Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/SMART/galaxy/changeTagName.xml @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
| author | yufei-luo |
|---|---|
| date | Thu, 17 Jan 2013 10:52:14 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:e0f8dcca02ed |
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| 1 <tool id="changeTagName" name="change tag name"> | |
| 2 <description>Changes the name of tag of a list of transcripts.</description> | |
| 3 <command interpreter="python"> | |
| 4 ../Java/Python/changeTagName.py -i $formatType.inputFileName | |
| 5 #if $formatType.FormatInputFileName == 'bed': | |
| 6 -f bed | |
| 7 #elif $formatType.FormatInputFileName == 'gff': | |
| 8 -f gff | |
| 9 #elif $formatType.FormatInputFileName == 'gff2': | |
| 10 -f gff2 | |
| 11 #elif $formatType.FormatInputFileName == 'gff3': | |
| 12 -f gff3 | |
| 13 #end if | |
| 14 | |
| 15 -t $Tag | |
| 16 -n $name | |
| 17 | |
| 18 -o $outputFileGff | |
| 19 </command> | |
| 20 | |
| 21 <inputs> | |
| 22 <conditional name="formatType"> | |
| 23 <param name="FormatInputFileName" type="select" label="Input File Format"> | |
| 24 <option value="bed">bed</option> | |
| 25 <option value="gff">gff</option> | |
| 26 <option value="gff2">gff2</option> | |
| 27 <option value="gff3">gff3</option> | |
| 28 </param> | |
| 29 <when value="bed"> | |
| 30 <param name="inputFileName" format="bed" type="data" label="Input File"/> | |
| 31 </when> | |
| 32 <when value="gff"> | |
| 33 <param name="inputFileName" format="gff" type="data" label="Input File"/> | |
| 34 </when> | |
| 35 <when value="gff2"> | |
| 36 <param name="inputFileName" format="gff2" type="data" label="Input File"/> | |
| 37 </when> | |
| 38 <when value="gff3"> | |
| 39 <param name="inputFileName" format="gff3" type="data" label="Input File"/> | |
| 40 </when> | |
| 41 </conditional> | |
| 42 | |
| 43 <param name="Tag" type="text" value="None" label="tag option" help="A given tag, you must choose a tag."/> | |
| 44 <param name="name" type="text" value="None" label="name option" help="new name for the tag, you must choose a new name."/> | |
| 45 | |
| 46 | |
| 47 | |
| 48 </inputs> | |
| 49 | |
| 50 <outputs> | |
| 51 <data name="outputFileGff" format="gff3" label="[changeTagName] Output File"/> | |
| 52 </outputs> | |
| 53 | |
| 54 </tool> |