diff aggregate_gd_indivs.xml @ 27:8997f2ca8c7a

Update to Miller Lab devshed revision bae0d3306d3b

--- a/aggregate_gd_indivs.xml	Mon Jun 03 12:29:29 2013 -0400
+++ b/aggregate_gd_indivs.xml	Mon Jul 15 10:47:35 2013 -0400
@@ -2,16 +2,22 @@
   <description>: Append summary columns for a population</description>
 
   <command interpreter="python">
-    aggregate_gd_indivs.py "$input" "$p1_input" "$output"
+    #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)
+    aggregate_gd_indivs.py '$input' '$p1_input' '$output'
     #if $input_type.choice == '0'
-      "gd_snp"
+      'gd_snp'
     #else if $input_type.choice == '1'
-      "gd_genotype"
+      'gd_genotype'
     #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>