<tool id="cravat_submit" name="CRAVAT Submit, Check, and Retrieve" version="0.1.0">
    <description>Submits, checks for, and retrieves data for cancer annotation</description>
  <command interpreter="python">cravat_submit.py $input $dropdown $GRCh $psm $Variant $Gene $Noncoding $Error</command>
  
  
  <inputs>
  
    <param format="tabular" name="input" type="data" label="Source file"> </param>
    <param format="tabular" name="dropdown" type="select" label="Analysis Program">
      <option value="">None</option>
      <option value="VEST">VEST</option>
      <option value="CHASM">CHASM</option>
      <option value="VEST;CHASM">VEST and CHASM</option>
    </param>
    <param format="tabular" name="GRCh" type="select" label="Genome Reference Consortium Human Build (GRCh)">
      <option value="GRCh38">GRCh38/hg38</option>
      <option value="GRCh37">GRCh37/hg19</option>
    </param>
    <param format="tabular" name="psm" type="data" optional="true" label="ProBED File(Optional)"> </param>
    
    
  </inputs>
  
  <outputs>
      <collection name="collection" type="list" label="CRAVAT Results: ${on_string} using ${dropdown}">
        <data format="cravat" label="CRAVAT: Gene Level Annotation Report" name="Gene" />
        <data format="cravat" label="CRAVAT: Variant Report" name="Variant" />
        <data format="cravat" label="CRAVAT: Non-coding Variant Report" name="Noncoding" />
        <data format="cravat" label="CRAVAT: Errors" name="Error" />
      </collection>
  </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 submits, checks for, and retrieves data for cancer annotation from the CRAVAT platform at cravat.us.
  </help>

</tool>