<tool id="cmpfastq" name="Compare two fast files">
  <description>Comparing two fastq files</description>
  <requirements>
    <requirement type="set_environment">CFQ_SCRIPT_PATH</requirement>
  </requirements>
  <command>\$CFQ_SCRIPT_PATH/cmpfastq $input1 $input2 $output1 $output2 $output3 $output4</command>
  <inputs>
    <param name="input1" type="data"  format="fastq" label="Source file 1"/>
    <param name="input2" type="data" format="fastq" label="Source file 2"/>
    <!--<param name="input3" type="select" label="Option">
        <option value="d">d</option>
        <option value="h ">h</option>
     </param> -->
  </inputs>
  <outputs>
    <data format="txt" name="output1" label="Common file 1"/>
    <data format="txt" name="output2" label="Common file 2"/>
    <data format="txt" name="output3" label="Unique file 1"/>
    <data format="txt" name="output4" label="Unique file 2"/>
  </outputs>

  <tests>
    <test>
     <!-- <param name="input" value="fa_gc_content_input.fa"/>
      <output name="out_file1" file="fa_gc_content_output.txt"/> -->
    </test> 
  </tests>

  <help>
This tool computes GC content from a FASTA file.
  </help>

</tool>