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synced 2026-09-24 16:30:27 +08:00
John Chilton
4c5c8a47db
Models: Track whether dataset collections have been populated yet. Dataset collections are still effectively immutable once populated - but dynamic output collections require them to be sort of like `final` fields in Java (analogy courtesy of JJ) - allowing them to be declared before they are initialized or populated. This is tracked by the `populated_state` field. Tools: Output collections can now describe `discover_datasets` elements just like datasets - except in this case instead of dynamically populating new datasets in the history - they will comprise the collection. `designation` has been reused to serve as the element_identifier for the collection element corresponding to the dataset. See Pull Request 356 for more information on the discover_datasets tag https://bitbucket.org/galaxy/galaxy-central/pull-request/356/enhancements-for-runtime-discovered. Workflows: Update workflow execution and recovery for dynamic output collections. Galaxy workflow data flow before collections * - * - * - * - * - * Galaxy worfklow data flow after collections (iteration 1) * - * - * \ * - * - * * - * - * / \ * - * - * * - * - * \ / * - * - * * - * - * / Galaxy worfklow data flow after this commit / * - * \ * - * * - * / \ * - * / \ / \ / \ / / * - * \ \ * - * -- * - * * - * -- * - * \ \ * - * / / \ / \ / \ / * - * \ / * - * * - * \ * - * /
31 lines
1.0 KiB
XML
31 lines
1.0 KiB
XML
<tool id="collection_split_on_column" name="collection_split_on_column" version="0.1.0">
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<command>
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mkdir outputs; cd outputs; awk '{ print \$2 > \$1 ".tabular" }' $input1
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</command>
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<inputs>
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<param name="input1" type="data" label="Input Table" help="Table to split on first column" format="tabular" />
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</inputs>
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<outputs>
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<collection name="split_output" type="list" label="Table split on first column">
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<discover_datasets pattern="__name_and_ext__" directory="outputs" />
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</collection>
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</outputs>
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<tests>
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<test>
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<param name="input1" value="tinywga.fam" />
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<output_collection name="split_output" type="list">
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<element name="101">
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<assert_contents>
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<has_text_matching expression="^1\n2\n3\n$" />
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</assert_contents>
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</element>
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<element name="1334">
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<assert_contents>
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<has_text_matching expression="^1\n10\n11\n12\n13\n2\n$" />
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</assert_contents>
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</element>
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</output_collection>
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</test>
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</tests>
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</tool>
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