Mercurial > repos > nick > dunovo

comparison correct_barcodes.xml @ 3:00dde366870a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'a3ad9fbb3f010253808fc0c7329897a741ec9feb\n'
author nick
date Mon, 11 Sep 2017 16:59:44 -0400
parents a9cb6fb9ea94
children 5fbeaa41b223
comparison
equal deleted inserted replaced
2:a9cb6fb9ea94 3:00dde366870a
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="0.7.6"> 2 <tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="0.8.1">
3 <description>of duplex sequencing reads</description> 3 <description>of duplex sequencing reads</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2.2.5">bowtie2</requirement> 5 <requirement type="package" version="2.2.5">bowtie2</requirement>
6 <requirement type="package" version="0.1.18">samtools</requirement> 6 <requirement type="package" version="0.1.18">samtools</requirement>
7 <requirement type="package" version="1.9">networkx</requirement> 7 <requirement type="package" version="1.9">networkx</requirement>
8 <requirement type="package" version="0.7.6">dunovo</requirement> 8 <requirement type="package" version="0.8.1">dunovo</requirement>
9 <!-- TODO: require Python 2.7 --> 9 <!-- TODO: require Python 2.7 -->
10 </requirements> 10 </requirements>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 baralign.sh '$input' refdir barcodes.bam 12 baralign.sh '$input' refdir barcodes.bam
13 && samtools view -f 256 barcodes.bam 13 && samtools view -f 256 barcodes.bam
14 | correct.py --galaxy $phone -d $dist -m $mapq -p $pos '$input' refdir/barcodes.fa 14 | correct.py --galaxy $phone --dist $dist --mapq $mapq --pos $pos '$input' refdir/barcodes.fa
15 | sort 15 | sort
16 > '$output' 16 > '$output'
17 ]]> 17 ]]>
18 </command> 18 </command>
19 <inputs> 19 <inputs>