<tool id="MergeScaffold" name="Merge Scaffold">
  <description></description>
  <command interpreter="python">MergeFiles.py $input1 $input2 $input3 $baitfile $merged \$INSTALL_RUN_PATH/</command>
  <requirements>
    <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
  </requirements>
  <inputs>
    <param format="txt" name="input1" type="data" label="Scaffold Output 1"/>
    <param format="txt" name="input2" type="data" label="Scaffold Output 2"/>
    <param format="txt" name="input3" type="data" label="Scaffold Output 3" optional = "true"/>
    <param format="txt" name="baitfile" type="data" label="baitfile"/>
  </inputs>
  <outputs>
    <data format="txt" name="merged" label="Merged Scaffold Report"/>    
  </outputs>
  <stdio>
    <regex match="Error|error"
     source="stdout"
           level="fatal"
           description="Unknown error"/>
    <regex match="Error|error"
     source="stderr"
           level="fatal"
           description="Unknown error"/>
    <regex match="Error: bad bait"
           source="stdout"
           level="fatal"
           description="Error: bad bait"/>
  </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>
Query CRAPome
-------------
This program will read in a SAINT formatted *Prey* file or a single column list (no column name) of Uniprot accessions (e.g. "P00533" or "EGFR_HUMAN"), query the  CRAPome database (v1.1) http://crapome.org, and return a file specifying the prevalence of each protein in the CRAPome.

**1) Input File**
SAINT formatted *Prey* file or a single column list (no column name) of Uniprot accessions.

**2) Species**
Please specify species. Supported species are Human and Yeast.
  </help>
</tool>