comparison SMART/galaxy/getWigProfile.xml @ 6:769e306b7933

Change the repository level.
author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
parents
children 440ceca58672
comparison
equal deleted inserted replaced
5:ea3082881bf8 6:769e306b7933
1 <tool id="getWigProfile" name="get wig profile">
2 <description>Compute the average profile of some genomic coordinates using WIG files (thus covering a large proportion of the genome).</description>
3 <command interpreter="python">
4 ../Java/Python/getWigProfile.py -i $formatType.inputFileName
5 #if $formatType.FormatInputFileName == 'bed':
6 -f bed
7 #elif $formatType.FormatInputFileName == 'gff':
8 -f gff
9 #elif $formatType.FormatInputFileName == 'gff2':
10 -f gff2
11 #elif $formatType.FormatInputFileName == 'gff3':
12 -f gff3
13 #end if
14 -w $inputWigFile
15 -p $nbPoints
16 -d $distance
17 $strands
18 -o $outputFilePNG
19 #if $optionSMO.SMO == 'Yes':
20 -m $optionSMO.smoothen
21 #end if
22
23 </command>
24
25 <inputs>
26 <conditional name="formatType">
27 <param name="FormatInputFileName" type="select" label="Input File Format">
28 <option value="bed">bed</option>
29 <option value="gff">gff</option>
30 <option value="gff2">gff2</option>
31 <option value="gff3">gff3</option>
32 </param>
33 <when value="bed">
34 <param name="inputFileName" format="bed" type="data" label="Input File"/>
35 </when>
36 <when value="gff">
37 <param name="inputFileName" format="gff" type="data" label="Input File"/>
38 </when>
39 <when value="gff2">
40 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
41 </when>
42 <when value="gff3">
43 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
44 </when>
45 </conditional>
46
47 <param name="inputWigFile" type="data" label="Input Wig File" format="wig"/>
48 <param name="nbPoints" type="integer" value="1000" label="number of points on the x-axis"/>
49 <param name="distance" type="integer" value="0" label="distance around genomic coordinates"/>
50 <param name="strands" type="boolean" truevalue="-s" falsevalue="" checked="false" label="consider both strands separately"/>
51
52 <conditional name="optionSMO">
53 <param name="SMO" type="select" label="smoothen the curve">
54 <option value="Yes">Yes</option>
55 <option value="No" selected="true">No</option>
56 </param>
57 <when value="Yes">
58 <param name="smoothen" type="integer" value="0"/>
59 </when>
60 <when value="No">
61 </when>
62 </conditional>
63
64 </inputs>
65
66 <outputs>
67 <data name="outputFilePNG" format="png" label="[getWigProfile]out file"/>
68 </outputs>
69
70 </tool>