annotate fimo2-old.xml @ 13:292186c14b08

Uploaded
author xuebing
date Sat, 10 Mar 2012 08:17:36 -0500
parents b7f1d9f8f3bc
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
1 <tool id="fimo" name="motif search">
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
2 <description>using FIMO</description>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
3 <command> fimo
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
4 #if $background_select.bg_select == "fromfile":
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
5 -bgfile $bgfile
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
6 #end if
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
7
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
8 $norc --output-pthresh $pth --verbosity 1 $motif $database
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
9 &amp;&amp; mv fimo_out/fimo.html ${html_outfile}
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
10
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
11 &amp;&amp; mv fimo_out/fimo.txt ${txt_outfile}
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
12
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
13 &amp;&amp; rm -rf fimo_out
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
14
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
15 </command>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
16 <inputs>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
17 <conditional name="motif_selection">
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
18 <param name="motif_sel" type="select" label="Motif Source">
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
19 <option value="user" selected="true">Use motif file in Your History</option>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
20 <option value="known" >Known motif</option>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
21 </param>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
22 ##<when value="known">
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
23 ## <param name="motif" type="select" label="Select motif">
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
24 ## <option value="/Users/xuebing/galaxy-dist/tool-data/motif-database/5primerSpliceSite" selected="true">mouse 5 primer splice site</option>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
25 ## <option value="/Users/xuebing/galaxy-dist/tool-data/motif-database/5primerSpliceSite">mouse 3 primer splice site</option>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
26 ## <option value="/Users/xuebing/galaxy-dist/tool-data/motif-database/TATA-Box.meme">TATA box</option>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
27 ## </param>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
28 ##</when>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
29 <when value="user">
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
30 <param name="motif" type="data" format="txt" label="Motif file" help="created using the tool create-motif-file, or import from Shared Data"/>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
31 </when>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
32 </conditional>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
33
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
34 <param name="database" type="data" format="fasta" label="Sequence file (FASTA)"/>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
35
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
36 <conditional name="background_select">
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
37 <param name="bg_select" type="select" label="Background model" >
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
38 <option value="uniform" selected="true">uniform</option>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
39 <option value="fromfile">load from file</option>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
40 </param>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
41 <when value="fromfile">
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
42 <param name="bgfile" type="data" format="txt" label="File for background model"/>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
43 </when>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
44 </conditional>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
45
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
46 <param name="pth" size="10" type="float" value="0.01" label="p-value threshold"/>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
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"/>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
48 </inputs>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
49 <outputs>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
50 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
51 <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (txt)"/>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
52 </outputs>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
53 <help>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
54
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
55 **What it does**
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
56
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
57 This tool uses FIMO to find matches of a motif in a fasta file. See more details:
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
58
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
59 http://meme.sdsc.edu/meme/fimo-intro.html
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
60
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
61
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
62 </help>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
63 </tool>