Mercurial > repos > trinity_ctat > clean_headers
changeset 0:1311b91e122d draft default tip
Adding profile info and exit code behavior. Making version numbers consistent. Upping test number.
| author | trinity_ctat |
|---|---|
| date | Fri, 06 Oct 2017 10:52:12 -0400 |
| parents | |
| children | |
| files | clean_headers.xml |
| diffstat | 1 files changed, 31 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/clean_headers.xml Fri Oct 06 10:52:12 2017 -0400 @@ -0,0 +1,31 @@ +<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>