Mercurial > repos > jpayne > snp_pipeline

comparison 5_call_consensus.xml @ 34:87f53c4a13df

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planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
author jpayne
date Thu, 01 Feb 2018 19:01:35 -0500
parents 8764af78e270
children 69216317baa7
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33:b6bc9158666c 34:87f53c4a13df
2 <description>for a sample, or lookup cached consensus SNP calls</description> 2 <description>for a sample, or lookup cached consensus SNP calls</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.6">bzip2</requirement> 4 <requirement type="package" version="1.0.6">bzip2</requirement>
5 <requirement type="package" version="1.0.1">snp-pipeline</requirement> 5 <requirement type="package" version="1.0.1">snp-pipeline</requirement>
6 <requirement type="package" version="1.5.11">boto3</requirement> 6 <requirement type="package" version="1.5.11">boto3</requirement>
7 <requirement type="package" version="3.4">python3</requirement> 7 <requirement type="package" version="3.5">python</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 #set $identifier = $call_pileup.name.split(' ')[0] 10 #set $identifier = $call_pileup.name.split(' ')[0]
11 python $__tool_directory__/snp-cache.py snp_consenus_calls 11 python $__tool_directory__/snp-cache.py snp_consenus_calls
12 "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)" 12 "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)"