diff integratedPlot.xml~ @ 0:46f7f689b929 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/integratedPlot.xml~	Tue Sep 17 11:29:11 2013 -0400
@@ -0,0 +1,95 @@
+<tool id="circosJunctions" name="Integrative Plot" version="1.56">
+	<description> Create a Circos plot with Complete Genomics and/or SNParray data </description>
+
+
+	<requirements>
+		<requirement type="set_environment">CIRCOS_SCRIPT_PATH</requirement>
+		<requirement type="package" version="0.64">circos</requirement>	    
+	</requirements>
+	
+
+	<command interpreter="bash">
+	galaxy_runCircos.sh 
+		$junctions 
+		$probes 
+		$snps 
+		$variants 
+		#if $imageformat == "png"
+			$wg_out 
+			$montage_out 			
+		#else
+			$wg_out2 
+			$montage_out2			
+		#end if
+		$chromosomes_out 
+		$reference
+		$custom_out
+		"$custom.region"		
+		$genetrack
+		$imageformat
+		\$CIRCOS_SCRIPT_PATH/scripts
+		\$CIRCOS_SCRIPT_PATH/config
+	</command>
+	
+	<inputs>
+
+		<param name="reference" type="select" label="Reference">
+				<option value="hg18" selected="true"> HG18 (build 36) </option>
+				<option value="hg19"> HG19 (build 37) </option>		
+		</param>
+		<param name="junctions" type="data" 	optional="true" 	format="tabular" label="CG Junctions file"/>
+		<param name="variants"  type="data" 	optional="true" 	format="tabular" label="Variants list (e.g. output from CG listvariants)"/>	
+		
+		<param name="snps" 		type="data" 	optional="true" 	format="tabular" label="Illumina (Nexus) snps.txt file"/>	
+		<param name="probes"  	type="data" 	optional="true" 	format="tabular" label="Illumina (Nexus) probes.txt file"/>	
+				
+		<param name="wg"  		type="boolean" 	truevalue="Y" 	falsevalue="N" 	checked="true" 	label="Generate Whole-Genome plot?"/>
+		<param name="chrplots" 	type="boolean" 	truevalue="Y" 	falsevalue="N" 	checked="false" label="Also generate per-chromosome plots?"/>
+		<param name="montage"  	type="boolean" 	truevalue="Y" 	falsevalue="N" 	checked="false" label="Also generate montage of per-chromosome plots?"/>
+		<param name="genetrack" type="boolean" 	truevalue="yes" falsevalue="no" checked="false" label="Add ImpactedGenes track (only for the per-chromosome or custom plots)" help="Shows which genes are impacted by the SV events (junctions)"/>
+	
+		<conditional name="custom">
+   			<param name="plot" type="select" label="Create a plot of a custom region?">
+				<option value="N" selected="true"> No </option>
+				<option value="Y"> Yes </option>		
+			</param>			      			
+   			<when value="N">
+      			<param name="region" type="hidden" value="None" />
+   			</when>
+   			<when value="Y">
+     			<param name="region" type="text" value="None" label="Region" help="For example: 'chr5;chr6;chrX' or 'chr12:12345-34567' or 'chr5:0-100,200-333;chrX:34567-78347'">
+				<sanitizer sanitize="False"/>
+				</param>
+   			</when>
+		</conditional>		
+		
+		<param name="imageformat" type="select" label="Image Format">
+				<option value="png" selected="true"> PNG </option>
+				<option value="svg"> SVG </option>		
+		</param>
+		
+		<param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>	
+		
+	</inputs>
+
+  <outputs>
+   	<data format="png" name="wg_out" 		label="Whole genome plot on ${on_string}">					<filter> imageformat == "png" </filter> <filter> wg </filter> </data>	
+    <data format="png" name="montage_out" 	label="Chromosomes_montage on ${on_string}">				<filter> imageformat == "png" </filter> <filter> montage </filter> </data>
+	<data format="png" name="custom_out"   	label="Plot of region ${custom.region} on ${on_string} "> 	<filter> imageformat == "png" </filter> <filter> custom['plot'] == "Y" </filter> </data>	
+	
+	<data format="svg" name="wg_out2" 		label="Whole genome plot on ${on_string}">					<filter> imageformat == "svg" </filter>	<filter> wg </filter> </data>	
+    <data format="svg" name="montage_out2" 	label="Chromosomes_montage on ${on_string}">				<filter> imageformat == "svg" </filter> <filter> montage </filter> </data>
+	<data format="svg" name="custom_out2"  	label="Plot of region ${custom.region} on ${on_string} "> 	<filter> imageformat == "svg" </filter>	<filter> custom['plot'] == "Y" </filter> </data>
+	
+	
+	<data format="gzip" name="chromosomes_out" label="Chromosome plots on ${on_string}"> <filter> chrplots </filter> </data>
+  </outputs>
+
+	<help> 
+
+
+	</help>
+
+</tool>
+
+