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comparison cutadapt.xml @ 4:0a872e59164c

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Added discard_stderr_wrapper.sh script to catch report and redirect to stdout
author Lance Parsons <lparsons@princeton.edu>
date Wed, 25 May 2011 19:33:40 -0400
parents 7ed26fc9fa8a
children 1dada50cca8a
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3:7ed26fc9fa8a 4:0a872e59164c
2 <description>from high-throughput sequence data</description> 2 <description>from high-throughput sequence data</description>
3 <requirements> 3 <requirements>
4 <requirement type="python-module">cutadapt</requirement> 4 <requirement type="python-module">cutadapt</requirement>
5 </requirements> 5 </requirements>
6 6
7 <command>cutadapt 7 <command interpreter="sh">discard_stderr_wrapper.sh cutadapt
8 #if $input.extension.startswith( "fastq"): 8 #if $input.extension.startswith( "fastq"):
9 --format=fastq 9 --format=fastq
10 #else 10 #else
11 --format=$input.extension 11 --format=$input.extension
12 #end if 12 #end if
28 #if $discard: 28 #if $discard:
29 --discard 29 --discard
30 #end if 30 #end if
31 '$input' 31 '$input'
32 --output='$output' 32 --output='$output'
33 2> $report 33 > $report
34 </command> 34 </command>
35 <inputs> 35 <inputs>
36 <param format="fastqsanger, fasta" name="input" type="data" optional="false" label="Fastq file to trim" length="100"/> 36 <param format="fastqsanger, fasta" name="input" type="data" optional="false" label="Fastq file to trim" length="100"/>
37 37
38 <repeat name="adapters" title="3' Adapters"> 38 <repeat name="adapters" title="3' Adapters">