Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/plotRepartition.xml @ 31:0ab839023fe4
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| author | m-zytnicki |
|---|---|
| date | Tue, 30 Apr 2013 14:33:21 -0400 |
| parents | 769e306b7933 |
| children |
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| 30:5677346472b5 | 31:0ab839023fe4 |
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| 1 <tool id="plotRepartition" name="plot repartition"> | |
| 2 <description>Plot the repartition of different data on a whole genome. (This tool uses only 1 input file, the different values are stored in the tags. )</description> | |
| 3 <command interpreter="python"> | |
| 4 ../Java/Python/WrappPlotRepartition.py -i $inputFileName | |
| 5 -n $names | |
| 6 $normalize | |
| 7 #if $optionColor.Color == 'Yes': | |
| 8 -c $optionColor.colValue | |
| 9 #end if | |
| 10 -f $format | |
| 11 | |
| 12 #if $optionLog.log == 'Yes': | |
| 13 -l $optionLog.logVal | |
| 14 #end if | |
| 15 | |
| 16 -o $outputFilePNG | |
| 17 </command> | |
| 18 | |
| 19 <inputs> | |
| 20 <param name="inputFileName" type="data" label="Input Gff3 File" format="gff3"/> | |
| 21 <param name="names" type="text" value="None" label="name for the tags (separated by commas and no space) [compulsory option]"/> | |
| 22 <param name="normalize" type="boolean" truevalue="-r" falsevalue="" checked="false" label="normalize data (when panels are different)"/> | |
| 23 <param name="format" type="text" value="png" label="format of the output file[default: png]"/> | |
| 24 | |
| 25 <conditional name="optionColor"> | |
| 26 <param name="Color" type="select" label="scolor of the lines (separated by commas and no space) "> | |
| 27 <option value="Yes">Yes</option> | |
| 28 <option value="No" selected="true">No</option> | |
| 29 </param> | |
| 30 <when value="Yes"> | |
| 31 <param name="colValue" type="text" value="None"/> | |
| 32 </when> | |
| 33 <when value="No"> | |
| 34 </when> | |
| 35 </conditional> | |
| 36 | |
| 37 <conditional name="optionLog"> | |
| 38 <param name="log" type="select" label="use log on x- or y-axis (write 'x', 'y' or 'xy')"> | |
| 39 <option value="Yes">Yes</option> | |
| 40 <option value="No" selected="true">No</option> | |
| 41 </param> | |
| 42 <when value="Yes"> | |
| 43 <param name="logVal" type="text" value=" "/> | |
| 44 </when> | |
| 45 <when value="No"> | |
| 46 </when> | |
| 47 </conditional> | |
| 48 | |
| 49 </inputs> | |
| 50 | |
| 51 <outputs> | |
| 52 <data name="outputFilePNG" format="tar" label="[plotRepartition]out file"/> | |
| 53 </outputs> | |
| 54 | |
| 55 <help> | |
| 56 This script gives a .tar out file, if you want to take look at the results, you have to download it. | |
| 57 </help> | |
| 58 | |
| 59 </tool> |