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

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author m-zytnicki
date Mon, 22 Apr 2013 11:08:07 -0400
parents 769e306b7933
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14:c79b9ae3f65f 15:440ceca58672
1 <tool id="cleanGff" name="clean Gff"> 1 <tool id="cleanGff" name="clean Gff">
2 <description>Cleans a GFF file as given by NCBI and outpus a Gff3 file.</description> 2 <description>Clean a GFF file (e.g. as given by NCBI) and produces a new GFF3 file, understood by S-MART.</description>
3 <command interpreter="python"> ../Java/Python/cleanGff.py -i $inputFile 3 <command interpreter="python"> ../Java/Python/cleanGff.py -i $inputFile
4 -t $type 4 -t $type
5 -o $outputFile 5 -o $outputFile
6 </command> 6 </command>
7 7
8 <inputs> 8 <inputs>
9 <param name="inputFile" type="data" label="Input File" format="gff"/> 9 <param name="inputFile" type="data" label="Input File" format="gff"/>
10 <param name="type" type="text" value="tRNA,rRNA,ncRNA,CDS" label="tag option, compulsory option" help="lists of comma separated types that you want to keep.EX: ncRNA,tRNA,rRNA,CDS"/> 10 <param name="type" type="text" value="tRNA,rRNA,ncRNA,CDS" label="Tags you keep" help="lists of comma separated types that you want to keep, e.g. ncRNA,tRNA,rRNA,CDS"/>
11 </inputs> 11 </inputs>
12 12
13 <outputs> 13 <outputs>
14 <data format="gff3" name="outputFile" label="[cleanGff] Output File"/> 14 <data format="gff3" name="outputFile" label="[cleanGff] Output File"/>
15 </outputs> 15 </outputs>
16 16
17 <help>
18 A GFF file (please consult http://www.sequenceontology.org/gff3.shtml to know more about it) may contain different sources of information: chromosome size, genes, transcripts, etc. S-MART mostly works on transcripts. This scripts filters the input GFF3 to keep the information you really want, based on the feature (3rd column).
19 </help>
17 </tool> 20 </tool>
18 21