<tool id="fimo" name="motif search">
  <description>using FIMO</description>
  <command> fimo 
    #if $background_select.bg_select == "fromfile":
    -bgfile $bgfile
    #end if
    
  $norc --max-stored-scores 5000000 --output-pthresh $pth --verbosity 1 $motif $database 
  &amp;&amp; mv fimo_out/fimo.html ${html_outfile}
  
  &amp;&amp; mv fimo_out/fimo.txt ${txt_outfile}
  
  &amp;&amp; rm -rf fimo_out
  
  </command>
  <inputs>
    
            <param name="motif" type="data" format="txt" label="Motif file" help="created using the tool create-motif-file, or import from Shared Data"/>         
    <param name="database" type="data" format="fasta" label="Sequence file (FASTA)"/>
      
    <conditional name="background_select">
    	<param name="bg_select" type="select" label="Background model" >
		  <option value="uniform" selected="true">uniform</option>
		  <option value="fromfile">load from file</option>
	    </param>
	    <when value="fromfile">
		    <param name="bgfile" type="data" format="txt" label="File for background model"/>
	    </when>
    </conditional>
      
      <param name="pth" size="10" type="float" value="0.0001" label="p-value threshold"/>
    <param name="norc" label="Do not score the reverse complement DNA strand. Both strands are scored by default" type="boolean" truevalue="-norc" falsevalue="" checked="False"/>
  </inputs>
  <outputs>
    <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/>
    <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (txt)"/>
  </outputs>
  <help>

**What it does**

This tool uses FIMO to find matches of a motif in a fasta file. See more details:

http://meme.sdsc.edu/meme/fimo-intro.html
 
  </help>
</tool>