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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools commit a35519a8cc09ea0a6e6ac5f57ff36fd738e5adb7
author iuc
date Mon, 20 Feb 2017 06:35:15 -0500
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1 <tool id="gvcftools_extract_variants" name="Extract Variants from gVCF files" version="0.1">
2 <description>Removes all non-variant blocks from a gVCF file to produce a smaller variant-only VCF file.</description>
3
4 <requirements>
5 <requirement type="package" version="0.17.0">gvcftools</requirement>
6 </requirements>
7
8 <command detect_errors="aggressive">
9 <![CDATA[
10 extract_variants
11 #if str( $advanced.advanced_options_selector ) == 'true':
12 '${advanced.skip_header}' '${advanced.invert}'
13 #end if
14 < '${gvcf_input}' > '${vcf_output}'
15 ]]>]
16 </command>
17
18 <inputs>
19 <param name="gvcf_input" type="data" format="vcf" label="Variants (gVCF format)" />
20 <conditional name="advanced">
21 <param name="advanced_options_selector" type="select" label="Advanced options">
22 <option value="true">Show advanced options</option>
23 <option value="false" selected="True">Don't show advanced options</option>
24 </param>
25 <when value="true">
26 <param type="boolean" name="skip_header" argument="--skip-header"
27 truevalue="--skip-header" falsevalue=""
28 label="Write the variants output file without a header" />
29 <param type="boolean" argument="--invert"
30 truevalue="--invert" falsevalue=""
31 label="Invert the filter so that only non-variant records are output" />
32 </when>
33 <when value="false"></when>
34 </conditional>
35 </inputs>
36
37 <outputs>
38 <data name="vcf_output" format="vcf" />
39 </outputs>
40
41 <tests>
42 <test>
43 <param name="gvcf_input" ftype="vcf" value="input1.gvcf" />
44 <output name="vcf_output" ftype="vcf" value="variants_output1.vcf" />
45 </test>
46 <test>
47 <param name="gvcf_input" ftype="vcf" value="input1.gvcf" />
48 <param name="advanced_options_selector" value="true" />
49 <param name="skip_header" value="True" />
50 <output name="vcf_output" ftype="vcf" value="variants_noheader_output1.vcf" />
51 </test>
52 <test>
53 <param name="gvcf_input" ftype="vcf" value="input1.gvcf" />
54 <param name="advanced_options_selector" value="true" />
55 <param name="invert" value="True" />
56 <output name="vcf_output" ftype="vcf" value="nonvariants_output1.vcf" />
57 </test>
58
59 </tests>
60
61 <help>
62 <![CDATA[
63 Extract variants from a gVCF field, removing all non-variant blocks to yield a smaller variant only VCF file.
64
65 From the `gvcftools`_ toolkit.
66
67 .. _gvcftools: https://sites.google.com/site/gvcftools/
68 ]]>
69 </help>
70 <citations>
71 <citation type="bibtex">
72 @unpublished{gvcftools,
73 author = {Illumina, Inc.},
74 title = {gvcftools},
75 url = {https://sites.google.com/site/gvcftools/}
76 }
77 </citation>
78 </citations>
79 </tool>