Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/getIntrons.xml @ 18:94ab73e8a190
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| author | m-zytnicki |
|---|---|
| date | Mon, 29 Apr 2013 03:20:15 -0400 |
| parents | 440ceca58672 |
| children | 0ab839023fe4 |
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| 17:b0e8584489e6 | 18:94ab73e8a190 |
|---|---|
| 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> | |
| 3 <command interpreter="python"> | 6 <command interpreter="python"> |
| 4 ../Java/Python/getIntrons.py -i $formatType.inputFileName | 7 ../Java/Python/getIntrons.py -i $formatType.inputFileName |
| 5 #if $formatType.FormatInputFileName == 'bed': | 8 #if $formatType.FormatInputFileName == 'bed': |
| 6 -f bed | 9 -f bed |
| 7 #elif $formatType.FormatInputFileName == 'gff': | 10 #elif $formatType.FormatInputFileName == 'gff': |
| 49 </conditional> | 52 </conditional> |
| 50 | 53 |
| 51 </inputs> | 54 </inputs> |
| 52 | 55 |
| 53 <outputs> | 56 <outputs> |
| 54 <data format="gff3" name="outputFileGff" label="[getIntrons -> gff3] Output File"/> | 57 <data format="gff3" name="outputFileGff" label="[get introns] output file"/> |
| 55 </outputs> | 58 </outputs> |
| 56 <tests> | 59 <tests> |
| 57 <test> | 60 <test> |
| 58 <param name="FormatInputFileName" value="gtf" /> | 61 <param name="FormatInputFileName" value="gtf" /> |
| 59 <param name="inputFileName" value="genes.gtf" /> | 62 <param name="inputFileName" value="genes.gtf" /> |