<tool id="ctat_clean_headers" name="ctat_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>