Mercurial > repos > fcaramia > custom_amplicon_alignment

comparison alignCustomAmplicon/alignCustomAmplicon_wrapper.xml @ 2:413ba6d9cc46 draft

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author fcaramia
date Wed, 09 Jan 2013 00:35:38 -0500
parents 6a1b222df393
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1:6a1b222df393 2:413ba6d9cc46
6 <requirement type="package" version="1.3.12">gzip</requirement> 6 <requirement type="package" version="1.3.12">gzip</requirement>
7 <requirement type="perl-module" version="0.42">Inline-CPP</requirement> 7 <requirement type="perl-module" version="0.42">Inline-CPP</requirement>
8 </requirements> 8 </requirements>
9 <command interpreter="perl"> 9 <command interpreter="perl">
10 alignCustomAmplicon.pl -s -r -p 4 -o $output $refFile.fields.path $read1 $read2 $primers 10 alignCustomAmplicon.pl -s -r -p 4 -o $output $refFile.fields.path $read1 $read2 $primers
11 -j "\$JAVA_JAR_PATH/MergeSamFiles.jar"
11 </command> 12 </command>
12 13
13 <inputs> 14 <inputs>
14 <param name="refFile" type="select" label="Select a reference genome"> 15 <param name="refFile" type="select" label="Select a reference genome">
15 <options from_data_table="all_fasta"> 16 <options from_data_table="all_fasta">