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

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="findTss" name="findTss">
2 <description>Find the transcription start site of a list of transcripts.</description>
3 <command interpreter="python">
4 ../Java/Python/findTss.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
15
16 -o $outputFileGff
17 $colinear
18 $normalize
19 -d $distance
20 $excel $excelOutput
21
22 </command>
23
24 <inputs>
25 <conditional name="formatType">
26 <param name="FormatInputFileName" type="select" label="Input File Format">
27 <option value="bed">bed</option>
28 <option value="gff">gff</option>
29 <option value="gff2">gff2</option>
30 <option value="gff3">gff3</option>
31 </param>
32 <when value="bed">
33 <param name="inputFileName" format="bed" type="data" label="Input File"/>
34 </when>
35 <when value="gff">
36 <param name="inputFileName" format="gff" type="data" label="Input File"/>
37 </when>
38 <when value="gff2">
39 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
40 </when>
41 <when value="gff3">
42 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
43 </when>
44 </conditional>
45
46 <param name="colinear" type="boolean" truevalue="-e" falsevalue="" checked="false" label="colinear option" help="This option clusterizes only the same strand reads"/>
47 <param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="normalize option for only GFF3 file format" help="This option normalize (Warning!! Only for GFF3 file!!!!!)"/>
48 <param name="distance" type="text" value="10" label="distance option" help="Limit the maximum distance between two reads"/>
49 <param name="excel" type="boolean" truevalue="-c" falsevalue="" checked="false" label="excel option" help="This option creates a csv file."/>
50 </inputs>
51
52 <outputs>
53 <data name="outputFileGff" format="gff3" label="[findTss] Output File"/>
54 <data name="excelOutput" format="csv" label="[findTss] CSV File">
55 <filter>excel</filter>
56 </data>
57 </outputs>
58
59 </tool>