Mercurial > repos > yufei-luo > s_mart

comparison SMART/galaxy/CleanTranscriptFile.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="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>
6 <command interpreter="python"> ../Java/Python/CleanTranscriptFile.py -i $formatType.inputFileName 3 <command interpreter="python"> ../Java/Python/CleanTranscriptFile.py -i $formatType.inputFileName
7 #if $formatType.FormatInputFileName == 'gff': 4 #if $formatType.FormatInputFileName == 'gff':
8 -f gff 5 -f gff
9 #elif $formatType.FormatInputFileName == 'gtf': 6 #elif $formatType.FormatInputFileName == 'gtf':
10 -f gtf 7 -f gtf
52 49
53 50
54 <outputs> 51 <outputs>
55 <data name="outputFile" format="gtf"> 52 <data name="outputFile" format="gtf">
56 <change_format> 53 <change_format>
57 <when input="formatType.FormatInputFileName" value="gtf" format="gtf" />
58 <when input="formatType.FormatInputFileName" value="gff" format="gff" /> 54 <when input="formatType.FormatInputFileName" value="gff" format="gff" />
59 <when input="formatType.FormatInputFileName" value="gff3" format="gff3" /> 55 <when input="formatType.FormatInputFileName" value="gff3" format="gff3" />
60 </change_format> 56 </change_format>
61 </data> 57 </data>
62 58
68 <param name="type" value="No" /> 64 <param name="type" value="No" />
69 <output name="outputFile" file="exp_cleantranscriptfile_genes.gtf" /> 65 <output name="outputFile" file="exp_cleantranscriptfile_genes.gtf" />
70 </test> 66 </test>
71 </tests> 67 </tests>
72 68
73 <help>
74 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).
75 </help>
76
77 </tool> 69 </tool>