Mercurial > repos > trinity_ctat > clean_headers
view clean_headers.xml @ 0:1311b91e122d draft default tip
Adding profile info and exit code behavior. Making version numbers consistent. Upping test number.
author | trinity_ctat |
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date | Fri, 06 Oct 2017 10:52:12 -0400 |
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<tool id="clean_headers" name="Clean Headers" version="1.0.0" profile="17.05"> <description>Clean read headers of fastq files</description> <requirements> <requirement type="package" version="5">perl</requirement> </requirements> <command detect_errors="exit_code"> perl -lpe 'if (m/^[@+]/){ s/ //g}' "$input" > "$output" </command> <macros> </macros> <stdio> <exit_code range="1:" level="fatal" description="Error returned from pipeline" /> </stdio> <regex match="Must investigate error above." source="stderr" level="fatal" description="Unknown error encountered" /> <inputs> <param format="fastq" name="input" type="data" label="Fastq file with reads to be cleaned" help=""/> </inputs> <outputs> <data format="fastq" name="output" label="Cleaned ${on_string}" /> </outputs> <tests> </tests> <help> Removes whitespace from the header of each read in a fastq file. If your Trinity run gives you errors with dying threads during the normalization step, try this tool on each input first. </help> <citations> </citations> </tool>