--- a/cwpair2.xml	Sat Jan 21 14:40:25 2017 -0500
+++ b/cwpair2.xml	Mon Nov 06 23:19:50 2017 -0500
@@ -5,32 +5,30 @@
         <import>cwpair2_macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <command detect_errors="aggressive">
-        <![CDATA[
-            python $__tool_directory__/cwpair2.py
-            #for $i in $input:
-                 --input "${i}" "${i.hid}"
-            #end for
-            --up_distance $up_distance
-            --down_distance $down_distance
-            --method $method
-            --binsize $binsize
-            --threshold_format $threshold_format_cond.threshold_format
-            #if str($threshold_format_cond.threshold_format) == "absolute_threshold":
-                --absolute_threshold $threshold_format_cond.absolute_threshold
-            #elif str($threshold_format_cond.threshold_format) == "relative_threshold":
-                --relative_threshold $threshold_format_cond.relative_threshold
-            #end if
-            --output_files $output_files
-            --statistics_output "$statistics_output"
-        ]]>
-    </command>
+    <command detect_errors="aggressive"><![CDATA[
+python '$__tool_directory__/cwpair2.py'
+#for $i in $input:
+    --input '${i}' '${i.hid}'
+#end for
+--up_distance $up_distance
+--down_distance $down_distance
+--method $method
+--binsize $binsize
+--threshold_format $threshold_format_cond.threshold_format
+#if str($threshold_format_cond.threshold_format) == "absolute_threshold":
+    --absolute_threshold $threshold_format_cond.absolute_threshold
+#elif str($threshold_format_cond.threshold_format) == "relative_threshold":
+    --relative_threshold $threshold_format_cond.relative_threshold
+#end if
+--output_files $output_files
+--statistics_output '$statistics_output'
+    ]]></command>
     <inputs>
-        <param  name="input" type="data" format="gff" multiple="True" label="Find matched pairs on" />
+        <param  name="input" type="data" format="gff" multiple="true" label="Find matched pairs on" />
         <param name="up_distance" type="integer" value="50" min="0" label="Distance upstream from a peak to allow a pair" help="The maximum distance upstream or 5’ to the primary peak"/>
         <param name="down_distance" type="integer" value="100" min="0" label="Distance downstream from a peak to allow a pair" help="The maximum distance downstream or 3’ to the primary peak"/>
         <param name="method" type="select" label="Method of finding a match">
-            <option value="mode" selected="True">Mode</option>
+            <option value="mode" selected="true">Mode</option>
             <option value="closest">Closest</option>
             <option value="largest">Largest</option>
             <option value="all">All</option>
@@ -179,7 +177,6 @@
  * **closest/largest/mode P** - pdf file that provides the preview plots graph (the initial iteration of the process for finding the mode).
  * **closest/largest/mode F** - pdf file that provides the final plots graph.
  * **Statistics Table** - provides the number of peaks in pairs (dividing this by 2 provides the number of peak-pairs).
-
     </help>
     <expand macro="citations" />
 </tool>