<tool id="nsaf_scoring" name="NSAF Scoring Table">
  <description></description>
  <command interpreter="python">nsaf_scoring.py $list_file $prey_file $crapome $inter_file $outfile \$INSTALL_RUN_PATH/ </command>
  <requirements>
    <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
  </requirements>
  <inputs>
    <param format="txt" name="list_file" type="data" label="List File"/>
    <param format="txt" name="prey_file" type="data" label="Prey File"/>
    <param format="txt" name="crapome" type="data" label="Crapome File" optional="true"/>
    <param format="txt" name="inter_file" type="data" label="Inter File" />
  </inputs>
  <outputs>
    <data format="txt" name="outfile" label="NSAF Scored Table"/>    
  </outputs>
  <stdio>
    <regex match="ValueError: 'PreyGene' is not in list"
       source="stdout"
       level="fatal"
       description="Error: Check Input file."/>
    <regex match="Error|error"
     source="stdout"
           level="fatal"
           description="Unknown error"/>
    <regex match="Error|error"
     source="stderr"
           level="fatal"
           description="Unknown error"/>
  </stdio> 
  <tests>
    <test>
      <param name="input" value="fa_gc_content_input.fa"/>
      <output name="out_file1" file="fa_gc_content_output.txt"/>
    </test>
  </tests>
  <help>
  </help>
</tool>