# HG changeset patch
# User mmonsoor
# Date 1442309179 14400
# Node ID 729991209550371e4526b8d08ca5d1352dcfc18b
# Parent  947793995ea248673a58e374f6d0cc8794303d46
Uploaded

diff -r 947793995ea2 -r 729991209550 abims_CAMERA_annotateDiffreport.xml
--- a/abims_CAMERA_annotateDiffreport.xml	Wed Sep 02 11:32:26 2015 -0400
+++ b/abims_CAMERA_annotateDiffreport.xml	Tue Sep 15 05:26:19 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.0.1">
+<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.0">
 
     <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description>
     
@@ -14,7 +14,7 @@
         <exit_code range="1:" level="fatal" />
     </stdio>
 
-    <command>
+    <command interpreter="Rscript">
         CAMERA.r 
         xfunction annotatediff image $image
         convert_param $convert_param num_digits $num_digits nSlaves \${GALAXY_SLOTS:-1}
@@ -137,16 +137,17 @@
     </inputs>
 
     <outputs>
-        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" >
-            <discover_datasets pattern="__designation_and_ext__" directory="zip" visible="true" />
-        </data>
+        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" />
         <data name="datamatrix" format="tabular" label="${image.name[:-6]}.annotate.dataMatrix.tsv" />
         <data name="rdata" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.polarity}.Rdata" >
             <change_format>
                 <when input="quick_block.polarity" value="positive" format="rdata.camera.positive" />
                 <when input="quick_block.polarity" value="negative" format="rdata.camera.negative" />
             </change_format>
-        </data>    
+        </data>
+	<data name="output_zip" format="zip" from_work_dir="Xdiffreport.zip" label="${image.name[:-6]}.annotateDiffreport.zip" >
+		 <filter>(options['option'] == 'show')</filter>
+	</data>    
     </outputs>
     
     <tests>