Commit 60be1ca5 authored by Takadonet's avatar Takadonet

added the ability to change two new parameters that were before hardcoded for...

added the ability to change two new parameters that were before hardcoded for freebayes filtering. Minumum mean mapping quality and alternative allele
parent 172eca22
<tool id="vcf2pseudoalignment" name="VCF 2 pseudoalignment" version ="0.0.12">
<tool id="vcf2pseudoalignment" name="VCF 2 pseudoalignment" version ="0.0.13">
<description>create a pseudo alignment from multiple VCFs files</description>
<requirements>
<requirement type="package" version="1.3.6">snvphyl</requirement>
......@@ -29,6 +29,8 @@
-c "$coverage"
-f fasta
-f phylip
--min-mean-mapping "$mean_mapping"
--ao "$ao"
-v
--numcpus \${GALAXY_SLOTS:-2}
--fasta "$ref_fasta"
......@@ -54,7 +56,8 @@
<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"/>
<param name="coverage" type="integer" value="15" label="minimum coverage"/>
<param name="mean_mapping" type="integer" value="30" label="minimum mean mapping quality"/>
<param name="ao" type="text" value="" label="Alternative allele ratio"/>
<param name="freebayes_collection" type="data_collection" label="FreeBayes filtered BCF" help="" optional="false" format="bcf_bgzip" collection_type="list" />
<param name="mpileup_collection" type="data_collection" label="Mpileup BCF" help="" optional="false" format="bcf_bgzip" collection_type="list" />
</inputs>
......
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