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comparison SMART/galaxy/getIntrons.xml @ 36:44d5973c188c

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author m-zytnicki
date Tue, 30 Apr 2013 15:02:29 -0400
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35:d94018ca4ada 36:44d5973c188c
1 <tool id="getIntrons" name="get introns">
2 <description>Get the introns of a set of transcripts.</description>
3 <command interpreter="python">
4 ../Java/Python/getIntrons.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 -o $outputFileGff
19 </command>
20
21 <inputs>
22 <conditional name="formatType">
23 <param name="FormatInputFileName" type="select" label="Input File Format">
24 <option value="bed">bed</option>
25 <option value="gff">gff</option>
26 <option value="gff2">gff2</option>
27 <option value="gff3">gff3</option>
28 <option value="sam">sam</option>
29 <option value="gtf">gtf</option>
30 </param>
31 <when value="bed">
32 <param name="inputFileName" format="bed" type="data" label="Input File"/>
33 </when>
34 <when value="gff">
35 <param name="inputFileName" format="gff" type="data" label="Input File"/>
36 </when>
37 <when value="gff2">
38 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
39 </when>
40 <when value="gff3">
41 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
42 </when>
43 <when value="sam">
44 <param name="inputFileName" format="sam" type="data" label="Input File"/>
45 </when>
46 <when value="gtf">
47 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
48 </when>
49 </conditional>
50
51 </inputs>
52
53 <outputs>
54 <data format="gff3" name="outputFileGff" label="[getIntrons -> gff3] Output File"/>
55 </outputs>
56 <tests>
57 <test>
58 <param name="FormatInputFileName" value="gtf" />
59 <param name="inputFileName" value="genes.gtf" />
60 <output name="outputFileGff" file="exp_getIntrons.gff3" />
61 </test>
62 </tests>
63
64 <help>
65 Provide all the introns of an annotation file.
66 </help>
67
68 </tool>