Commit 8b8791a6 authored by Matthias Bernt's avatar Matthias Bernt
Browse files

xsd: add OutputDiscoverDatasetsCommon 

to describe attributes common to OutputDiscoverDatasets and OutputCollectionDiscoverDatasets
parent 3b3a65d1

lib/galaxy/tool_util/xsd/galaxy.xsd

+22 −62
Original line number Diff line number Diff line
@@ -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>
@@ -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>
@@ -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>