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xsd: add OutputDiscoverDatasetsCommon
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to describe attributes common to OutputDiscoverDatasets and OutputCollectionDiscoverDatasets
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@bernt-matthias
bernt-matthias committed Jul 29, 2024
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Showing 1 changed file with 22 additions and 62 deletions.
84 changes: 22 additions & 62 deletions lib/galaxy/tool_util/xsd/galaxy.xsd
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Expand Up @@ -6004,23 +6004,7 @@ Therefore a filter for such a variable looks like the following example.
</xs:simpleContent>
</xs:complexType>

<xs:complexType name="OutputDiscoverDatasets">
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[
Describe datasets to dynamically collect after the job complete.
There are many simple tools with examples of this element distributed with
Galaxy, including:
* [multi_output.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/multi_output.xml)
* [multi_output_assign_primary.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/multi_output_assign_primary.xml)
* [multi_output_configured.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/multi_output_configured.xml)
More information can be found on Planemo's documentation for
[multiple output files](https://planemo.readthedocs.io/en/latest/writing_advanced.html#multiple-output-files).
]]></xs:documentation>
</xs:annotation>
<xs:attributeGroup name="OutputDiscoverDatasetsCommon">
<xs:attribute name="from_provided_metadata" type="xs:boolean" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">Indicate that dataset filenames should simply be read from the provided metadata file (e.g. galaxy.json). If this is set - pattern and sort must not be set.</xs:documentation>
Expand Down Expand Up @@ -6071,6 +6055,26 @@ More information can be found on Planemo's documentation for
<xs:documentation xml:lang="en">Indication if this dataset is visible in output history. This defaults to ``false``, but probably shouldn't - be sure to set to ``true`` if that is your intention.</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:attributeGroup>

<xs:complexType name="OutputDiscoverDatasets">
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[
Describe datasets to dynamically collect after the job complete.
There are many simple tools with examples of this element distributed with
Galaxy, including:
* [multi_output.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/multi_output.xml)
* [multi_output_assign_primary.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/multi_output_assign_primary.xml)
* [multi_output_configured.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/multi_output_configured.xml)
More information can be found on Planemo's documentation for
[multiple output files](https://planemo.readthedocs.io/en/latest/writing_advanced.html#multiple-output-files).
]]></xs:documentation>
</xs:annotation>
<xs:attributeGroup ref="OutputDiscoverDatasetsCommon"/>
<xs:attribute name="assign_primary_output" type="xs:boolean" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">Replace the primary dataset described by the parameter ``data`` parameter with the first output discovered.</xs:documentation>
Expand All @@ -6094,51 +6098,7 @@ Galaxy, including:
]]></xs:documentation>
</xs:annotation>
<xs:attribute name="from_provided_metadata" type="xs:boolean" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">Indicate that dataset filenames should simply be read from the provided metadata file (e.g. galaxy.json). If this is set - pattern and sort_by must not be set.</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="pattern" type="xs:string" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">Regular expression used to find filenames and parse dynamic properties.</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="directory" type="xs:string" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">Directory (relative to working directory) to search for files.</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="recurse" type="xs:boolean" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">Indicates that the specified directory should be searched recursively for matching files.</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="match_relative_path" type="xs:boolean" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">Indicates that the entire path of the discovered dataset relative to the specified directory should be available for matching patterns.</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="format" type="xs:string" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">Format (or datatype) of discovered datasets (an alias with ``ext``).</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="ext" type="xs:string" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">Format (or datatype) of discovered datasets (an alias with ``format``).</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="sort_by" type="xs:string" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">A string `[reverse_][SORT_COMP_]SORTBY` describing the desired sort order of the collection elements. `SORTBY` can be `filename`, `name`, `designation`, `dbkey` and the optional `SORT_COMP` can be either `lexical` or `numeric`. Default is lexical sorting by filename.</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="visible" type="xs:boolean" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">Indication if this dataset is visible in the history. This defaults to ``false``, but probably shouldn't - be sure to set to ``true`` if that is your intention.</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attributeGroup ref="OutputDiscoverDatasetsCommon"/>
</xs:complexType>
<xs:complexType name="Actions">
<xs:annotation>
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