Mercurial > repos > greg > affy2vcf

comparison affy2vcf.xml @ 9:e981015b6b46 draft

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author greg
date Thu, 11 Oct 2018 14:22:25 -0400
parents 192da25388ec
children 8f1660b17f90
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8:192da25388ec 9:e981015b6b46
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 #set text_outputs_dir = 'text_outputs' 7 #set text_outputs_dir = 'text_outputs'
8 export BCFTOOLS_PLUGINS=\$(dirname `which bcftools`)/../libexec/bcftools && 8 export BCFTOOLS_PLUGINS=\$(dirname `which bcftools`)/../libexec/bcftools &&
9 mkdir $text_outputs_dir && 9 mkdir $text_outputs_dir &&
10 bcftools +$BCFTOOLS_PLUGINS/affy2vcf.so 10 bcftools +\$BCFTOOLS_PLUGINS/affy2vcf.so
11 #if str($reference_genome_source_cond.reference_genome_source) == "history": 11 #if str($reference_genome_source_cond.reference_genome_source) == "history":
12 --fasta_ref '$reference_genome_source_cond.history_item' 12 --fasta_ref '$reference_genome_source_cond.history_item'
13 #else: 13 #else:
14 --fasta_ref '$reference_genome_source_cond.locally_cached_item' 14 --fasta_ref '$reference_genome_source_cond.locally_cached_item'
15 #end if 15 #end if