Mercurial > repos > jpayne > snp_pipeline

comparison 5_call_consensus.xml @ 6:62191abf5426

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planemo upload commit b'7f6183b769772449fbcee903686b8d5ec5b7439f\n'-dirty
author jpayne
date Mon, 29 Jan 2018 13:56:19 -0500
parents eefdd97a6749
children 13539c458a6e
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5:5191246bc2e2 6:62191abf5426
1 <tool id="call_consensus" name="5. Call consensus SNPs" version="1.0.1" profile="16.10"> 1 <tool id="call_consensus" name="5. Call consensus SNPs" version="1.0.1" profile="16.10">
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="1.0.1">snp-pipeline</requirement> 4 <requirement type="package" version="1.0.1">snp-pipeline</requirement>
5 <requirement type="package" version="1.5.11">boto3</requirement> 5 <requirement type="package" version="1.5.11">boto3</requirement>
6 <requirement type="package">package_python_3_5</requirement>
6 </requirements> 7 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
8 #set $identifier = $call_pileup.name.split(' ')[0] 9 #set $identifier = $call_pileup.name.split(' ')[0]
9 $__tool_directory__/snp-cache.py snp_consenus_calls 10 $__tool_directory__/snp-cache.py snp_consenus_calls
10 "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)" 11 "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)"