Mercurial > repos > iuc > packaged_annotation_loader
diff 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"
author | iuc |
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date | Tue, 04 Jan 2022 18:34:48 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/load_annotations.xml Tue Jan 04 18:34:48 2022 +0000 @@ -0,0 +1,133 @@ +<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	Version" /> + <has_line line="CIViC variants	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>