Mercurial > repos > saskia-hiltemann > cgatools_v17

annotate tools/cgatools17/tv2vcf.xml @ 1:3a2e0f376f26 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Minor change to tv2vcf.xml to allow for workflow automation
author dgdekoning
date Wed, 21 Oct 2015 10:09:15 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
1 <tool id="tv2vcf" name="TestVariants-2-VCF" version="v2">
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
2
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
3 <description> Convert CG MasterVar format to VCF format </description>
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
4
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
5 <requirements>
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
6 <requirement type="package" version="1">cgatools17</requirement>
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
7 </requirements>
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
8
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
9 <command interpreter="perl">
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
10 testvariants2VCF-v2.pl $testvarIn ${crr.fields.crr_path} > $output
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
11 </command>
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
12
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
13 <inputs>
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
14 <param name="testvarIn" type="data" format="tabular" label="TestVariants file to be converted to VCF"/>
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
15 <param name="crr" type="select" label="Reference Build">
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
16 <options from_data_table="cg_anno_files" />
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
17 </param>
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
18 </inputs>
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
19
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
20 <outputs>
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
21 <data format="vcf" name="output" label="${tool.name} on ${on_string}"/>
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
22 </outputs>
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
23
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
24 <help>
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
25 This program converts the output of the cgatools *testvariants* command into a multi-sample VCF file.
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
26
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
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.
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
28 Samples that are positive for more than two alleles within the same locus will be flagged and their genotype calls set to unknown (./.).
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
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.
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
30
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
31 Author: Zuoming Deng, zdeng@completegenomics.com
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
32
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
33 </help>
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
dgdekoning
parents:
diff changeset
34 </tool>