--- a/coverage_distributions.xml	Mon Jun 03 12:29:29 2013 -0400
+++ b/coverage_distributions.xml	Mon Jul 15 10:47:35 2013 -0400
@@ -2,22 +2,27 @@
   <description>: Examine sequence coverage for SNPs</description>
 
   <command interpreter="python">
-    coverage_distributions.py "$input" "0" "$output" "$output.files_path"
+    #import json
+    #import base64
+    #import zlib
+    #set $ind_names = $input.dataset.metadata.individual_names
+    #set $ind_colms = $input.dataset.metadata.individual_columns
+    #set $ind_dict = dict(zip($ind_names, $ind_colms))
+    #set $ind_json = json.dumps($ind_dict, separators=(',',':'))
+    #set $ind_comp = zlib.compress($ind_json, 9)
+    #set $ind_arg = base64.b64encode($ind_comp)
+    coverage_distributions.py '$input' '0' '$output' '$output.files_path' '$ind_arg'
     #if $individuals.choice == '0'
-      "all_individuals"
+      'all_individuals'
     #else if $individuals.choice == '1'
       #set $arg = 'individuals:%s' % str($individuals.p1_input)
-        "$arg"
+        '$arg'
     #else if $individuals.choice == '2'
       #for $population in $individuals.populations
         #set $arg = 'population:%s:%s' % (str($population.p_input), str($population.p_input.name))
-        "$arg"
+        '$arg'
       #end for
     #end if
-    #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
-      #set $individual_arg = 'individual:%s:%s' % ($individual_col, $individual)
-      "$individual_arg"
-    #end for
   </command>
 
   <inputs>