "pattern", | ||
| "name": "Input parameter", | ||
| "outputs": [], | ||
| "position": { | ||
| "left": 43, | ||
| "top": 177.5 | ||
| }, | ||
| "tool_id": null, | ||
| "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}", | ||
| "tool_version": null, | ||
| "type": "parameter_input", | ||
| "uuid": "3070ffe4-0f1a-47f4-92a2-98024da29942", | ||
| "when": null, | ||
| "workflow_outputs": [] | ||
| }, | ||
| "2": { | ||
| "annotation": "", | ||
| "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2", | ||
| "errors": null, | ||
| "id": 2, | ||
| "input_connections": { | ||
| "input_collection": { | ||
| "id": 0, | ||
| "output_name": "output" | ||
| } | ||
| }, | ||
| "inputs": [], | ||
| "label": null, | ||
| "name": "Extract element identifiers", | ||
| "outputs": [ | ||
| { | ||
| "name": "output", | ||
| "type": "txt" | ||
| } | ||
| ], | ||
| "position": { | ||
| "left": 299, | ||
| "top": 0 | ||
| }, | ||
| "post_job_actions": { | ||
| "HideDatasetActionoutput": { | ||
| "action_arguments": {}, | ||
| "action_type": "HideDatasetAction", | ||
| "output_name": "output" | ||
| } | ||
| }, | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2", | ||
| "tool_shed_repository": { | ||
| "changeset_revision": "d3c07d270a50", | ||
| "name": "collection_element_identifiers", | ||
| "owner": "iuc", | ||
| "tool_shed": "toolshed.g2.bx.psu.edu" | ||
| }, | ||
| "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_collection\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", | ||
| "tool_version": "0.0.2", | ||
| "type": "tool", | ||
| "uuid": "0abdf45b-5993-4645-ae05-a9f5f0efa1f8", | ||
| "when": null, | ||
| "workflow_outputs": [] | ||
| }, | ||
| "3": { | ||
| "annotation": "", | ||
| "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1", | ||
| "errors": null, | ||
| "id": 3, | ||
| "input_connections": { | ||
| "infile": { | ||
| "id": 2, | ||
| "output_name": "output" | ||
| }, | ||
| "url_paste": { | ||
| "id": 1, | ||
| "output_name": "output" | ||
| } | ||
| }, | ||
| "inputs": [], | ||
| "label": "Select identifiers with pattern", | ||
| "name": "Search in textfiles", | ||
| "outputs": [ | ||
| { | ||
| "name": "output", | ||
| "type": "input" | ||
| } | ||
| ], | ||
| "position": { | ||
| "left": 577, | ||
| "top": 106 | ||
| }, | ||
| "post_job_actions": { | ||
| "HideDatasetActionoutput": { | ||
| "action_arguments": {}, | ||
| "action_type": "HideDatasetAction", | ||
| "output_name": "output" | ||
| } | ||
| }, | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1", | ||
| "tool_shed_repository": { | ||
| "changeset_revision": "86755160afbf", | ||
| "name": "text_processing", | ||
| "owner": "bgruening", | ||
| "tool_shed": "toolshed.g2.bx.psu.edu" | ||
| }, | ||
| "tool_state": "{\"case_sensitive\": \"-i\", \"color\": \"NOCOLOR\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"\", \"lines_after\": \"0\", \"lines_before\": \"0\", \"regex_type\": \"-P\", \"url_paste\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", | ||
| "tool_version": "9.3+galaxy1", | ||
| "type": "tool", | ||
| "uuid": "ec998903-14ca-463e-bbde-1d0ff8c5d0f8", | ||
| "when": null, | ||
| "workflow_outputs": [] | ||
| }, | ||
| "4": { | ||
| "annotation": "", | ||
| "content_id": "__FILTER_FROM_FILE__", | ||
| "errors": null, | ||
| "id": 4, | ||
| "input_connections": { | ||
| "how|filter_source": { | ||
| "id": 3, | ||
| "output_name": "output" | ||
| }, | ||
| "input": { | ||
| "id": 0, | ||
| "output_name": "output" | ||
| } | ||
| }, | ||
| "inputs": [ | ||
| { | ||
| "description": "runtime parameter for tool Filter collection", | ||
| "name": "how" | ||
| } | ||
| ], | ||
| "label": "Split collection into 2", | ||
| "name": "Filter collection", | ||
| "outputs": [ | ||
| { | ||
| "name": "output_filtered", | ||
| "type": "input" | ||
| }, | ||
| { | ||
| "name": "output_discarded", | ||
| "type": "input" | ||
| } | ||
| ], | ||
| "position": { | ||
| "left": 797, | ||
| "top": 106 | ||
| }, | ||
| "post_job_actions": { | ||
| "RenameDatasetActionoutput_discarded": { | ||
| "action_arguments": { | ||
| "newname": "not ${pattern}" | ||
| }, | ||
| "action_type": "RenameDatasetAction", | ||
| "output_name": "output_discarded" | ||
| }, | ||
| "RenameDatasetActionoutput_filtered": { | ||
| "action_arguments": { | ||
| "newname": "${pattern}" | ||
| }, | ||
| "action_type": "RenameDatasetAction", | ||
| "output_name": "output_filtered" | ||
| } | ||
| }, | ||
| "tool_id": "__FILTER_FROM_FILE__", | ||
| "tool_state": "{\"how\": {\"how_filter\": \"remove_if_absent\", \"__current_case__\": 0, \"filter_source\": {\"__class__\": \"ConnectedValue\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", | ||
| "tool_version": "1.0.0", | ||
| "type": "tool", | ||
| "uuid": "68b2babb-f4c1-4e5f-ba3c-e00704baa798", | ||
| "when": null, | ||
| "workflow_outputs": [ | ||
| { | ||
| "label": "unselected_collection", | ||
| "output_name": "output_discarded", | ||
| "uuid": "c94a017b-41bd-41a1-9eb5-c2a26c475c53" | ||
| }, | ||
| { | ||
| "label": "selected_collection", | ||
| "output_name": "output_filtered", | ||
| "uuid": "5a70e977-f0fc-48ca-8ec1-947b2da01a67" | ||
| } | ||
| ] | ||
| } | ||
| }, | ||
| "tags": [], | ||
| "uuid": "67c71ce5-ce8e-4d09-8e6c-e45d2ced17b6", | ||
| "version": 3 | ||
| } | ||
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Is that a regex pattern or literal words ?
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It uses grep so it is a regex. However, as this workflow is targeting a "user" audience I was trying to make it understandable for non bioinformaticians but I am happy to get suggestions.
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They might be surpised if they do enter special characters, so best to mention this I think ?
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Actually, do you expect users to run this workflow as a standalone workflow ? I thought this was useful as a thing to embed in another workflow ? Would it maybe make more sense to add what is not covered by the filter filter to the tool itself ?
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I feel like I am using this workflow as a standalone. For example, to select only part of my samples for deeper analysis or for a specific heatmap etc...
You are right about the word/regex, I should warn the users.