Mercurial > repos > iuc > packaged_annotation_loader
comparison 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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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	Version" /> | |
122 <has_line line="CIViC variants	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> |