diff prepare_population_structure.xml @ 27:8997f2ca8c7a

Update to Miller Lab devshed revision bae0d3306d3b

--- a/prepare_population_structure.xml	Mon Jun 03 12:29:29 2013 -0400
+++ b/prepare_population_structure.xml	Mon Jul 15 10:47:35 2013 -0400
@@ -1,26 +1,31 @@
-<tool id="gd_prepare_population_structure" name="Prepare Input" version="1.1.0">
+<tool id="gd_prepare_population_structure" name="Prepare Input" version="1.2.0">
   <description>: Filter and convert to the format needed for these tools</description>
 
   <command interpreter="python">
-    prepare_population_structure.py "$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)
+    prepare_population_structure.py '$input'
     #if $input_type.choice == '0'
-      "gd_snp" "$input_type.min_reads" "$input_type.min_qual"
+      'gd_snp' '$input_type.min_reads' '$input_type.min_qual'
     #else if $input_type.choice == '1'
-      "gd_genotype" "0" "0"
+      'gd_genotype' '0' '0'
     #end if
-    "$min_spacing" "$output" "$output.files_path"
+    '0' '$output' '$output.files_path' '$ind_arg'
     #if $individuals.choice == '0'
-        "all_individuals"
+        'all_individuals'
     #else if $individuals.choice == '1'
         #for $population in $individuals.populations
           #set $pop_arg = 'population:%s:%s' % (str($population.p_input), str($population.p_input.name))
-          "$pop_arg"
+          '$pop_arg'
         #end for
     #end if
-    #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
-        #set $arg = 'individual:%s:%s' % ($individual_col, $individual)
-        "$arg"
-    #end for
   </command>
 
   <inputs>
@@ -52,7 +57,10 @@
       </when>
     </conditional>
 
+    <!--
     <param name="min_spacing" type="integer" min="0" value="0" label="Minimum spacing between SNPs" />
+    "$min_spacing" "$output" "$output.files_path"
+    -->
   </inputs>
 
   <outputs>