Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/SMART/galaxy/plot.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="plot" name="Plot"> | |
| 2 <description>Plot some information from a list of transcripts.</description> | |
| 3 <command interpreter="python"> | |
| 4 ../Java/Python/plot.py -i $formatType.inputFileName | |
| 5 #if $formatType.FormatInputFileName == 'gff': | |
| 6 -f gff | |
| 7 #elif $formatType.FormatInputFileName == 'gff2': | |
| 8 -f gff2 | |
| 9 #elif $formatType.FormatInputFileName == 'gff3': | |
| 10 -f gff3 | |
| 11 #end if | |
| 12 | |
| 13 -x $xLabel | |
| 14 | |
| 15 -y $yLabel | |
| 16 | |
| 17 -X $XVal | |
| 18 -Y $YVal | |
| 19 | |
| 20 #if $optionLog.log == 'Yes' : | |
| 21 -l $optionLog.logOnAxisLabel | |
| 22 #end if | |
| 23 | |
| 24 -s $shape | |
| 25 -o $outputFile | |
| 26 | |
| 27 </command> | |
| 28 | |
| 29 <inputs> | |
| 30 <conditional name="formatType"> | |
| 31 <param name="FormatInputFileName" type="select" label="Input File Format"> | |
| 32 <option value="gff">gff</option> | |
| 33 <option value="gff2">gff2</option> | |
| 34 <option value="gff3">gff3</option> | |
| 35 </param> | |
| 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="xLabel" type="text" value="value1" label="x label option" help="Choose one of the tags of 9th column in GFF file to be plotted as X-axis. Warning: You can only choose the tag value is digital."/> | |
| 48 <param name="yLabel" type="text" value="value2" label="y label option" help="Choose one of the tags of 9th column in GFF file to be plotted as Y-axis. You can only choose the tag value is digital."/> | |
| 49 <param name="XVal" type="float" value="0.0" label="value for x when tag is not present "/> | |
| 50 | |
| 51 <param name="YVal" type="float" value="0.0" label="value for y when tag is not present"/> | |
| 52 | |
| 53 | |
| 54 <conditional name="optionLog"> | |
| 55 <param name="log" type="select" label="calculate log option" help="use log on x- or y-axis (write 'x', 'y' or 'xy')"> | |
| 56 <option value="Yes">Yes</option> | |
| 57 <option value="No" selected="true">No</option> | |
| 58 </param> | |
| 59 <when value="Yes"> | |
| 60 <param name="logOnAxisLabel" type="text" value="y" label="use log on x- or y-axis (write 'x', 'y' or 'xy')"/> | |
| 61 </when> | |
| 62 <when value="No"> | |
| 63 </when> | |
| 64 </conditional> | |
| 65 <param name="shape" type="text" value="barplot" label="shape of the plot [format: choice (barplot, line, points, heatPoints)]"/> | |
| 66 </inputs> | |
| 67 | |
| 68 <outputs> | |
| 69 <data name="outputFile" format="png" label="[plot] Output file"/> | |
| 70 </outputs> | |
| 71 </tool> |