comparison smart_toolShed/SMART/galaxy/getExons.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="getExons" name="get exons">
2 <description>Get the exons of a set of transcripts.</description>
3 <command interpreter="python">
4 ../Java/Python/getExons.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 == 'sam':
14 -f sam
15 #elif $formatType.FormatInputFileName == 'gtf':
16 -f gtf
17 #end if
18
19 #if $optionSelect.Value == "Yes":
20 -s $optionSelect.selectValue
21 #end if
22
23 -o $outputFileGff
24 </command>
25
26 <inputs>
27 <conditional name="formatType">
28 <param name="FormatInputFileName" type="select" label="Input File Format">
29 <option value="bed">bed</option>
30 <option value="gff">gff</option>
31 <option value="gff2">gff2</option>
32 <option value="gff3">gff3</option>
33 <option value="sam">sam</option>
34 <option value="gtf">gtf</option>
35 </param>
36 <when value="bed">
37 <param name="inputFileName" format="bed" type="data" label="Input File"/>
38 </when>
39 <when value="gff">
40 <param name="inputFileName" format="gff" type="data" label="Input File"/>
41 </when>
42 <when value="gff2">
43 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
44 </when>
45 <when value="gff3">
46 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
47 </when>
48 <when value="sam">
49 <param name="inputFileName" format="sam" type="data" label="Input File"/>
50 </when>
51 <when value="gtf">
52 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
53 </when>
54 </conditional>
55
56 <conditional name="optionSelect">
57 <param name="Value" type="select" label="select some of the exons (like '1,2,5..-3,-1')">
58 <option value="Yes">Yes</option>
59 <option value="No" selected="true">No</option>
60 </param>
61 <when value="Yes">
62 <param name="selectValue" type="text" value="None" label="select option" help="like '1,2,5..-3,-1'"/>
63 </when>
64 <when value="No">
65 </when>
66 </conditional>
67 </inputs>
68
69 <outputs>
70 <data format="gff3" name="outputFileGff" label="[getExons -> gff3] Output File"/>
71 </outputs>
72 </tool>