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comparison fastq_screen.xml @ 2:81a0c1c27ec8 draft default tip

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author iuc
date Fri, 16 May 2014 19:46:52 -0400
parents 3480daf4ed27
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1:3480daf4ed27 2:81a0c1c27ec8
1 <tool id="fastq_screen" name="fastq_screen" version="0.4.2"> 1 <tool id="fastq_screen" name="fastq_screen" version="0.4.2">
2 <description>Screen for contamination</description> 2 <description>Screen for contamination</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.1.0">bowtie2</requirement>
4 <requirement type="package" version="0.4.2">fastq_screen</requirement> 5 <requirement type="package" version="0.4.2">fastq_screen</requirement>
5 <requirement type="package" version="2.1.0">package_bowtie2</requirement>
6 </requirements> 6 </requirements>
7 <command> 7 <command>
8 fastq_screen --aligner="bowtie2" --outdir="." --conf="$fastqrunconf" 8 fastq_screen --aligner="bowtie2" --outdir="." --conf="$fastqrunconf"
9 #if $sampN &gt; 0: 9 #if $sampN &gt; 0:
10 --subset "$sampN" 10 --subset "$sampN"
60 <data format="png" name="outpng" label="${jobName}.png"/> 60 <data format="png" name="outpng" label="${jobName}.png"/>
61 </outputs> 61 </outputs>
62 <configfiles> 62 <configfiles>
63 <configfile name="fastqrunconf"> 63 <configfile name="fastqrunconf">
64 ###### autogenerated by fastq_screen.xml for fastq_screen run 64 ###### autogenerated by fastq_screen.xml for fastq_screen run
65 BOWTIE2 /data/app/bin/bowtie2 65 BOWTIE2 bowtie2
66 #for $refs in $refGenomes: 66 #for $refs in $refGenomes:
67 DATABASE $refs.ref.fields.value $refs.ref.fields.path BOWTIE2 67 DATABASE $refs.ref.fields.value $refs.ref.fields.path BOWTIE2
68 #end for 68 #end for
69 </configfile> 69 </configfile>
70 </configfiles> 70 </configfiles>