Mercurial > repos > nml > vcf2snvalignment
diff 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 |
parents | |
children | d2096d0c149e |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcf2snvalignment.xml Tue Aug 27 12:33:24 2019 -0400 @@ -0,0 +1,96 @@ +<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>