Mercurial > repos > yufei-luo > s_mart

diff smart_toolShed/SMART/galaxy/plotRepartition.xml @ 0:e0f8dcca02ed

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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
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/galaxy/plotRepartition.xml	Thu Jan 17 10:52:14 2013 -0500
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+<tool id="plotRepartition" name="plot repartition">
+	<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>
+	<command interpreter="python">
+		../Java/Python/WrappPlotRepartition.py -i $inputFileName
+		-n $names
+		$normalize
+		#if $optionColor.Color == 'Yes':
+			-c $optionColor.colValue
+		#end if		
+		-f $format
+		
+		#if $optionLog.log == 'Yes':
+			-l $optionLog.logVal
+		#end if	
+		
+		-o $outputFilePNG
+	</command>
+
+	<inputs>
+		<param name="inputFileName" type="data" label="Input Gff3 File" format="gff3"/>
+		<param name="names" type="text" value="None" label="name for the tags (separated by commas and no space) [compulsory option]"/>
+		<param name="normalize" type="boolean" truevalue="-r" falsevalue="" checked="false" label="normalize data (when panels are different)"/>
+		<param name="format" type="text" value="png" label="format of the output file[default: png]"/>
+		
+		<conditional name="optionColor">
+			<param name="Color" type="select" label="scolor of the lines (separated by commas and no space) ">
+					<option value="Yes">Yes</option>
+					<option value="No" selected="true">No</option>
+			</param>
+			<when value="Yes">
+				<param name="colValue" type="text" value="None"/>
+			</when>
+			<when value="No">
+			</when>
+		</conditional>
+		
+		<conditional name="optionLog">
+			<param name="log" type="select" label="use log on x- or y-axis (write 'x', 'y' or 'xy')">
+					<option value="Yes">Yes</option>
+					<option value="No" selected="true">No</option>
+			</param>
+			<when value="Yes">
+				<param name="logVal" type="text" value=" "/>
+			</when>
+			<when value="No">
+			</when>
+		</conditional>	
+		
+	</inputs>
+
+	<outputs>
+		<data name="outputFilePNG" format="tar" label="[plotRepartition]out file"/>
+	</outputs> 
+	
+	<help>
+        This script gives a .tar out file, if you want to take look at the results, you have to download it.
+    </help>	
+	
+</tool>