Mercurial > repos > jpayne > snp_pipeline

comparison 7_smp_matrix.xml @ 18:97abaa8b8384

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planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
author jpayne
date Wed, 31 Jan 2018 12:33:00 -0500
parents 8626ed5eb356
children 4bb7e4a360bc
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17:8626ed5eb356 18:97abaa8b8384
7 <requirement type="package">tabix</requirement> 7 <requirement type="package">tabix</requirement>
8 <requirement type="package" version="3.4">python3</requirement> 8 <requirement type="package" version="3.4">python3</requirement>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 env && 11 env &&
12 which bcftools &&
13 which bunzip &&
14 which snp-pipeline &&
15 which python &&
12 python $__tool_directory__/snp-wind.py ./ -p "consensus.fasta" 16 python $__tool_directory__/snp-wind.py ./ -p "consensus.fasta"
13 #for $fa in sorted($cons, key=lambda f: f.element_identifier) 17 #for $fa in sorted($cons, key=lambda f: f.element_identifier)
14 -n $fa.element_identifier -f $fa 18 -n $fa.element_identifier -f $fa
15 #end for 19 #end for
16 > ./file && 20 > ./file &&