Mercurial > repos > iuc > gvcftools_extract_variants
comparison extract_variants.xml @ 0:bf8841b0a6b0 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools commit a35519a8cc09ea0a6e6ac5f57ff36fd738e5adb7
author | iuc |
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date | Mon, 20 Feb 2017 06:35:42 -0500 |
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-1:000000000000 | 0:bf8841b0a6b0 |
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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> |