annotate tools/mytools/fimo2.xml @ 3:33c067c3ae34

Deleted selected files
author xuebing
date Fri, 09 Mar 2012 19:47:53 -0500
parents 9071e359b9a3
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
1 <tool id="fimo" name="motif search">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
2 <description>using FIMO</description>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
3 <command> fimo
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
4 #if $background_select.bg_select == "fromfile":
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
5 -bgfile $bgfile
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
6 #end if
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
7
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
8 $norc --max-stored-scores 5000000 --output-pthresh $pth --verbosity 1 $motif $database
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
9 &amp;&amp; mv fimo_out/fimo.html ${html_outfile}
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
10
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
11 &amp;&amp; mv fimo_out/fimo.txt ${txt_outfile}
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
12
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
13 &amp;&amp; rm -rf fimo_out
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
14
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
15 </command>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
16 <inputs>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
17
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
18 <param name="motif" type="data" format="txt" label="Motif file" help="created using the tool create-motif-file, or import from Shared Data"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
19 <param name="database" type="data" format="fasta" label="Sequence file (FASTA)"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
20
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
21 <conditional name="background_select">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
22 <param name="bg_select" type="select" label="Background model" >
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
23 <option value="uniform" selected="true">uniform</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
24 <option value="fromfile">load from file</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
25 </param>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
26 <when value="fromfile">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
27 <param name="bgfile" type="data" format="txt" label="File for background model"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
28 </when>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
29 </conditional>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
30
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
31 <param name="pth" size="10" type="float" value="0.0001" label="p-value threshold"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
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"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
33 </inputs>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
34 <outputs>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
35 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
36 <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (txt)"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
37 </outputs>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
38 <help>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
39
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
40 **What it does**
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
41
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
42 This tool uses FIMO to find matches of a motif in a fasta file. See more details:
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
43
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
44 http://meme.sdsc.edu/meme/fimo-intro.html
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
45
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
46 </help>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
47 </tool>