--- a/make_phylip.xml	Mon Sep 23 13:37:19 2013 -0400
+++ b/make_phylip.xml	Wed Nov 20 13:46:10 2013 -0500
@@ -1,19 +1,19 @@
-<tool id="gd_make_phylip" name="Phylip" version="1.0.0" force_history_refresh="True">
+<tool id="gd_make_phylip" name="Phylip" version="1.1.0" force_history_refresh="True">
   <description>: prepare data for phylogenetic analysis</description>
 
   <command interpreter="python">
     #set $zero_based = 1
-    #set $gen_chrClmn = int($input.metadata.scaffold) - $zero_based
-    #set $gen_posClmn = int($input.metadata.pos) - $zero_based
+    #set $gen_chrClmn = int($input.metadata.ref) - $zero_based
+    #set $gen_posClmn = int($input.metadata.rPos) - $zero_based
     #set $gen_refClmn = int($input.metadata.pos) - $zero_based + 1
     #set $gen_altrClmn = int($input.metadata.pos) - $zero_based + 2
-    make_phylip.py '--altrClmn=$gen_altrClmn' '--chrClmn=$gen_chrClmn' '--gd_indivs=$indivs_input' '--input=$input' '--output=$output1' '--output_id=$output1.id' '--output_dir=$__new_file_path__' '--posClmn=$gen_posClmn' '--refClmn=$gen_refClmn'
+    make_phylip.py '--altrClmn=$gen_altrClmn' '--chrClmn=$gen_chrClmn' '--gd_indivs=$indivs_input' '--input=$input' '--input_type=$input.ext' '--output=$output1' '--output_id=$output1.id' '--output_dir=$__new_file_path__' '--posClmn=$gen_posClmn' '--refClmn=$gen_refClmn'
     #if $input_type.choice == '0'
-      #set $cov_chrClmn = int($input_type.coverage_input.metadata.scaffold) - $zero_based
-      #set $cov_posClmn = int($input_type.coverage_input.metadata.pos) - $zero_based
+      #set $cov_chrClmn = int($input_type.coverage_input.metadata.ref) - $zero_based
+      #set $cov_posClmn = int($input_type.coverage_input.metadata.rPos) - $zero_based
       #set $cov_refClmn = int($input_type.coverage_input.metadata.pos) - $zero_based + 1
       #set $cov_altrClmn = int($input_type.coverage_input.metadata.pos) - $zero_based + 2
-      '--altrClmnCvrg=$cov_altrClmn' '--chrClmnCvrg=$cov_chrClmn' '--cvrgTreshold=$input_type.coverage_threshold' '--gd_indivs_cover=$indivs_input' '--indvlsPrctTrshld=$input_type.indivs_threshold' '--inputCover=$input_type.coverage_input' '--posClmnCvrg=$cov_posClmn' '--refClmnCvrg=$cov_refClmn'
+      '--altrClmnCvrg=$cov_altrClmn' '--chrClmnCvrg=$cov_chrClmn' '--cvrgTreshold=$input_type.coverage_threshold' '--gd_indivs_cover=$indivs_input' '--indvlsPrctTrshld=$input_type.indivs_threshold' '--inputCover=$input_type.coverage_input' '--inputCover_type=$input_type.coverage_input.ext' '--posClmnCvrg=$cov_posClmn' '--refClmnCvrg=$cov_refClmn'
     #else if $input_type.choice == '1'
       #set $fchrClmn = int($input_type.annotation_input.metadata.chromCol) - $zero_based
       #set $strandClmn = int($input_type.annotation_input.metadata.strandCol) - $zero_based
@@ -28,6 +28,8 @@
     #end if
   </command>
 
+  <code file="make_phylip_hooks.py" />
+
   <inputs>
     <param name="input" type="data" format="gd_genotype,gd_snp" label="Genotype/SNP dataset">
       <validator type="metadata" check="scaffold" message="scaffold missing" />