Mercurial > repos > yufei-luo > s_mart

comparison SMART/galaxy/CleanTranscriptFile.xml @ 15:440ceca58672

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Uploaded
author m-zytnicki
date Mon, 22 Apr 2013 11:08:07 -0400
parents 769e306b7933
children 94ab73e8a190
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14:c79b9ae3f65f 15:440ceca58672
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 <command interpreter="python"> ../Java/Python/CleanTranscriptFile.py -i $formatType.inputFileName 3 <command interpreter="python"> ../Java/Python/CleanTranscriptFile.py -i $formatType.inputFileName
4 #if $formatType.FormatInputFileName == 'gff': 4 #if $formatType.FormatInputFileName == 'gff':
5 -f gff 5 -f gff
6 #elif $formatType.FormatInputFileName == 'gtf': 6 #elif $formatType.FormatInputFileName == 'gtf':
7 -f gtf 7 -f gtf
55 <when input="formatType.FormatInputFileName" value="gff3" format="gff3" /> 55 <when input="formatType.FormatInputFileName" value="gff3" format="gff3" />
56 </change_format> 56 </change_format>
57 </data> 57 </data>
58 58
59 </outputs> 59 </outputs>
60 <tests>
61 <test>
62 <param name="FormatInputFileName" value="gtf" />
63 <param name="inputFileName" value="genes.gtf" />
64 <param name="type" value="No" />
65 <output name="outputFile" file="exp_cleantranscriptfile_genes.gtf" />
66 </test>
67 </tests>
68
69 <help>
70 A GFF/GTF file (please consult http://www.sequenceontology.org/gff3.shtml to know more about the GFF3 format, and http://mblab.wustl.edu/GTF22.html for the GTF format) may contain different sources of information: chromosome size, genes, transcripts, etc. S-MART mostly works on transcripts. This scripts filters the input file to keep the information you really want, based on the feature (3rd column).
71 </help>
72
60 </tool> 73 </tool>