Mercurial > repos > yufei-luo > s_mart

comparison SMART/galaxy/Clusterize.xml @ 60:90f4b29d884f

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Uploaded
author m-zytnicki
date Fri, 21 Feb 2014 08:32:36 -0500
parents 97aa2e42bfdf
children 5f210bc9f486
comparison
equal deleted inserted replaced
59:2a4884ba3e5c 60:90f4b29d884f
2 <description>Clusterize features when their genomic intervals overlap.</description> 2 <description>Clusterize features when their genomic intervals overlap.</description>
3 <requirements> 3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement> 4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python"> 6 <command interpreter="python">
7 ../Java/Python/clusterize.py -i $formatType.inputFileName 7 #set $inputFiles = ",".join(["%s" % (s) for s in $formatType.inputFileName])
8 #if $formatType.FormatInputFileName == 'bed': 8 ../Java/Python/clusterize.py -i $inputFiles -f $formatType.FormatInputFileName -o $outputFileGff $colinear $normalize -d $distance
9 -f bed
10 #elif $formatType.FormatInputFileName == 'gff':
11 -f gff
12 #elif $formatType.FormatInputFileName == 'gff2':
13 -f gff2
14 #elif $formatType.FormatInputFileName == 'gff3':
15 -f gff3
16 #elif $formatType.FormatInputFileName == 'sam':
17 -f sam
18 #elif $formatType.FormatInputFileName == 'bam':
19 -f bam
20 #elif $formatType.FormatInputFileName == 'gtf':
21 -f gtf
22 #end if
23 -o $outputFileGff
24 $colinear
25 $normalize
26 -d $distance
27 </command> 9 </command>
28 10
29 <inputs> 11 <inputs>
30 <conditional name="formatType"> 12 <conditional name="formatType">
31 <param name="FormatInputFileName" type="select" label="Input File Format"> 13 <param name="FormatInputFileName" type="select" label="Input File Format">
32 <option value="bed">bed</option> 14 <option value="bed">bed</option>
33 <option value="gff">gff</option> 15 <option value="gff">gff</option>
34 <option value="gff2">gff2</option> 16 <option value="gff2">gff2</option>
35 <option value="gff3">gff3</option> 17 <option value="gff3">gff3</option>
36 <option value="sam">sam</option> 18 <option value="sam">sam</option>
19 <option value="gtf">gtf</option>
37 <option value="bam">bam</option> 20 <option value="bam">bam</option>
38 <option value="gtf">gtf</option>
39 </param> 21 </param>
40 <when value="bed"> 22 <when value="bed">
41 <param name="inputFileName" format="bed" type="data" label="Input File"/> 23 <param name="inputFileName" format="bed" type="data" multiple="true" label="Input File"/>
42 </when> 24 </when>
43 <when value="gff"> 25 <when value="gff">
44 <param name="inputFileName" format="gff" type="data" label="Input File"/> 26 <param name="inputFileName" format="gff" type="data" multiple="true" label="Input File"/>
45 </when> 27 </when>
46 <when value="gff2"> 28 <when value="gff2">
47 <param name="inputFileName" format="gff2" type="data" label="Input File"/> 29 <param name="inputFileName" format="gff2" type="data" multiple="true" label="Input File"/>
48 </when> 30 </when>
49 <when value="gff3"> 31 <when value="gff3">
50 <param name="inputFileName" format="gff3" type="data" label="Input File"/> 32 <param name="inputFileName" format="gff3" type="data" multiple="true" label="Input File"/>
51 </when> 33 </when>
52 <when value="sam"> 34 <when value="sam">
53 <param name="inputFileName" format="sam" type="data" label="Input File"/> 35 <param name="inputFileName" format="sam" type="data" multiple="true" label="Input File"/>
36 </when>
37 <when value="gtf">
38 <param name="inputFileName" format="gtf" type="data" multiple="true" label="Input File"/>
54 </when> 39 </when>
55 <when value="bam"> 40 <when value="bam">
56 <param name="inputFileName" format="bam" type="data" label="Input File"/> 41 <param name="inputFileName" format="bam" type="data" multiple="true" label="Input File"/>
57 </when>
58 <when value="gtf">
59 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
60 </when> 42 </when>
61 </conditional> 43 </conditional>
62 44
63 <param name="colinear" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Only merge collinear features"/> 45 <param name="colinear" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Only merge collinear features"/>
64 <param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Normalize counts" help="Only works if the nbOccurrences tag is set."/> 46 <param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Normalize counts" help="Only works if the nbOccurrences tag is set."/>