Unverified Commit 7c2be774 authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #20854 from bernt-matthias/undo-accidental-push

parents 716e3607 0b6cf742

lib/galaxy/config/sample/datatypes_conf.xml.sample

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@@ -329,7 +329,6 @@ 
    <datatype extension='qiime2.tabular' type="galaxy.datatypes.qiime2:QIIME2Metadata" display_in_upload="true"/>

    <datatype extension="zip" type="galaxy.datatypes.binary:CompressedZipArchive" display_in_upload="true">

        <converter file="archive_to_directory.xml" target_datatype="directory" />

        <converter file="archive_to_directory.xml" target_datatype="lexicmap_index"/>

    </datatype>

    <datatype extension="ncbi_genome_dataset.zip" type="galaxy.datatypes.binary:CompressedZipArchive" subclass="true" display_in_upload="true"/>

    <datatype extension="zarr.zip" type="galaxy.datatypes.binary:CompressedZarrZipArchive" display_in_upload="true">
@@ -340,7 +339,6 @@ 
    </datatype>

    <datatype extension="tar" auto_compressed_types="gz,bz2" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true">

      <converter file="archive_to_directory.xml" target_datatype="directory"/>

      <converter file="archive_to_directory.xml" target_datatype="lexicmap_index"/>

    </datatype>

    <datatype extension="directory" type="galaxy.datatypes.data:Directory"/>

    <datatype extension="bwa_mem2_index" display_in_upload="true" type="galaxy.datatypes.data:Directory" subclass="true"/>

lib/galaxy/datatypes/converters/archive_to_directory.xml

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@@ -22,7 +22,6 @@ 
            <option value="directory">directory</option>

            <option value="zarr">zarr</option>

            <option value="ome_zarr">ome_zarr</option>

            <option value="lexicmap_index">lexicmap_index</option>

        </param>

    </inputs>

    <outputs provided_metadata_file="metadata_json">

test/functional/tools/directory_datatype.xml

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<tool id="directory_datatype" name="Directory datatype" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.0" license="MIT">

    <description>Test with the directory</description>

    <macros>

        <token name="@TOOL_VERSION@">0.1.0</token>

        <token name="@VERSION_SUFFIX@">0</token>

    </macros>

    <command detect_errors="exit_code"><![CDATA[

        ls '$directory_in.files_path'/* &&

        mkdir '$directory_out.files_path' &&

        cp -r '$directory_in.files_path'/* '$directory_out.files_path'/ &&

        ls '$directory_out.files_path'/* &&



        ls '$directory_derived_in.files_path'/* &&

        mkdir '$directory_derived_out.files_path' &&

        cp -r '$directory_derived_in.files_path'/* '$directory_derived_out.files_path'/ &&

        ls '$directory_derived_out.files_path'/*



    ]]></command>

    <inputs>

        <param name="directory_in" type="data" format="directory" label="Directory input" />

        <param name="directory_derived_in" type="data" format="lexicmap_index" label="Lexicmap Index input" />

    </inputs>

    <outputs>

        <data name="directory_out" format="directory" label="${tool.name} on ${on_string}: Directory" />

        <data name="directory_derived_out" format="lexicmap_index" label="${tool.name} on ${on_string}: Lexic Map Index" />

    </outputs>

    <tests>

        <test>

            <param name="directory_in" value="testdir1.tar"/>

            <param name="directory_derived_in" value="testdir1.tar"/>

            <output name="directory_out" value="testdir1.tar.directory"/>

            <output name="directory_derived_out" value="testdir1.tar.directory"/>

        </test>

        <test>

            <param name="directory_in" value="testdir1.zip"/>

            <param name="directory_derived_in" value="testdir1.zip"/>

            <output name="directory_out">

                <assert_contents>

                    <has_size size="0"/>

                </assert_contents>

            </output>

            <output name="directory_derived_out">

                <assert_contents>

                    <has_size size="0"/>

                </assert_contents>

            </output>

            <assert_stdout>

                <has_line line="dir1" n="4"/>

                <has_line line="file1" n="4"/>

                <has_line line="file2" n="4"/>

            </assert_stdout>

        </test>

    </tests>

</tool>
 
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test/functional/tools/sample_tool_conf.xml

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@@ -17,7 +17,6 @@ 
  <tool file="inheritance_simple.xml" />

  <tool file="boolean_conditional.xml" />

  <tool file="composite.xml" />

  <tool file="directory_datatype.xml" />

  <tool file="environment_variables.xml" />

  <tool file="environment_variables_inject.xml" />

  <tool file="code_file.xml" />