<tool id="fimo" name="motif search">
  <description>using FIMO</description>
  <command> fimo 
    #if $background_select.bg_select == "fromfile":
    -bgfile $bgfile
    #end if
    
  $norc --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>
    <conditional name="motif_selection">   
        <param name="motif_sel" type="select" label="Motif Source">
            <option value="user" selected="true">Use motif file in Your History</option>
            <option value="known" >Known motif</option>
        </param>
        ##<when value="known">
        ##    <param name="motif" type="select" label="Select motif">
        ##        <option value="/Users/xuebing/galaxy-dist/tool-data/motif-database/5primerSpliceSite" selected="true">mouse 5 primer splice site</option>
        ##        <option value="/Users/xuebing/galaxy-dist/tool-data/motif-database/5primerSpliceSite">mouse 3 primer splice site</option>
        ##        <option value="/Users/xuebing/galaxy-dist/tool-data/motif-database/TATA-Box.meme">TATA box</option>
        ##    </param>
        ##</when>
        <when value="user">
            <param name="motif" type="data" format="txt" label="Motif file" help="created using the tool create-motif-file, or import from Shared Data"/>
        </when>
    </conditional>     
         
    <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="0.01" 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>
