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comparison vcf2tsv.xml @ 4:fd6e01595a72 draft default tip

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author anton
date Mon, 15 Sep 2014 14:47:06 -0400
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3:4a464f44b556 4:fd6e01595a72
1 <tool id="vcf2tsv" name="VCFtoTab-delimited:" version="0.0.2">
2 <requirements>
3 <requirement type="package" version="8a5602bf07">vcflib</requirement>
4 </requirements>
5 <description>Convert VCF data into TAB-delimited format</description>
6 <command>vcf2tsv ${g_option} -n "${null_filler}" "${input}" > "${out_file1}"</command>
7 <inputs>
8 <param format="vcf" name="input" type="data" label="Select VCF dataset to convert"/>
9 <param name="g_option" type="boolean" checked="true" truevalue="-g" falsevalue="" label="Report data per sample" help="-g option"/>
10 <param name="null_filler" type="select" label="Fill empty fields with" help="-n option" >
11 <option value="">Nothing</option>
12 <option value=".">.</option>
13 <option value="*">*</option>
14 <option value="NULL">NULL</option>
15 </param>
16 </inputs>
17 <outputs>
18 <data format="tabular" name="out_file1" />
19 </outputs>
20 <tests>
21 <test>
22 <param name="g_option" value="true"/>
23 <param name="null_filler" value="."/>
24 <param name="input" value="vcflib.vcf"/>
25 <output name="out_file1" file="vcf2tsv-test1.tab"/>
26 </test>
27 <test>
28 <param name="g_option" value="false"/>
29 <param name="null_filler" value="."/>
30 <param name="input" value="vcflib.vcf"/>
31 <output name="out_file1" file="vcf2tsv-test2.tab"/>
32 </test>
33 </tests>
34 <help>
35
36 Converts VCF dataset to tab-delimited format, using null string to replace empty values in the table.
37 Specifying "**Report data per sample**" (-g) will output one line per sample with genotype information.
38
39 ----
40
41 Vcf2Tsv is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
42
43 </help>
44 </tool>