Mercurial > repos > iuc > packaged_annotation_loader

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

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