Mercurial > repos > yufei-luo > s_mart

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

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Uploaded
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="getExons" name="get exons"> 1 <tool id="getExons" name="get exons">
2 <description>Get the exons of a set of transcripts.</description> 2 <description>Get the exons 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/getExons.py -i $formatType.inputFileName 4 ../Java/Python/getExons.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':
68 </when> 65 </when>
69 </conditional> 66 </conditional>
70 </inputs> 67 </inputs>
71 68
72 <outputs> 69 <outputs>
73 <data format="gff3" name="outputFileGff" label="[get exons] output file"/> 70 <data format="gff3" name="outputFileGff" label="[getExons -> gff3] Output File"/>
74 </outputs> 71 </outputs>
75 <tests> 72 <tests>
76 <test> 73 <test>
77 <param name="FormatInputFileName" value="gtf" /> 74 <param name="FormatInputFileName" value="gtf" />
78 <param name="inputFileName" value="genes.gtf" /> 75 <param name="inputFileName" value="genes.gtf" />
79 <param name="Value" value="No"/> 76 <param name="Value" value="No"/>
80 <output name="outputFileGff" file="exp_getExons.gff3" /> 77 <output name="outputFileGff" file="exp_getExons.gff3" />
81 </test> 78 </test>
82 </tests> 79 </tests>
83
84 <help>
85 Provide all the exons of an annotation file.
86 </help>
87 </tool> 80 </tool>