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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 --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 ${txt_outfile}
12
13 &amp;&amp; rm -rf fimo_out
14
15 </command>
16 <inputs>
17 <conditional name="motif_selection">
18 <param name="motif_sel" type="select" label="Motif Source">
19 <option value="user" selected="true">Use motif file in Your History</option>
20 <option value="known" >Known motif</option>
21 </param>
22 ##<when value="known">
23 ## <param name="motif" type="select" label="Select motif">
24 ## <option value="/Users/xuebing/galaxy-dist/tool-data/motif-database/5primerSpliceSite" selected="true">mouse 5 primer splice site</option>
25 ## <option value="/Users/xuebing/galaxy-dist/tool-data/motif-database/5primerSpliceSite">mouse 3 primer splice site</option>
26 ## <option value="/Users/xuebing/galaxy-dist/tool-data/motif-database/TATA-Box.meme">TATA box</option>
27 ## </param>
28 ##</when>
29 <when value="user">
30 <param name="motif" type="data" format="txt" label="Motif file" help="created using the tool create-motif-file, or import from Shared Data"/>
31 </when>
32 </conditional>
33
34 <param name="database" type="data" format="fasta" label="Sequence file (FASTA)"/>
35
36 <conditional name="background_select">
37 <param name="bg_select" type="select" label="Background model" >
38 <option value="uniform" selected="true">uniform</option>
39 <option value="fromfile">load from file</option>
40 </param>
41 <when value="fromfile">
42 <param name="bgfile" type="data" format="txt" label="File for background model"/>
43 </when>
44 </conditional>
45
46 <param name="pth" size="10" type="float" value="0.01" label="p-value threshold"/>
47 <param name="norc" label="Do not score the reverse complement DNA strand. Both strands are scored by default" type="boolean" truevalue="-norc" falsevalue="" checked="False"/>
48 </inputs>
49 <outputs>
50 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/>
51 <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (txt)"/>
52 </outputs>
53 <help>
54
55 **What it does**
56
57 This tool uses FIMO to find matches of a motif in a fasta file. See more details:
58
59 http://meme.sdsc.edu/meme/fimo-intro.html
60
61
62 </help>
63 </tool>