annotate 6_merge_vcfs.xml @ 61:2af5e948dd5c

planemo upload
author jpayne
date Wed, 26 Jun 2024 00:58:54 -0400
parents 49d672730d3e
children d497922d6caa
rev   line source
jpayne@0 1 <tool id="merge_vcfs" name="6. Merge VCFs" version="1.0.1" profile="16.10">
jpayne@0 2 <description>into a multi-sample VCF with consensus SNPs</description>
jpayne@0 3 <requirements>
jpayne@61 4 <!-- <container type="docker">quay.io/biocontainers/mulled-v2-72d480da2f80e0804df2fc75273988c6dba1648d:f354c444b518b0ada8e031aa2984346e2f5d8837-0</container> -->
jpayne@61 5 <requirement type="package" version="1.9">bcftools</requirement>
jpayne@58 6 <requirement type="package" version="1.0.8">bzip2</requirement>
jpayne@58 7 <requirement type="package" version="2.2.1">snp-pipeline</requirement>
jpayne@58 8 <requirement type="package" version="0.2.6">tabix</requirement>
jpayne@61 9 <requirement type="package" version="1.9">htslib</requirement>
jpayne@58 10 <!-- <requirement type="package" version="3.6.8">python</requirement> -->
jpayne@0 11 </requirements>
jpayne@0 12 <command detect_errors="exit_code"><![CDATA[
jpayne@28 13 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
jpayne@9 14 python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf"
jpayne@0 15 #for $vcf in $vcfs
jpayne@0 16 -n $vcf.element_identifier -f $vcf
jpayne@0 17 #end for
jpayne@0 18 > ./file
jpayne@0 19 && cat ./file
jpayne@56 20 && cfsan_snp_pipeline merge_vcfs ./file
jpayne@0 21 ]]></command>
jpayne@0 22 <inputs>
jpayne@0 23 <param type="data_collection" format="vcf" collection_type="list" name="vcfs" label="List of VCFs" />
jpayne@0 24 </inputs>
jpayne@0 25 <outputs>
jpayne@0 26 <data format="vcf" label="SNP matrix" name="snpmav" from_work_dir="snpma.vcf"/>
jpayne@0 27 </outputs>
jpayne@0 28 <tests>
jpayne@0 29 <test>
jpayne@0 30 <param name="vcfs">
jpayne@0 31 <collection type="list">
jpayne@0 32 <element name="sample1" value="samples/sample1/consensus.vcf" />
jpayne@0 33 <element name="sample2" value="samples/sample2/consensus.vcf" />
jpayne@0 34 <element name="sample3" value="samples/sample3/consensus.vcf" />
jpayne@0 35 <element name="sample4" value="samples/sample4/consensus.vcf" />
jpayne@0 36 </collection>
jpayne@0 37 </param>
jpayne@50 38 <output name="snpmav" value="snpma.vcf" lines_diff="4" />
jpayne@0 39 </test>
jpayne@0 40 </tests>
jpayne@0 41 <help><![CDATA[
jpayne@0 42 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>
jpayne@0 43 ]]></help>
jpayne@0 44 <citations>
jpayne@0 45 <citation type="doi">10.7717/peerj-cs.20</citation>
jpayne@0 46 </citations>
jpayne@0 47 </tool>