Mercurial > repos > iuc > packaged_annotation_loader

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:0de428c589f3
1 <tool id="packaged_annotation_loader" name="Load packaged annotation data" version="0.1" profile="20.05">
2 <description>as a collection</description>
3 <requirements>
4 <requirement type="package" version="3.9">python</requirement>
5 <requirement type="package" version="6.0">pyyaml</requirement>
6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[
8 cp $c1 galaxy.json
9 #if str($retrieve_meta):
10 && python '$__tool_directory__/retrieve_meta.py' --format $retrieve_meta -o meta.out galaxy.json
11 #end if
12 ]]> </command>
13 <configfiles>
14 <configfile name="c1">
15 #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(','))])
16 #set $elems=$elems.format($packaged_data.fields.path, $packaged_data.fields.dbkey)
17 {"list_output": {"elements": [$elems]}}
18 </configfile>
19 </configfiles>
20 <inputs>
21 <param name="packaged_data" type="select" label="Annotation data package to load">
22 <options from_data_table="packaged_annotation_data">
23 <column name="name" index="6" />
24 <column name="value" index="5" />
25 <column name="path" index="7" />
26 <column name="dbkey" index="1" />
27 <filter type="unique_value" column="value" />
28 <filter type="sort_by" column="name" />
29 <validator type="no_options" message="No annotation paackage available" />
30 </options>
31 </param>
32 <param name="annotation" type="select" multiple="true" optional="false" label="Packaged annotations to load into collection">
33 <options from_data_table="packaged_annotation_data">
34 <column name="name" index="2" />
35 <column name="value" index="3" />
36 <column name="format" index="4" />
37 <column name="package_id" index="5" />
38 <filter type="param_value" ref="packaged_data" column="package_id" />
39 <validator type="no_options" message="No annotation data available" />
40 </options>
41 </param>
42 <param name="retrieve_meta" type="select" label="Retrieve annotation sources metadata as separate dataset?">
43 <option value="">No metadata</option>
44 <option value="yaml">Return the metadata in orignal yaml format</option>
45 <option value="tab">Return tabular annotation source/version info</option>
46 </param>
47 </inputs>
48 <outputs>
49 <collection name="list_output" type="list" label="Output List">
50 <discover_datasets from_provided_metadata="true" visible="false" />
51 </collection>
52 <data name="meta_out" format="tabular" label="Loaded annotations metadata" from_work_dir="meta.out">
53 <filter>bool(str(retrieve_meta))</filter>
54 <change_format>
55 <when input="retrieve_meta" value="yaml" format="yaml" />
56 </change_format>
57 </data>
58 </outputs>
59 <tests>
60 <test expect_num_outputs="1">
61 <param name="packaged_data" value="Cancer_variant_data__hg19__1__2021-12-16" />
62 <param name="annotation" value="hotspots.data.test" />
63 <output_collection name="list_output" type="list" count="1">
64 <element name="hotspots.data.test" ftype="bed" file="test-annotation-data/hotspots.data.test">
65 <metadata name="dbkey" value="hg19" />
66 </element>
67 </output_collection>
68 </test>
69 <test expect_num_outputs="1">
70 <param name="packaged_data" value="Cancer_variant_data__hg19__1__2021-12-16" />
71 <param name="annotation" value="hotspots.data.test,civic.variants.test" />
72 <output_collection name="list_output" type="list" count="2">
73 <element name="hotspots.data.test" ftype="bed" file="test-annotation-data/hotspots.data.test">
74 <metadata name="dbkey" value="hg19" />
75 </element>
76 <element name="civic.variants.test" ftype="bed" file="test-annotation-data/civic.variants.test">
77 <metadata name="dbkey" value="hg19" />
78 </element>
79 </output_collection>
80 </test>
81 <test expect_num_outputs="2">
82 <param name="packaged_data" value="Cancer_variant_data__hg19__1__2021-12-16" />
83 <param name="annotation" value="hotspots.data.test,civic.variants.test" />
84 <param name="retrieve_meta" value="yaml" />
85 <output_collection name="list_output" type="list" count="2">
86 <element name="hotspots.data.test" ftype="bed" file="test-annotation-data/hotspots.data.test">
87 <metadata name="dbkey" value="hg19" />
88 </element>
89 <element name="civic.variants.test" ftype="bed" file="test-annotation-data/civic.variants.test">
90 <metadata name="dbkey" value="hg19" />
91 </element>
92 </output_collection>
93 <output name="meta_out" ftype="yaml" file="test-annotation-data/meta.yml" />
94 </test>
95 <test expect_num_outputs="2">
96 <param name="packaged_data" value="Cancer_variant_data__hg19__1__2021-12-16" />
97 <param name="annotation" value="hotspots.data.test,civic.variants.test" />
98 <param name="retrieve_meta" value="tab" />
99 <output_collection name="list_output" type="list" count="2">
100 <element name="hotspots.data.test" ftype="bed" file="test-annotation-data/hotspots.data.test">
101 <metadata name="dbkey" value="hg19" />
102 </element>
103 <element name="civic.variants.test" ftype="bed" file="test-annotation-data/civic.variants.test">
104 <metadata name="dbkey" value="hg19" />
105 </element>
106 </output_collection>
107 <output name="meta_out" ftype="tabular" file="anno-version.tsv"/>
108 </test>
109 <test expect_num_outputs="2">
110 <param name="packaged_data" value="Cancer_variant_data__hg19__1__2021-12-16" />
111 <param name="annotation" value="civic.variants.test" />
112 <param name="retrieve_meta" value="tab" />
113 <output_collection name="list_output" type="list" count="1">
114 <element name="civic.variants.test" ftype="bed" file="test-annotation-data/civic.variants.test">
115 <metadata name="dbkey" value="hg19" />
116 </element>
117 </output_collection>
118 <output name="meta_out" ftype="tabular">
119 <assert_contents>
120 <has_n_lines n="2" />
121 <has_line line="Annotation&#009;Version" />
122 <has_line line="CIViC variants&#009;01-Feb-2019" />
123 </assert_contents>
124 </output>
125 </test>
126 </tests>
127 <help><![CDATA[
128 This tool can be used to make genome annotation data installed via the
129 `data manager for packaged_annotation data
130 <https://toolshed.g2.bx.psu.edu/view/wolma/data_manager_packaged_annotation_data>`__
131 accessible as a list of datasets collection.
132 ]]></help>
133 </tool>