changeset 16:16310f8b24d5 draft

Uploaded

--- a/bamCorrelate.xml	Mon Dec 16 14:08:15 2013 -0500
+++ b/bamCorrelate.xml	Mon Dec 16 15:13:08 2013 -0500
@@ -24,7 +24,7 @@
 
         --plotFile $outFileName
 
-        #if $outputOpt.showOutputOpt == "yes"
+        #if $output.showOutputSettings == "yes"
             --outRawCounts '$outFileRawCounts' 
             --outFileCorMatrix '$outFileCorMatrix'
             --plotFileFormat $output.outFileFormat
@@ -100,8 +100,8 @@
 
         </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>
@@ -117,10 +117,20 @@
     <outputs>
         <expand macro="output_image_file_format" />
         <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
-            <filter>(outputOpt['showOutputOpt'] == 'yes' and outputOpt['saveRawCounts'] == True)</filter>
+            <filter>
+            ((
+                output['showOutputSettings'] == 'yes' and 
+                output['saveRawCounts'] is True
+            ))
+            </filter>
         </data>
         <data format="tabular" name="outFileCorMatrix" label="${tool.name} on ${on_string}: correlation matrix">
-            <filter>(outputOpt['showOutputOpt'] == 'yes' and outputOpt['saveCorMatrix'] == True)</filter>
+            <filter>
+            ((
+                output['showOutputSettings'] == 'yes' and 
+                output['saveCorMatrix'] is True
+            ))
+            </filter>
         </data>
     </outputs>
     <help>

--- a/bamFingerprint.xml	Mon Dec 16 14:08:15 2013 -0500
+++ b/bamFingerprint.xml	Mon Dec 16 15:13:08 2013 -0500
@@ -6,12 +6,6 @@
         <import>deepTools_macros.xml</import>
     </macros>
     <command>
-        #import tempfile
-        #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
-
-        #set files=[]
-        #set labels=[]
-
         @multiple_input_bams@
 
     bamFingerprint
@@ -35,7 +29,6 @@
         --plotFileFormat 'png'
       #end if
 
-
       #if $advancedOpt.showAdvancedOpt == "yes":
         
         #if str($advancedOpt.region.value) != '':
@@ -117,8 +110,8 @@
         <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
             <filter>
             ((
-                outputOpt['showOutputOpt'] == 'yes' and 
-                outputOpt['saveRawCounts'] is True
+                output['showOutputSettings'] == 'yes' and 
+                output['saveRawCounts'] is True
             ))
             </filter>
         </data>

--- a/computeGCBias.xml	Mon Dec 16 14:08:15 2013 -0500
+++ b/computeGCBias.xml	Mon Dec 16 15:13:08 2013 -0500
@@ -83,8 +83,8 @@
             </when>
         </conditional>
         <param name="image_format" type="select" label="GC bias plot" help="If given, a diagnostic image summarizing the GC bias found on the sample will be created.">
-            <option value="none" selected="true">No image</option>
-            <option value="png">Image in png format</option>
+            <option value="none">No image</option>
+            <option value="png" selected="true">Image in png format</option>
             <option value="pdf">Image in pdf format</option>
             <option value="svg">Image in svg format</option>
             <option value="eps">Image in eps format</option>