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author xuebing
date Tue, 13 Mar 2012 19:05:10 -0400
parents 292186c14b08
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13:292186c14b08 14:76e1b1b21cce
1 <tool id="fimo" name="motif search">
2 <description>using FIMO</description>
3 <command> fimo
4 #if $background_select.bg_select == "fromfile":
5 -bgfile $bgfile
6 #end if
7
8 $norc --max-stored-scores 5000000 --output-pthresh $pth --verbosity 1 $motif $database
9 &amp;&amp; mv fimo_out/fimo.html ${html_outfile}
10
11 &amp;&amp; mv fimo_out/fimo.txt ${txt_outfile}
12
13 &amp;&amp; rm -rf fimo_out
14
15 </command>
16 <inputs>
17
18 <param name="motif" type="data" format="txt" label="Motif file" help="created using the tool create-motif-file, or import from Shared Data"/>
19 <param name="database" type="data" format="fasta" label="Sequence file (FASTA)"/>
20
21 <conditional name="background_select">
22 <param name="bg_select" type="select" label="Background model" >
23 <option value="uniform" selected="true">uniform</option>
24 <option value="fromfile">load from file</option>
25 </param>
26 <when value="fromfile">
27 <param name="bgfile" type="data" format="txt" label="File for background model"/>
28 </when>
29 </conditional>
30
31 <param name="pth" size="10" type="float" value="0.0001" label="p-value threshold"/>
32 <param name="norc" label="Do not score the reverse complement DNA strand. Both strands are scored by default" type="boolean" truevalue="-norc" falsevalue="" checked="False"/>
33 </inputs>
34 <outputs>
35 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/>
36 <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (txt)"/>
37 </outputs>
38 <help>
39
40 **What it does**
41
42 This tool uses FIMO to find matches of a motif in a fasta file. See more details:
43
44 http://meme.sdsc.edu/meme/fimo-intro.html
45
46 </help>
47 </tool>