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comparison 6_merge_vcfs.xml @ 0:eefdd97a6749

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planemo upload commit b'7f6183b769772449fbcee903686b8d5ec5b7439f\n'-dirty
author jpayne
date Wed, 24 Jan 2018 14:18:21 -0500
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1 <tool id="merge_vcfs" name="6. Merge VCFs" version="1.0.1" profile="16.10">
2 <description>into a multi-sample VCF with consensus SNPs</description>
3 <requirements>
4 <requirement type="package" version="1.3.1">bcftools</requirement>
5 <requirement type="package" version="1.0.1">snp-pipeline</requirement>
6 <requirement type="package">tabix</requirement>
7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[
9 $__tool_directory__/snp-wind.py ./ -p "consensus.vcf"
10 #for $vcf in $vcfs
11 -n $vcf.element_identifier -f $vcf
12 #end for
13 > ./file
14 && cat ./file
15 && cfsan_snp_pipeline merge_vcfs ./file
16 ]]></command>
17 <inputs>
18 <param type="data_collection" format="vcf" collection_type="list" name="vcfs" label="List of VCFs" />
19 </inputs>
20 <outputs>
21 <data format="vcf" label="SNP matrix" name="snpmav" from_work_dir="snpma.vcf"/>
22 </outputs>
23 <tests>
24 <test>
25 <param name="vcfs">
26 <collection type="list">
27 <element name="sample1" value="samples/sample1/consensus.vcf" />
28 <element name="sample2" value="samples/sample2/consensus.vcf" />
29 <element name="sample3" value="samples/sample3/consensus.vcf" />
30 <element name="sample4" value="samples/sample4/consensus.vcf" />
31 </collection>
32 </param>
33 <output name="snpmav" value="snpma.vcf" lines_diff="2" />
34 </test>
35 </tests>
36 <help><![CDATA[
37 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>
38 ]]></help>
39 <citations>
40 <citation type="doi">10.7717/peerj-cs.20</citation>
41 </citations>
42 </tool>