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comparison smart_toolShed/SMART/galaxy/clusterize.xml @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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-1:000000000000 0:e0f8dcca02ed
1 <tool id="MergingDataClusterize" name="Clusterize">
2 <description>Clusterizes the reads when their genomic intervals overlap.</description>
3 <command interpreter="python">
4 ../Java/Python/clusterize.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 #elif $formatType.FormatInputFileName == 'csv':
14 -f csv
15 #elif $formatType.FormatInputFileName == 'sam':
16 -f sam
17 #end if
18 -o $outputFileGff
19 $colinear
20 $normalize
21 -d $distance
22 $log $outputFileLog
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 <option value="csv">csv</option>
33 <option value="sam">sam</option>
34 </param>
35 <when value="bed">
36 <param name="inputFileName" format="bed" type="data" label="Input File"/>
37 </when>
38 <when value="gff">
39 <param name="inputFileName" format="gff" type="data" label="Input File"/>
40 </when>
41 <when value="gff2">
42 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
43 </when>
44 <when value="gff3">
45 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
46 </when>
47 <when value="csv">
48 <param name="inputFileName" format="csv" type="data" label="Input File"/>
49 </when>
50 <when value="sam">
51 <param name="inputFileName" format="sam" type="data" label="Input File"/>
52 </when>
53 </conditional>
54
55 <param name="colinear" type="boolean" truevalue="-c" falsevalue="" checked="false" label="colinear option" help="This option clusterizes only the same strand reads"/>
56 <param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="normalize option for only GFF3 file format" help="This option normalize (attention!! Only for GFF3 file!!!!!)"/>
57 <param name="log" type="boolean" truevalue="-l" falsevalue="" checked="false" label="log option" help="This option create a log file"/>
58 <param name="distance" type="integer" value="0" label="distance option" help="Limit the maximum distance between two reads"/>
59 </inputs>
60
61 <outputs>
62 <data name="outputFileGff" format="gff3" label="[clusterize]output file"/>
63 <data name="outputFileLog" format="txt" label="[clusterize]output file">
64 <filter>log</filter>
65 </data>
66 </outputs>
67 </tool>