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comparison cfsan_snp_pipeline_snp_matrix.xml @ 3:f959d99d1758 draft default tip

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author greg
date Thu, 23 Nov 2023 19:02:52 +0000
parents f3485a9e51a3
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2:610251aac6ef 3:f959d99d1758
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #if str($reference_cond.reference_source) == 'cached' 8 #if str($reference_cond.reference_source) == 'cached'
9 set reference = '$reference_cond.reference.fields.path' 9 #set reference = $reference_cond.reference.fields.path
10 #else: 10 #else:
11 set reference = '$reference_cond.reference' 11 #set reference = $reference_cond.reference
12 #end if 12 #end if
13 13
14 python '$__tool_directory__/snp_wind.py' ./ -p 'consensus.fasta' 14 python '$__tool_directory__/snp_wind.py' ./ -p 'consensus.fasta'
15 #for $fa in sorted($input_fasta_collection, key=lambda f: f.element_identifier): 15 #for $fa in sorted($input_fasta_collection, key=lambda f: f.element_identifier):
16 -n '$fa.element_identifier' -f '$fa' 16 -n '$fa.element_identifier' -f '$fa'