# HG changeset patch
# User Richard Burhans <burhans@bx.psu.edu>
# Date 1384983823 18000
# Node ID 884ccb07885bedd74f86a1cab3379caef232d58a
# Parent  51cd0307fb70bf1b49726e65c24f05b14cee73e7
Fixed output_id

diff -r 51cd0307fb70 -r 884ccb07885b make_phylip.py
--- a/make_phylip.py	Wed Nov 20 16:32:01 2013 -0500
+++ b/make_phylip.py	Wed Nov 20 16:43:43 2013 -0500
@@ -402,6 +402,7 @@
     parser.add_argument('--refClmn',metavar='int',type=int,help='the column with the reference nucleotide.',required=True)
     parser.add_argument('--altrClmn',metavar='int',type=int,help='the column with the derived nucleotide.',required=True)
     parser.add_argument('--output',metavar='output',type=str,help='the output',required=True)
+    parser.add_argument('--output_id',metavar='int',type=int,help='the output id',required=True)
     parser.add_argument('--gd_indivs',metavar='input gd_indivs file',type=str,help='the input reference species columns in the input file.',required=True)
     #~ 
     parser.add_argument('--inputCover',metavar='input gd_snp cover file',type=str,help='the input file with the table in gd_snp/gd_genotype cover format.',required=False,default=False)
@@ -431,6 +432,7 @@
     inSNPf = args.input
     inSNPf_type = args.input_type
     outfile = args.output
+    outfile_id = args.output_id
     gd_indivs = args.gd_indivs    
     pxchrx = args.chrClmn
     pxpos = args.posClmn
diff -r 51cd0307fb70 -r 884ccb07885b make_phylip.xml
--- a/make_phylip.xml	Wed Nov 20 16:32:01 2013 -0500
+++ b/make_phylip.xml	Wed Nov 20 16:43:43 2013 -0500
@@ -7,7 +7,7 @@
     #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=$input' '--input_type=$input.ext' '--output=$output1' '--posClmn=$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' '--posClmn=$gen_posClmn' '--refClmn=$gen_refClmn'
     #if $input_type.choice == '0'
       #set $cov_chrClmn = int($input_type.coverage_input.metadata.ref) - $zero_based
       #set $cov_posClmn = int($input_type.coverage_input.metadata.rPos) - $zero_based