Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/SMART/galaxy/getWigProfile.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="getWigProfile" name="get wig profile"> | |
| 2 <description>Compute the average profile of some genomic coordinates using WIG files (thus covering a large proportion of the genome).</description> | |
| 3 <command interpreter="python"> | |
| 4 ../Java/Python/getWigProfile.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 -w $inputWigFile | |
| 15 -p $nbPoints | |
| 16 -d $distance | |
| 17 $strands | |
| 18 -o $outputFilePNG | |
| 19 #if $optionSMO.SMO == 'Yes': | |
| 20 -m $optionSMO.smoothen | |
| 21 #end if | |
| 22 | |
| 23 </command> | |
| 24 | |
| 25 <inputs> | |
| 26 <conditional name="formatType"> | |
| 27 <param name="FormatInputFileName" type="select" label="Input File Format"> | |
| 28 <option value="bed">bed</option> | |
| 29 <option value="gff">gff</option> | |
| 30 <option value="gff2">gff2</option> | |
| 31 <option value="gff3">gff3</option> | |
| 32 </param> | |
| 33 <when value="bed"> | |
| 34 <param name="inputFileName" format="bed" type="data" label="Input File"/> | |
| 35 </when> | |
| 36 <when value="gff"> | |
| 37 <param name="inputFileName" format="gff" type="data" label="Input File"/> | |
| 38 </when> | |
| 39 <when value="gff2"> | |
| 40 <param name="inputFileName" format="gff2" type="data" label="Input File"/> | |
| 41 </when> | |
| 42 <when value="gff3"> | |
| 43 <param name="inputFileName" format="gff3" type="data" label="Input File"/> | |
| 44 </when> | |
| 45 </conditional> | |
| 46 | |
| 47 <param name="inputWigFile" type="data" label="Input Wig File" format="wig"/> | |
| 48 <param name="nbPoints" type="integer" value="1000" label="number of points on the x-axis"/> | |
| 49 <param name="distance" type="integer" value="0" label="distance around genomic coordinates"/> | |
| 50 <param name="strands" type="boolean" truevalue="-s" falsevalue="" checked="false" label="consider both strands separately"/> | |
| 51 | |
| 52 <conditional name="optionSMO"> | |
| 53 <param name="SMO" type="select" label="smoothen the curve"> | |
| 54 <option value="Yes">Yes</option> | |
| 55 <option value="No" selected="true">No</option> | |
| 56 </param> | |
| 57 <when value="Yes"> | |
| 58 <param name="smoothen" type="integer" value="0"/> | |
| 59 </when> | |
| 60 <when value="No"> | |
| 61 </when> | |
| 62 </conditional> | |
| 63 | |
| 64 </inputs> | |
| 65 | |
| 66 <outputs> | |
| 67 <data name="outputFilePNG" format="png" label="[getWigProfile]out file"/> | |
| 68 </outputs> | |
| 69 | |
| 70 </tool> |