Mercurial > repos > saskia-hiltemann > cgatools_v17
comparison tools/cgatools17/tv2vcf.xml @ 1:3a2e0f376f26 draft
Minor change to tv2vcf.xml to allow for workflow automation
| author | dgdekoning |
|---|---|
| date | Wed, 21 Oct 2015 10:09:15 -0400 |
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| 0:751b62d30ae1 | 1:3a2e0f376f26 |
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| 1 <tool id="tv2vcf" name="TestVariants-2-VCF" version="v2"> | |
| 2 | |
| 3 <description> Convert CG MasterVar format to VCF format </description> | |
| 4 | |
| 5 <requirements> | |
| 6 <requirement type="package" version="1">cgatools17</requirement> | |
| 7 </requirements> | |
| 8 | |
| 9 <command interpreter="perl"> | |
| 10 testvariants2VCF-v2.pl $testvarIn ${crr.fields.crr_path} > $output | |
| 11 </command> | |
| 12 | |
| 13 <inputs> | |
| 14 <param name="testvarIn" type="data" format="tabular" label="TestVariants file to be converted to VCF"/> | |
| 15 <param name="crr" type="select" label="Reference Build"> | |
| 16 <options from_data_table="cg_anno_files" /> | |
| 17 </param> | |
| 18 </inputs> | |
| 19 | |
| 20 <outputs> | |
| 21 <data format="vcf" name="output" label="${tool.name} on ${on_string}"/> | |
| 22 </outputs> | |
| 23 | |
| 24 <help> | |
| 25 This program converts the output of the cgatools *testvariants* command into a multi-sample VCF file. | |
| 26 | |
| 27 Variants that share the same location (chr,begin,end) will be merged into one locus and their flags (0,1,N) will be converted into genotype calls. | |
| 28 Samples that are positive for more than two alleles within the same locus will be flagged and their genotype calls set to unknown (./.). | |
| 29 For a non-SNP locus, the VCF format requires that an extra reference base immediately upstream of the variant locus be included in the REF and ALT columns. | |
| 30 | |
| 31 Author: Zuoming Deng, zdeng@completegenomics.com | |
| 32 | |
| 33 </help> | |
| 34 </tool> |