diff cummerbund_wrapper.xml @ 1:6a9bc26ab8d9

Added cuffdata and cuffdatadb datatypes, cuffdiff multiselect outputs

--- a/cummerbund_wrapper.xml	Mon Oct 01 14:08:13 2012 -0400
+++ b/cummerbund_wrapper.xml	Mon Oct 08 15:26:47 2012 -0500
@@ -29,7 +29,7 @@
                 <param name="rebuild" type="hidden" value="TRUE"/>
             </when>
             <when value="history">
-                <param name="input_database" type="data" format="data" label="Select backend database (sqlite)"/>
+                <param name="input_database" type="data" format="cuffdatadb" label="Select backend database (sqlite)"/>
             </when>
         </conditional>
         <repeat name="plots" title="Plots">
@@ -38,6 +38,9 @@
 			<conditional name="plot">
 				<param name="type" type="select" label="Plot type">
 					<option value="density" selected="true">Density</option>
+					<option value="dispersion">Dispersion</option>
+					<option value="fpkmSCV">Squared Coefficient of Variation</option>
+					<option value="scatterMatrix">Scatter Matrix</option>
 					<option value="boxplot">Boxplot</option>
 					<option value="scatter">Scatter</option>
 					<option value="volcano">Volcano</option>
@@ -48,6 +51,13 @@
 				</param>
 				<when value="density">
 					<param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
+					<param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Replicates?"/>
+				</when>
+				<when value="dispersion">
+				</when>
+				<when value="fpkmSCV">
+				</when>
+				<when value="scatterMatrix">
 				</when>
 				<when value="boxplot">
 					<param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
@@ -220,7 +230,22 @@
 
     ## Density plot ##
 	#if $p.plot['type'] == "density":
-csDensity(genes(cuff))
+csDensity(genes(cuff),replicates=$p.plot.replicates)
+devname = dev.off()
+
+    ## Dispersion plot ##
+	#elif $p.plot['type'] == "dispersion":
+dispersionPlot(genes(cuff))
+devname = dev.off()
+
+    ## Squared Coefficient of Variation plot ##
+	#elif $p.plot['type'] == "fpkmSCV":
+fpkmSCVPlot(genes(cuff))
+devname = dev.off()
+
+    ## Scatter Matrix ##
+	#elif $p.plot['type'] == "scatterMatrix":
+csScatterMatrix(genes(cuff))
 devname = dev.off()
 
     ## Boxplot ##