Mercurial > repos > anton > vcf2tsv
comparison vcf2tsv.xml @ 0:8e1a693e7a52
Imported from capsule None
| author | anton |
|---|---|
| date | Wed, 11 Jun 2014 17:11:55 -0400 |
| parents | |
| children | 1258fa7a2744 |
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| -1:000000000000 | 0:8e1a693e7a52 |
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| 1 <tool id="vcf2tsv" name="VCFtoTab-delimited:" version="0.0.1"> | |
| 2 <requirements> | |
| 3 <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">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 stdin or given VCF file 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> |