--- a/average_fst.xml	Mon Jun 03 12:29:29 2013 -0400
+++ b/average_fst.xml	Mon Jul 15 10:47:35 2013 -0400
@@ -2,27 +2,33 @@
   <description>: Estimate the relative fixation index between two populations</description>
 
   <command interpreter="python">
-    average_fst.py "$input" "$p1_input" "$p2_input"
+    #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)
+    average_fst.py '$input' '$p1_input' '$p2_input'
     #if $input_type.choice == '0'
-      "gd_snp" "$input_type.data_source.choice"
+      'gd_snp' '$input_type.data_source.choice'
       #if $input_type.data_source.choice == '0'
-        "$input_type.data_source.min_value"
+        '$input_type.data_source.min_value'
       #else if $input_type.data_source.choice == '1'
-        "1"
+        '1'
       #end if
     #else if $input_type.choice == '1'
-      "gd_genotype" "1" "1"
+      'gd_genotype' '1' '1'
     #end if
-    "$discard_fixed" "$output"
+    '$discard_fixed' '$output'
     #if $use_randomization.choice == '0'
-      "0" "/dev/null"
+      '0' '/dev/null'
     #else if $use_randomization.choice == '1'
-      "$use_randomization.shuffles" "$use_randomization.p0_input"
+      '$use_randomization.shuffles' '$use_randomization.p0_input'
     #end if
-    #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
-        #set $arg = '%s:%s' % ($individual_col, $individual)
-        "$arg"
-    #end for
+    '$ind_arg'
   </command>
 
   <inputs>