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comparison 1_map_reads.xml @ 9:41bd2a5793ee

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planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
author jpayne
date Tue, 30 Jan 2018 15:55:32 -0500
parents 360e1c2bf24d
children 25b858c2f21d
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8:360e1c2bf24d 9:41bd2a5793ee
1 <tool id="map_reads" name="1. Map Reads" version="1.0.1" profile="16.10"> 1 <tool id="map_reads" name="1. Map Reads" version="1.0.1" profile="16.10">
2 <description>to index, or lookup cached alignment</description> 2 <description>to index, or lookup cached alignment</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.3.4">bowtie2</requirement> 4 <requirement type="package" version="2.3.4">bowtie2</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" version="3.5">python</requirement> 6 <requirement type="package" version="3.4">python</requirement>
7 </requirements> 7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 #if $reads.reads_select == 'collection' 9 #if $reads.reads_select == 'collection'
10 export files="$reads.coll.forward $reads.coll.reverse" && 10 export files="$reads.coll.forward $reads.coll.reverse" &&
11 export params="-1 $reads.coll.forward -2 $reads.coll.reverse" && 11 export params="-1 $reads.coll.forward -2 $reads.coll.reverse" &&
12 #else 12 #else
13 export files="$forward $reverse" && 13 export files="$forward $reverse" &&
14 export params="-1 $forward -2 $reverse" && 14 export params="-1 $forward -2 $reverse" &&
15 #end if 15 #end if
16 ${__tool_directory__}/snp-cache.py snp_mapped_reads 16 python ${__tool_directory__}/snp-cache.py snp_mapped_reads
17 "\$(md5sum $reference 17 "\$(md5sum $reference
18 \$files 18 \$files
19 | cut -c -32 | md5sum | cut -c -32)" 19 | cut -c -32 | md5sum | cut -c -32)"
20 -c " 20 -c "
21 cp $reference ./reference.fasta 21 cp $reference ./reference.fasta