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comparison SMART/galaxy/getIntrons.xml @ 38:2c0c0a89fad7

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author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
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37:d22fadc825e3 38:2c0c0a89fad7
1 <tool id="getIntrons" name="get introns">
2 <description>Get the introns of a set of transcripts.</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python">
7 ../Java/Python/getIntrons.py -i $formatType.inputFileName
8 #if $formatType.FormatInputFileName == 'bed':
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 == 'gtf':
19 -f gtf
20 #end if
21 -o $outputFileGff
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 <option value="sam">sam</option>
32 <option value="gtf">gtf</option>
33 </param>
34 <when value="bed">
35 <param name="inputFileName" format="bed" type="data" label="Input File"/>
36 </when>
37 <when value="gff">
38 <param name="inputFileName" format="gff" type="data" label="Input File"/>
39 </when>
40 <when value="gff2">
41 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
42 </when>
43 <when value="gff3">
44 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
45 </when>
46 <when value="sam">
47 <param name="inputFileName" format="sam" type="data" label="Input File"/>
48 </when>
49 <when value="gtf">
50 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
51 </when>
52 </conditional>
53
54 </inputs>
55
56 <outputs>
57 <data format="gff3" name="outputFileGff" label="[get introns] output file"/>
58 </outputs>
59 <tests>
60 <test>
61 <param name="FormatInputFileName" value="gtf" />
62 <param name="inputFileName" value="genes.gtf" />
63 <output name="outputFileGff" file="exp_getIntrons.gff3" />
64 </test>
65 </tests>
66
67 <help>
68 Provide all the introns of an annotation file.
69 </help>
70
71 </tool>