Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/SMART/galaxy/findTss.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="findTss" name="findTss"> | |
| 2 <description>Find the transcription start site of a list of transcripts.</description> | |
| 3 <command interpreter="python"> | |
| 4 ../Java/Python/findTss.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 | |
| 16 -o $outputFileGff | |
| 17 $colinear | |
| 18 $normalize | |
| 19 -d $distance | |
| 20 $excel $excelOutput | |
| 21 | |
| 22 </command> | |
| 23 | |
| 24 <inputs> | |
| 25 <conditional name="formatType"> | |
| 26 <param name="FormatInputFileName" type="select" label="Input File Format"> | |
| 27 <option value="bed">bed</option> | |
| 28 <option value="gff">gff</option> | |
| 29 <option value="gff2">gff2</option> | |
| 30 <option value="gff3">gff3</option> | |
| 31 </param> | |
| 32 <when value="bed"> | |
| 33 <param name="inputFileName" format="bed" type="data" label="Input File"/> | |
| 34 </when> | |
| 35 <when value="gff"> | |
| 36 <param name="inputFileName" format="gff" type="data" label="Input File"/> | |
| 37 </when> | |
| 38 <when value="gff2"> | |
| 39 <param name="inputFileName" format="gff2" type="data" label="Input File"/> | |
| 40 </when> | |
| 41 <when value="gff3"> | |
| 42 <param name="inputFileName" format="gff3" type="data" label="Input File"/> | |
| 43 </when> | |
| 44 </conditional> | |
| 45 | |
| 46 <param name="colinear" type="boolean" truevalue="-e" falsevalue="" checked="false" label="colinear option" help="This option clusterizes only the same strand reads"/> | |
| 47 <param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="normalize option for only GFF3 file format" help="This option normalize (Warning!! Only for GFF3 file!!!!!)"/> | |
| 48 <param name="distance" type="text" value="10" label="distance option" help="Limit the maximum distance between two reads"/> | |
| 49 <param name="excel" type="boolean" truevalue="-c" falsevalue="" checked="false" label="excel option" help="This option creates a csv file."/> | |
| 50 </inputs> | |
| 51 | |
| 52 <outputs> | |
| 53 <data name="outputFileGff" format="gff3" label="[findTss] Output File"/> | |
| 54 <data name="excelOutput" format="csv" label="[findTss] CSV File"> | |
| 55 <filter>excel</filter> | |
| 56 </data> | |
| 57 </outputs> | |
| 58 | |
| 59 </tool> |