Mercurial > repos > yufei-luo > s_mart

comparison SMART/galaxy/CleanTranscriptFile.xml @ 18:94ab73e8a190

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Uploaded
author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
parents 440ceca58672
children 0ab839023fe4
comparison
equal deleted inserted replaced
17:b0e8584489e6 18:94ab73e8a190
1 <tool id="CleanTranscriptFile" name="clean Transcript File"> 1 <tool id="CleanTranscriptFile" name="clean transcript file">
2 <description>Clean a transcript file so that it is useable for S-MART.</description> 2 <description>Clean a transcript file so that it is useable for S-MART.</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
3 <command interpreter="python"> ../Java/Python/CleanTranscriptFile.py -i $formatType.inputFileName 6 <command interpreter="python"> ../Java/Python/CleanTranscriptFile.py -i $formatType.inputFileName
4 #if $formatType.FormatInputFileName == 'gff': 7 #if $formatType.FormatInputFileName == 'gff':
5 -f gff 8 -f gff
6 #elif $formatType.FormatInputFileName == 'gtf': 9 #elif $formatType.FormatInputFileName == 'gtf':
7 -f gtf 10 -f gtf
49 52
50 53
51 <outputs> 54 <outputs>
52 <data name="outputFile" format="gtf"> 55 <data name="outputFile" format="gtf">
53 <change_format> 56 <change_format>
57 <when input="formatType.FormatInputFileName" value="gtf" format="gtf" />
54 <when input="formatType.FormatInputFileName" value="gff" format="gff" /> 58 <when input="formatType.FormatInputFileName" value="gff" format="gff" />
55 <when input="formatType.FormatInputFileName" value="gff3" format="gff3" /> 59 <when input="formatType.FormatInputFileName" value="gff3" format="gff3" />
56 </change_format> 60 </change_format>
57 </data> 61 </data>
58 62