Mercurial > repos > devteam > vcf2tsv
comparison vcf2tsv.xml @ 0:77e1141bbd29 draft
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author | devteam |
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date | Thu, 19 Mar 2015 11:35:32 -0400 |
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children | d6c944f1581a |
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1 <tool id="vcf2tsv" name="VCFtoTab-delimited:" version="0.0.2"> | |
2 <description>Convert VCF data into TAB-delimited format</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"></expand> | |
7 <expand macro="stdio" /> | |
8 <command>vcf2tsv ${g_option} -n "${null_filler}" "${input}" > "${out_file1}"</command> | |
9 <inputs> | |
10 <param format="vcf" name="input" type="data" label="Select VCF dataset to convert"/> | |
11 <param name="g_option" type="boolean" checked="true" truevalue="-g" falsevalue="" label="Report data per sample" help="-g option"/> | |
12 <param name="null_filler" type="select" label="Fill empty fields with" help="-n option" > | |
13 <option value="">Nothing</option> | |
14 <option value=".">.</option> | |
15 <option value="*">*</option> | |
16 <option value="NULL">NULL</option> | |
17 </param> | |
18 </inputs> | |
19 <outputs> | |
20 <data format="tabular" name="out_file1" /> | |
21 </outputs> | |
22 <tests> | |
23 <test> | |
24 <param name="g_option" value="true"/> | |
25 <param name="null_filler" value="."/> | |
26 <param name="input" value="vcflib.vcf"/> | |
27 <output name="out_file1" file="vcf2tsv-test1.tab"/> | |
28 </test> | |
29 <test> | |
30 <param name="g_option" value="false"/> | |
31 <param name="null_filler" value="."/> | |
32 <param name="input" value="vcflib.vcf"/> | |
33 <output name="out_file1" file="vcf2tsv-test2.tab"/> | |
34 </test> | |
35 </tests> | |
36 <help> | |
37 | |
38 Converts VCF dataset to tab-delimited format, using null string to replace empty values in the table. | |
39 Specifying "**Report data per sample**" (-g) will output one line per sample with genotype information. | |
40 | |
41 ---- | |
42 | |
43 Vcf2Tsv @IS_PART_OF_VCFLIB@ | |
44 </help> | |
45 <expand macro="citations" /> | |
46 </tool> |