diff vennerable/Vennerable.xml @ 0:77bbf955e8de default tip

initial commit

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vennerable/Vennerable.xml	Thu Nov 06 15:07:54 2014 +0100
@@ -0,0 +1,135 @@
+<tool id="Vennerable" name="Vennerable" version="1.2c" >
+	<description>: Plot data in Venn or Edwards/Venn-like diagrams</description>
+	<command>
+		R --slave --vanilla --file=\$VENNERABLE_SCRIPT_PATH/vennerable/Vennerable.R 
+		--args $inputFile
+		#if $opt.userSpecified == "Yes" 
+			default
+		#else
+			"$opt.xNames"
+		#end if
+		$weighting
+		#if $imagetype.value == "svg"
+			$outputFile_svg
+			$plottype
+			$resolution
+			svg
+		#else if $imagetype.value == "png"
+			$outputFile_png
+			$plottype
+			$resolution
+			png
+		#else
+			$outputFile_pdf
+			$plottype
+			$resolution
+			pdf
+		#end if
+		2&gt;$Vennerable_log
+		1&gt;&gt;$Vennerable_log
+	</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 up to 5 datasets)</option>
+			<option value="ChowRuskey">Chow-Ruskey (always weigthed max 9 sets common intersect not 0)</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>
+            <option value="battle">Edwards-Venn Squares battle (max 9 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 (PNG only). Lower (50) is larger text.&lt;br /&gt;&lt;i&gt;Default is vector graphics format SVG!&lt;/i&gt;" />
+        <param name="imagetype" type="select" label="Image output format" help="Scalable Vector Graphics (SVG) format is best for post processing" >
+            <option value="pdf" selected="True">PDF</option>
+            <option value="svg">SVG</option>
+            <option value="png">PNG</option>
+        </param>
+	</inputs>
+	<outputs>
+		<data name="outputFile_svg" format="svg" label="Venn diagram svg of ${inputFile.name}">
+			<filter>imagetype=="svg"</filter>
+		</data>
+		<data name="outputFile_png" format="png" label="Venn diagram png of ${inputFile.name}">
+			<filter>imagetype=="png"</filter>
+		</data>
+		<data name="outputFile_pdf" format="pdf" label="Venn diagram pdf of ${inputFile.name}">
+			<filter>imagetype=="pdf"</filter>
+		</data>
+		<data name="Vennerable_log" format="tabular" label="Vennerable output and error log file" />
+	</outputs>
+	<tests>
+		<test>
+		</test>
+	</tests>
+	<requirements>
+ 		<requirement type="package" version="3.0.3">R</requirement>
+		<requirement type="package" version="1.0">vennerable_r_packages</requirement>
+		<requirement type="set_environment">VENNERABLE_SCRIPT_PATH</requirement>
+	</requirements>
+	<help>
+| 
+
+
+**What it does**
+
+Vennerable V3.0 (07-10-2014)
+
+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 from 2 to 9 collumns (in battle mode) of data but more are adviced not to be used (for speed and clarity).
+
+Since version Vennerable version 3 it supports up to 9 datasets in battle mode. Wrapper version 1.2 and up support output in svg, pdf and png.
+
+-----
+
+**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**
+
+- [e-mail]
+- Vennerable R package: http://r-forge.r-project.org/projects/vennerable/ 
+
+-----
+
+.. class:: infomark
+
+**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
+
+
+  </help>
+</tool>