Mercurial > repos > nml > vcf2snvalignment
view vcf2snvalignment.xml @ 0:7d66bf698382 draft
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
author | nml |
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date | Tue, 27 Aug 2019 12:33:24 -0400 |
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children | d2096d0c149e |
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<tool id="vcf2snvalignment" name="VCF 2 snvalignment" version ="1.8.2"> <description>create a snv alignment from multiple merged VCF files</description> <requirements> <requirement type="package" version="1.8.2">snvphyl-tools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #for $f in $vcf_collection.keys# #set $name = str($vcf_collection[$f]).split('/')[-1] ln -f -s '$vcf_collection[$f]' && #if $vcf_collection[$f].metadata.bcf_index: ln -s '${$vcf_collection[$f].metadata.bcf_index}' ${name}.csi && #else bcftools index $name && #end if #end for# vcf2snv_alignment.pl -r "$reference" #if str($invalid) != 'None': --invalid-pos "$invalid" #end if -f fasta -f phylip --numcpus \${GALAXY_SLOTS:-2} --fasta "$ref_fasta" #for $f in $vcf_collection.keys# #set $path = str($vcf_collection[$f]).split('/')[-1] --consolidate_vcf "$f=$path" #end for# #if $strain_list.select_list == "include": --include '$strain_list.include' #elif $strain_list.select_list == "exclude": --exclude '$strain_list.exclude' #end if ##mark where the output files will be sent to, simply have to match them up later in the xml output section -o 'snvalign' ]]> </command> <inputs> <param name="reference" type="text" label="Reference Name" value='reference' /> <param name="ref_fasta" type="data" label="Reference Fasta File" format="fasta"/> <param name="invalid" type="data" label="Invalid position file" format="gff,bed" optional="true"/> <conditional name="strain_list"> <param name="select_list" type="select" label="Strain Selecting options"> <option value="all">Use all strains in collection</option> <option value="include">Provide list of subset of strains to only include</option> <option value="exclude">Provide list of subset of strains to exclude</option> </param> <when value="include"> <param name="include" type="data" label="List of strains to be include" format="text" optional="false"/> </when> <when value="exclude"> <param name="exclude" type="data" label="List of strains to be excluded" format="text" optional="false"/> </when> <when value="all"/> </conditional> <param name="vcf_collection" type="data_collection" label="Combined VCF Files" help="" optional="false" format="bcf,bcf_bgzip" collection_type="list" /> </inputs> <outputs> <data format="tabular" name="positions" from_work_dir="snvalign-positions.tsv" /> <data format="fasta" name="fasta" from_work_dir="snvalign.fasta"/> <data format="phylip" name="phylip" from_work_dir="snvalign.phy" /> <data format="tabular" name="vcf2core" from_work_dir="snvalign-stats.csv" /> </outputs> <tests> <test> <param name="reference" value="ref"/> <param name="ref_fasta" value="reference.fasta"/> <param name="vcf_collection"> <collection type="list"> <element name="v1" value="consolidate_vcf/v1.bcf.gz"/> <element name="v2" value="consolidate_vcf/v2.bcf.gz"/> </collection> </param> <output name="positions" file="expected_positions.tsv"/> <output name="fasta" file="expected_fasta.fasta"/> <output name="phylip" file="expected_phylip.phy"/> <output name="vcf2core" file="expected_stats.csv"/> </test> </tests> <help> Produces an alignment of SNVs from the merged variant/non-variant calls produced from the "consolidate_vcfs" tool. </help> <citations> </citations> </tool>