diff cummerbund_wrapper.xml @ 2:fdf01b3c1841

Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output

--- a/cummerbund_wrapper.xml	Mon Feb 04 21:23:20 2013 -0600
+++ b/cummerbund_wrapper.xml	Fri Nov 08 14:54:01 2013 -0600
@@ -1,5 +1,4 @@
-<tool id="cummerbund" name="cummeRbund" version="0.0.6">
-    
+<tool id="cummerbund" name="cummeRbund" version="0.0.7">
     <description>R package designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output</description>
     
     <command interpreter="python">
@@ -64,8 +63,12 @@
 					<param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/>
 				</when>
 				<when value="maplot">
-					<param name="x" type="text" label="Sample name 1"/>
-					<param name="y" type="text" label="Sample name 2"/>
+					<param name="x" type="text" label="Sample name 1" help="Condition1 name used in cuffdiff">
+                                        <validator type="empty_field" message="A Condition name from the cuffdiff run is required"/>
+                                        </param>
+					<param name="y" type="text" label="Sample name 2" help="Condition2 name used in cuffdiff">
+                                        <validator type="empty_field" message="A Condition name from the cuffdiff run is required"/>
+                                        </param>
 					<param name="use_count" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Use Count?"/>
 				</when>
 				<when value="dendrogram">
@@ -185,7 +188,7 @@
         <exit_code range="1:"  level="fatal"   description="CummerBund Error" />
     </stdio>
     <outputs>
-        <data format="data" name="output_database" label="${tool.name} on ${on_string}: Database File (sqlite)">
+        <data format="cuffdatadb" name="output_database" label="${tool.name} on ${on_string}: Database File (sqlite)">
             <filter>backend_database_source['backend_database_selector'] == "cuffdiff_output"</filter>
         </data>
     	<data format="html" name="output_html" label="${tool.name} on ${on_string} (HTML)"/>
@@ -244,6 +247,18 @@
                          rebuild = F)
 #end if
 
+## Print out info
+print(cuff)
+sink("cuffdb_info.txt")
+print(cuff)
+print("SAMPLES:")
+samples(cuff)
+print("REPLICATES:")
+replicates(cuff)
+print("FEATURES:")
+print(annotation(genes(cuff)))
+sink()
+
 #for $i, $p in enumerate($plots, start=1):
 	#set $filename = "plot%02d-%s.png" % ($i, $p.plot['type'])
 png(filename = "${filename}", width = ${p.width}, height = ${p.height})