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comparison vcf2tsv.xml @ 0:77e1141bbd29 draft

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author devteam
date Thu, 19 Mar 2015 11:35:32 -0400
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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>