-
Notifications
You must be signed in to change notification settings - Fork 73
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Split collections into 2 #593
Open
lldelisle
wants to merge
9
commits into
galaxyproject:main
Choose a base branch
from
lldelisle:split_collection
base: main
Could not load branches
Branch not found: {{ refName }}
Loading
Could not load tags
Nothing to show
Loading
Are you sure you want to change the base?
Some commits from the old base branch may be removed from the timeline,
and old review comments may become outdated.
Open
Changes from all commits
Commits
Show all changes
9 commits
Select commit
Hold shift + click to select a range
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
lldelisle ea558b3
Apply suggestions from @mvdbeek
lldelisle File filter
Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
There are no files selected for viewing
29 changes: 29 additions & 0 deletions
29
workflows/data-manipulation/split-collection/.dockstore.yml
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| 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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| # Changelog | ||
|
|
||
| ## [0.1] 2024-11-12 | ||
|
|
||
| First release |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| # Split collection | ||
|
|
||
| These workflows allow to split a collection into 2 using identifiers. | ||
|
|
||
| The common input to all workflows is a collection of type 'list'. | ||
|
|
||
| The way to split the collection differs with the workflow. | ||
|
|
||
| - 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. | ||
|
|
||
| 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
51
...s/data-manipulation/split-collection/Split-collection-by-pattern-in-identifiers-tests.yml
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,51 @@ | ||
| - 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
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,244 @@ | ||
| { | ||
| "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 element identifiers", | ||
| "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 | ||
| } |
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Is that a regex pattern or literal words ?
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
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.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
They might be surpised if they do enter special characters, so best to mention this I think ?
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
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 ?
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
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.