diff bamFingerprint.xml @ 28:1e5fcb1555de draft

Uploaded

--- a/bamFingerprint.xml	Sat Dec 14 16:13:11 2013 -0500
+++ b/bamFingerprint.xml	Mon Dec 16 04:51:41 2013 -0500
@@ -26,12 +26,16 @@
       #set newoutFileName=str($outFileName)+".png"
       --plotFile $newoutFileName
 
-      #if $outputOpt.showOutputOpt == "yes"
-          #if $outputOpt.saveRawCounts:
+      #if $output.showOutputSettings == "yes"
+          --plotFileFormat $output.outFileFormat
+          #if $output.saveRawCounts:
             --outRawCounts '$outFileRawCounts' 
           #end if
+      #else
+        --plotFileFormat 'png'
       #end if
 
+
       #if $advancedOpt.showAdvancedOpt == "yes":
         
         #if str($advancedOpt.region.value) != '':
@@ -95,22 +99,28 @@
             </when>
         </conditional>
 
-        <conditional name="outputOpt">
-            <param name="showOutputOpt" type="select" label="Show additional output options" >
+        <conditional name="output">
+            <param name="showOutputSettings" type="select" label="Show advanced output settings">
                 <option value="no" selected="true">no</option>
                 <option value="yes">yes</option>
             </param>
             <when value="no" />
             <when value="yes">
+                <expand macro="input_image_file_format" />
                 <param name="saveRawCounts" type="boolean" label="Save the bin counts"/>
             </when>
         </conditional>
 
     </inputs>
     <outputs>
-        <data format="png" name="outFileName" />
+        <expand macro="output_image_file_format" />
         <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
-            <filter>(outputOpt['showOutputOpt'] == 'yes' and outputOpt['saveRawCounts'] == True)</filter>
+            <filter>
+            ((
+                outputOpt['showOutputOpt'] == 'yes' and 
+                outputOpt['saveRawCounts'] is True
+            ))
+            </filter>
         </data>
     </outputs>
     <help>