--- a/phylogenetic_tree.py	Wed May 22 15:58:18 2013 -0400
+++ b/phylogenetic_tree.py	Tue May 28 16:24:19 2013 -0400
@@ -19,22 +19,102 @@
 
 ################################################################################
 
-if len(sys.argv) < 11:
-    print >> sys.stderr, "Usage"
+#  <command interpreter="python">
+#    phylogenetic_tree.py "$input" "$output" "$output.files_path"
+#
+#    #if $input_type.choice == '0'
+#      "gd_snp"
+#      #if $input_type.data_source.choice == '0'
+#        "sequence_coverage"
+#        "$input_type.data_source.minimum_coverage"
+#        "$input_type.data_source.minimum_quality"
+#      #else if $input_type.data_source.choice == '1'
+#        "estimated_genotype"
+#    #else if $input_type.choice == '1'
+#      "gd_genotype"
+#    #end if
+#
+#    #if $individuals.choice == '0'
+#      "all_individuals"
+#    #else if $individuals.choice == '1'
+#      "$individuals.p1_input"
+#    #end if
+#
+#    #if ((str($input.metadata.scaffold) == str($input.metadata.ref)) and (str($input.metadata.pos) == str($input.metadata.rPos))) or (str($include_reference) == '0')
+#        "none"
+#    #else
+#        "$input.metadata.dbkey"
+#    #end if
+#
+#    #set $draw_tree_options = ''.join(str(x) for x in [$branch_style, $scale_style, $length_style, $layout_style])
+#    #if $draw_tree_options == ''
+#        ""
+#    #else
+#        "-$draw_tree_options"
+#    #end if
+#
+#    #for $individual_name, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
+#        #set $arg = '%s:%s' % ($individual_col, $individual_name)
+#        "$arg"
+#    #end for
+#  </command>
+
+################################################################################
+
+# if len(sys.argv) < 11:
+#     print >> sys.stderr, "Usage"
+#     sys.exit(1)
+#
+# input, p1_input, output, extra_files_path, minimum_coverage, minimum_quality, dbkey, data_source, draw_tree_options = sys.argv[1:10]
+# 
+# individual_metadata = sys.argv[10:]
+# 
+# # note: TEST THIS
+# if dbkey in ['', '?', 'None']:
+#     dbkey = 'none'
+# 
+# p_total = Population()
+# p_total.from_tag_list(individual_metadata)
+
+if len(sys.argv) < 5:
+    print >> sys.stderr, 'Usage'
     sys.exit(1)
 
-input, p1_input, output, extra_files_path, minimum_coverage, minimum_quality, dbkey, data_source, draw_tree_options = sys.argv[1:10]
+input, output, extra_files_path, input_type = sys.argv[1:5]
+args = sys.argv[5:]
+
+data_source = '1'
+minimum_coverage = '0'
+minimum_quality = '0'
 
-individual_metadata = sys.argv[10:]
+if input_type == 'gd_snp':
+    data_source_arg = args.pop(0)
+    if data_source_arg == 'sequence_coverage':
+        data_source = '0'
+        minimum_coverage = args.pop(0)
+        minimum_quality = args.pop(0)
+    elif data_source_arg == 'estimated_genotype':
+        pass
+    else:
+        print >> sys.stderr, 'Unsupported data_source:', data_source_arg
+        sys.exit(1)
+elif input_type == 'gd_genotype':
+    pass
+else:
+    print >> sys.stderr, 'Unsupported input_type:', input_type
+    sys.exit(1)
+
+p1_input, dbkey, draw_tree_options = args[:3]
 
 # note: TEST THIS
 if dbkey in ['', '?', 'None']:
     dbkey = 'none'
 
+individual_metadata = args[3:]
+
 p_total = Population()
 p_total.from_tag_list(individual_metadata)
 
-
 ################################################################################
 
 mkdir_p(extra_files_path)
@@ -88,6 +168,9 @@
     tags = p1.tag_list()
 
 for tag in tags:
+    if input_type == 'gd_genotype':
+        column, name = tag.split(':')
+        tag = '{0}:{1}'.format(int(column) - 2, name)
     args.append(tag)
 
 fh = open(phylip_outfile, 'w')