Mercurial > repos > kuyt002 > vennerable_r
diff vennerable/unused/Vennerable.xml_backup_png @ 0:77bbf955e8de default tip
initial commit
| author | eric |
|---|---|
| date | Thu, 06 Nov 2014 15:07:54 +0100 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vennerable/unused/Vennerable.xml_backup_png Thu Nov 06 15:07:54 2014 +0100 @@ -0,0 +1,112 @@ +<tool id="Vennerable" name="Vennerable" version="0.9" > + <description>: Plot data in Venn or Venn-like diagrams</description> + <command> + #if $opt.userSpecified == "Yes" + R --slave --vanilla --file=$GALAXY_ROOT_DIR/tools/WURtools/R_tools/Vennerable.R + --args $inputFile + default + $weighting + $outputFile + $plottype + $resolution + 2>$Vennerable_log + 1>>$Vennerable_log + #else + R --slave --vanilla --file=$GALAXY_ROOT_DIR/tools/WURtools/R_tools/Vennerable.R + --args $inputFile + "$opt.xNames" + $weighting + $outputFile + $plottype + $resolution + 2>$Vennerable_log + 1>>$Vennerable_log + #end if + </command> + <inputs> + <param name="inputFile" format="tabular" type="data" label="Data set" /> + <conditional name="opt"> + <param name="userSpecified" type="select" label="Use column headers as dataset names?"> + <option value="Yes">Yes</option> + <option value="No">No</option> + </param> + <when value="Yes"> + </when> + <when value="No"> + <param name="xNames" type="text" label="Alternative data names" value="A,B,C,D" help="(comma-separated)"/> + </when> + </conditional> + <param name="plottype" type="select" label="Plot type to use" help="some other options might get disabled for certain plottypes" > + <option value="AWFE" selected="True">AWFE: Edwards-Venn (Non-weighted)</option> + <option value="ChowRuskey">Chow-Ruskey (always weigthed)</option> + <option value="ellipses">Ellipses (4 datasets only and always non-weighted)</option> + <option value="circles">Circles (max 3 datasets)</option> + <option value="squares">Squares (max 4 datasets non-weighted)</option> + </param> + <param name="weighting" type="select" label="Use weighting for data in plot" > + <option value="FALSE" selected="True">Non-weighted</option> + <option value="TRUE">Weighted</option> + </param> + <param name="resolution" type="integer" label="Resolution to use (dpi)" value="150" help="Plot features can be sized with this setting. Lower (50) is larger text." /> + </inputs> + <outputs> + <data name="outputFile" format="png" label="Venn diagram of ${inputFile.name}"/> + <data name="Vennerable_log" format="tabular" label="Vennerable output and error log file" /> + </outputs> + <tests> + <test> + </test> + </tests> + <requirements> + <requirement type="binary">R</requirement> + </requirements> + <help> +| + + +**What it does** + +Vennerable V2.0 (09-10-2009) + +This tool will use the Vennerable R package to plot data as weighted or un-weighted diagrams such as Venn, Edwards-Venn and Chow-Rusky. + +The tool can take 2 to 7 collumns of data but more are adviced not to be used (for speed and clarity). + +----- + +**Input** + +It takes a tabular file containing identifiers. Matches will be calculated automatically. + +Be sure to specify headers if you haven't any in your dataset! Otherwise the top row of data will be excluded. + +:: + + DataA DataB DataC DataD + HUM1 AGK2 AGK2 RTT3 + AGK2 ZZE3 ERT3 ZPD3 + ZPD3 AAW3 RTT3 WER2 + WER2 HUM1 RRW4 DUM1 + +----- + +**Example** + +.. image:: ../static/images/WURtools/VennerablePlot.png + +----- + +**References** + +- alex.bossers@wur.nl +- Vennerable R package: http://r-forge.r-project.org/projects/vennerable/ + +----- + +.. class:: infomark + +**TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* + + + </help> +</tool>