annotate load_annotations.xml @ 0:0de428c589f3 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"

<tool id="packaged_annotation_loader" name="Load packaged annotation data" version="0.1" profile="20.05">
    <description>as a collection</description>
    <requirements>
        <requirement type="package" version="3.9">python</requirement>
        <requirement type="package" version="6.0">pyyaml</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        cp $c1 galaxy.json
        #if str($retrieve_meta):
            && python '$__tool_directory__/retrieve_meta.py' --format $retrieve_meta -o meta.out galaxy.json
        #end if
    ]]>    </command>
    <configfiles>
        <configfile name="c1">
            #set $elems=",".join(['{{"name": "%s", "ext": "%s", "filename": "{0}/%s", "dbkey": "{1}"}}' % (i, f, i) for i, f in zip($annotation, $annotation.fields.format.split(','))])
            #set $elems=$elems.format($packaged_data.fields.path, $packaged_data.fields.dbkey)
{"list_output": {"elements": [$elems]}}
        </configfile>
    </configfiles>
    <inputs>
        <param name="packaged_data" type="select" label="Annotation data package to load">
            <options from_data_table="packaged_annotation_data">
                <column name="name" index="6" />
                <column name="value" index="5" />
                <column name="path" index="7" />
                <column name="dbkey" index="1" />
                <filter type="unique_value" column="value" />
                <filter type="sort_by" column="name" />
                <validator type="no_options" message="No annotation paackage available" />
            </options>
        </param>
        <param name="annotation" type="select" multiple="true" optional="false" label="Packaged annotations to load into collection">
            <options from_data_table="packaged_annotation_data">
                <column name="name" index="2" />
                <column name="value" index="3" />
                <column name="format" index="4" />
                <column name="package_id" index="5" />
                <filter type="param_value" ref="packaged_data" column="package_id" />
                <validator type="no_options" message="No annotation data available" />
            </options>
        </param>
        <param name="retrieve_meta" type="select" label="Retrieve annotation sources metadata as separate dataset?">
            <option value="">No metadata</option>
            <option value="yaml">Return the metadata in orignal yaml format</option>
            <option value="tab">Return tabular annotation source/version info</option>
        </param>
    </inputs>
    <outputs>
        <collection name="list_output" type="list" label="Output List">
            <discover_datasets from_provided_metadata="true" visible="false" />
        </collection>
        <data name="meta_out" format="tabular" label="Loaded annotations metadata" from_work_dir="meta.out">
            <filter>bool(str(retrieve_meta))</filter>
            <change_format>
                <when input="retrieve_meta" value="yaml" format="yaml" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="packaged_data" value="Cancer_variant_data__hg19__1__2021-12-16" />
            <param name="annotation" value="hotspots.data.test" />
            <output_collection name="list_output" type="list" count="1">
                <element name="hotspots.data.test" ftype="bed" file="test-annotation-data/hotspots.data.test">
                    <metadata name="dbkey" value="hg19" />
                </element>
            </output_collection>
        </test>
        <test expect_num_outputs="1">
            <param name="packaged_data" value="Cancer_variant_data__hg19__1__2021-12-16" />
            <param name="annotation" value="hotspots.data.test,civic.variants.test" />
            <output_collection name="list_output" type="list" count="2">
                <element name="hotspots.data.test" ftype="bed" file="test-annotation-data/hotspots.data.test">
                    <metadata name="dbkey" value="hg19" />
                </element>
                <element name="civic.variants.test" ftype="bed" file="test-annotation-data/civic.variants.test">
                    <metadata name="dbkey" value="hg19" />
                </element>
            </output_collection>
        </test>
        <test expect_num_outputs="2">
            <param name="packaged_data" value="Cancer_variant_data__hg19__1__2021-12-16" />
            <param name="annotation" value="hotspots.data.test,civic.variants.test" />
            <param name="retrieve_meta" value="yaml" />
            <output_collection name="list_output" type="list" count="2">
                <element name="hotspots.data.test" ftype="bed" file="test-annotation-data/hotspots.data.test">
                    <metadata name="dbkey" value="hg19" />
                </element>
                <element name="civic.variants.test" ftype="bed" file="test-annotation-data/civic.variants.test">
                    <metadata name="dbkey" value="hg19" />
                </element>
            </output_collection>
            <output name="meta_out" ftype="yaml" file="test-annotation-data/meta.yml" />
        </test>
        <test expect_num_outputs="2">
            <param name="packaged_data" value="Cancer_variant_data__hg19__1__2021-12-16" />
            <param name="annotation" value="hotspots.data.test,civic.variants.test" />
            <param name="retrieve_meta" value="tab" />
            <output_collection name="list_output" type="list" count="2">
                <element name="hotspots.data.test" ftype="bed" file="test-annotation-data/hotspots.data.test">
                    <metadata name="dbkey" value="hg19" />
                </element>
                <element name="civic.variants.test" ftype="bed" file="test-annotation-data/civic.variants.test">
                    <metadata name="dbkey" value="hg19" />
                </element>
            </output_collection>
            <output name="meta_out" ftype="tabular" file="anno-version.tsv"/>
        </test>
        <test expect_num_outputs="2">
            <param name="packaged_data" value="Cancer_variant_data__hg19__1__2021-12-16" />
            <param name="annotation" value="civic.variants.test" />
            <param name="retrieve_meta" value="tab" />
            <output_collection name="list_output" type="list" count="1">
                <element name="civic.variants.test" ftype="bed" file="test-annotation-data/civic.variants.test">
                    <metadata name="dbkey" value="hg19" />
                </element>
            </output_collection>
            <output name="meta_out" ftype="tabular">
                <assert_contents>
                    <has_n_lines n="2" />
                    <has_line line="Annotation&#009;Version" />
                    <has_line line="CIViC variants&#009;01-Feb-2019" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
This tool can be used to make genome annotation data installed via the
`data manager for packaged_annotation data
<https://toolshed.g2.bx.psu.edu/view/wolma/data_manager_packaged_annotation_data>`__
accessible as a list of datasets collection.
    ]]></help>
</tool>