Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/getNb.xml @ 6:769e306b7933
Change the repository level.
| author | yufei-luo |
|---|---|
| date | Fri, 18 Jan 2013 04:54:14 -0500 |
| parents | |
| children |
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| 5:ea3082881bf8 | 6:769e306b7933 |
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| 1 <tool id="getNumber" name="get number"> | |
| 2 <description>Get the distribution of exons per transcripts, or mapping per read, or transcript per cluster.</description> | |
| 3 <command interpreter="python"> | |
| 4 ../Java/Python/getNb.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 #elif $formatType.FormatInputFileName == 'sam': | |
| 14 -f sam | |
| 15 #elif $formatType.FormatInputFileName == 'gtf': | |
| 16 -f gtf | |
| 17 #end if | |
| 18 -o $outputFilePNG | |
| 19 -q $query | |
| 20 $barPlot | |
| 21 #if $optionXMAX.XMAX == 'Yes': | |
| 22 -x $optionXMAX.xMaxValue | |
| 23 #end if | |
| 24 | |
| 25 </command> | |
| 26 | |
| 27 <inputs> | |
| 28 <conditional name="formatType"> | |
| 29 <param name="FormatInputFileName" type="select" label="Input File Format"> | |
| 30 <option value="bed">bed</option> | |
| 31 <option value="gff">gff</option> | |
| 32 <option value="gff2">gff2</option> | |
| 33 <option value="gff3">gff3</option> | |
| 34 <option value="sam">sam</option> | |
| 35 <option value="gtf">gtf</option> | |
| 36 </param> | |
| 37 <when value="bed"> | |
| 38 <param name="inputFileName" format="bed" type="data" label="Input File"/> | |
| 39 </when> | |
| 40 <when value="gff"> | |
| 41 <param name="inputFileName" format="gff" type="data" label="Input File"/> | |
| 42 </when> | |
| 43 <when value="gff2"> | |
| 44 <param name="inputFileName" format="gff2" type="data" label="Input File"/> | |
| 45 </when> | |
| 46 <when value="gff3"> | |
| 47 <param name="inputFileName" format="gff3" type="data" label="Input File"/> | |
| 48 </when> | |
| 49 <when value="sam"> | |
| 50 <param name="inputFileName" format="sam" type="data" label="Input File"/> | |
| 51 </when> | |
| 52 <when value="gtf"> | |
| 53 <param name="inputFileName" format="gtf" type="data" label="Input File"/> | |
| 54 </when> | |
| 55 </conditional> | |
| 56 | |
| 57 <param name="query" type="text" value="None" label="compulsory option, choice (exon, transcript, cluster)" /> | |
| 58 <param name="barPlot" type="boolean" truevalue="-b" falsevalue="" checked="false" label="use barplot representation"/> | |
| 59 | |
| 60 <conditional name="optionXMAX"> | |
| 61 <param name="XMAX" type="select" label="maximum value on the x-axis to plot "> | |
| 62 <option value="Yes">Yes</option> | |
| 63 <option value="No" selected="true">No</option> | |
| 64 </param> | |
| 65 <when value="Yes"> | |
| 66 <param name="xMaxValue" type="integer" value="0" /> | |
| 67 </when> | |
| 68 <when value="No"> | |
| 69 </when> | |
| 70 </conditional> | |
| 71 | |
| 72 </inputs> | |
| 73 | |
| 74 <outputs> | |
| 75 <data name="outputFilePNG" format="png" label="[getNB]out file"/> | |
| 76 </outputs> | |
| 77 | |
| 78 </tool> |