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comparison SMART/galaxy/getIntrons.xml @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
1 <tool id="getIntrons" name="get introns"> 1 <tool id="getIntrons" name="get introns">
2 <description>Get the introns of a set of transcripts.</description> 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"> 3 <command interpreter="python">
7 ../Java/Python/getIntrons.py -i $formatType.inputFileName 4 ../Java/Python/getIntrons.py -i $formatType.inputFileName
8 #if $formatType.FormatInputFileName == 'bed': 5 #if $formatType.FormatInputFileName == 'bed':
9 -f bed 6 -f bed
10 #elif $formatType.FormatInputFileName == 'gff': 7 #elif $formatType.FormatInputFileName == 'gff':
52 </conditional> 49 </conditional>
53 50
54 </inputs> 51 </inputs>
55 52
56 <outputs> 53 <outputs>
57 <data format="gff3" name="outputFileGff" label="[get introns] output file"/> 54 <data format="gff3" name="outputFileGff" label="[getIntrons -> gff3] Output File"/>
58 </outputs> 55 </outputs>
59 <tests> 56 <tests>
60 <test> 57 <test>
61 <param name="FormatInputFileName" value="gtf" /> 58 <param name="FormatInputFileName" value="gtf" />
62 <param name="inputFileName" value="genes.gtf" /> 59 <param name="inputFileName" value="genes.gtf" />
63 <output name="outputFileGff" file="exp_getIntrons.gff3" /> 60 <output name="outputFileGff" file="exp_getIntrons.gff3" />
64 </test> 61 </test>
65 </tests> 62 </tests>
66 63
67 <help>
68 Provide all the introns of an annotation file.
69 </help>
70
71 </tool> 64 </tool>