Mercurial > repos > lparsons > cutadapt
comparison cutadapt.xml @ 4:0a872e59164c
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"> |