Unverified Commit 745913df authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #18605 from bernt-matthias/xsd-data-action 

[24.1] xsd: allow `change_format` and `actions` also in statically defined collection elements, and break recursion
parents fe6d2e30 262b4b69

doc/schema_template.md

+1 −1
Original line number Diff line number Diff line
@@ -82,7 +82,7 @@ $tag:tool|outputs|data|actions|action://complexType[@name='Action'] 
$tag:tool|outputs|data|actions|action|option://complexType[@name='ActionsOption']

$tag:tool|outputs|data|discover_datasets://complexType[@name='OutputDiscoverDatasets']

$tag:tool|outputs|collection://complexType[@name='OutputCollection']

$tag:tool|outputs|collection|data://complexType[@name='OutputCollectionDataElement']

$tag:tool|outputs|collection|data://complexType[@name='OutputCollectionData']

$tag:tool|outputs|collection|filter://complexType[@name='OutputFilter']

$tag:tool|outputs|collection|discover_datasets://complexType[@name='OutputCollectionDiscoverDatasets']

$tag:tool|tests://complexType[@name='Tests']

lib/galaxy/tool_util/xsd/galaxy.xsd

+34 −65
Original line number Diff line number Diff line
@@ -5827,15 +5827,24 @@ on Human (hg18)``. 
    <xs:attributeGroup ref="OutputDataAttributes"/>

  </xs:complexType>



  <!-- Allowed tags included in collection-data -->

  <xs:group name="OutputCollectionDataElement">

    <xs:choice>

      <xs:element name="actions" type="Actions" />

      <xs:element name="change_format" type="ChangeFormat" />

    </xs:choice>

  </xs:group>



  <!-- Allowed tags included in collection -->

  <xs:group name="OutputCollectionElement">

    <xs:choice>

      <xs:element name="data" type="OutputCollectionDataElement" />

      <xs:element name="data" type="OutputCollectionData" />

      <xs:element name="discover_datasets" type="OutputCollectionDiscoverDatasets" />

      <xs:element name="filter" type="OutputFilter" />

    </xs:choice>

  </xs:group>



  <xs:complexType name="OutputCollectionDataElement">

  <xs:complexType name="OutputCollectionData">

    <xs:annotation>

      <xs:documentation xml:lang="en"><![CDATA[
@@ -5844,7 +5853,7 @@ define the elements of a collection statically. See also [Planemo's documentatio 
]]></xs:documentation>

    </xs:annotation>

    <xs:sequence>

      <xs:group ref="OutputCollectionElement" minOccurs="0" maxOccurs="unbounded" />

      <xs:group ref="OutputCollectionDataElement" minOccurs="0" maxOccurs="unbounded" />

    </xs:sequence>

    <xs:attributeGroup ref="OutputCommon" />

    <xs:attributeGroup ref="OutputDataAttributes" />
@@ -6002,23 +6011,7 @@ 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>
@@ -6069,6 +6062,26 @@ 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>
@@ -6092,51 +6105,7 @@ 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>

test/functional/tools/collection_creates_pair_format.xml

+42 −2
Original line number Diff line number Diff line
@@ -7,16 +7,28 @@ 
  </command>

  <inputs>

    <param name="input1" type="data" label="Input" help="Input to be split." />

    <param name="out_format" type="select" label="Output data type">

      <option value="">do not change</option>

      <option value="interval">interval</option>

  </param>

  </inputs>

  <outputs>

    <!-- format is specified separately for the elements, i.e. default format (fasta in this case) is ignored -->

    <collection name="paired_output" format="fasta" type="paired" label="Split Pair">

      <data name="forward" format="txt" />

      <data name="forward" format="txt">

        <change_format>

          <when input="out_format" value="interval" format="interval" />

        </change_format>

      </data>

      <data name="reverse" format_source="input1" from_work_dir="reverse.txt" />

    </collection>

    <!-- no format is specified separately for the elements, i.e. default format (fasta in this case) is used -->

    <collection name="paired_output_default_format" format="fasta" type="paired" label="Split Pair">

      <data name="forward" />

      <data name="forward">

        <change_format>

          <when input="out_format" value="interval" format="interval" />

        </change_format>

      </data>

      <data name="reverse" from_work_dir="reverse.txt" />

    </collection>

  </outputs>
@@ -48,5 +60,33 @@ 
        </element>

      </output_collection>

    </test>

    <test>

      <param name="input1" ftype="bed" value="simple_lines_interleaved.txt" />

      <param name="out_format" value="interval"/>

      <output_collection name="paired_output" type="paired">

        <element name="forward" ftype="interval">

          <assert_contents>

            <has_text_matching expression="^This is a line of text.\nThis is a line of text.\n$" />

          </assert_contents>

        </element>

        <element name="reverse" ftype="bed">

          <assert_contents>

            <has_text_matching expression="^This is a different line of text.\nThis is a different line of text.\n$" />

          </assert_contents>

        </element>

      </output_collection>

      <output_collection name="paired_output_default_format" type="paired">

        <element name="forward" ftype="interval">

          <assert_contents>

            <has_text_matching expression="^This is a line of text.\nThis is a line of text.\n$" />

          </assert_contents>

        </element>

        <element name="reverse" ftype="fasta">

          <assert_contents>

            <has_text_matching expression="^This is a different line of text.\nThis is a different line of text.\n$" />

          </assert_contents>

        </element>

      </output_collection>

    </test>

  </tests>

</tool>

test/functional/tools/metadata_column_names.xml

+23 −1
Original line number Diff line number Diff line 
<tool id="metadata_columns" name="metadata_columns" version="1.0.0">

    <description>Tests whether metadata is being set correctly.</description>

    <command><![CDATA[

        cp '$input' '$output'

        cp '$input' '$output';

        cp '$input' '$paired_output.forward' ;

        cp '$input' '$paired_output.reverse' ;

    ]]></command>

    <inputs>

        <param name="input" type="data" multiple="false" />
@@ -12,6 +14,18 @@ 
                <action name="column_names" type="metadata" default="First,${input.name}" />

            </actions>

        </data>

        <collection name="paired_output" format="tabular" type="paired" label="Split Pair">

            <data name="forward">

                <actions>

                    <action name="dbkey" type="metadata" default="hg38" />

                </actions>

            </data>

            <data name="reverse">

                <actions>

                    <action name="column_names" type="metadata" default="A,B,C" />

                </actions>

            </data>

    </collection>

    </outputs>

    <tests>

        <test>
@@ -19,6 +33,14 @@ 
            <output name="output">

                <metadata name="column_names" value="First,2.tabular"/>

            </output>

            <output_collection name="paired_output" type="paired">

                <element name="forward" ftype="tabular" value="2.tabular">

                    <metadata name="dbkey" value="hg38"/>

                </element>

                <element name="reverse" ftype="tabular" value="2.tabular">

                    <metadata name="column_names" value="A,B,C"/>

                </element>

              </output_collection>

        </test>

    </tests>

</tool>