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comparison make_phylip.xml @ 37:884ccb07885b

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Fixed output_id
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 20 Nov 2013 16:43:43 -0500
parents 51cd0307fb70
children
comparison
equal deleted inserted replaced
36:51cd0307fb70 37:884ccb07885b
5 #set $zero_based = 1 5 #set $zero_based = 1
6 #set $gen_chrClmn = int($input.metadata.ref) - $zero_based 6 #set $gen_chrClmn = int($input.metadata.ref) - $zero_based
7 #set $gen_posClmn = int($input.metadata.rPos) - $zero_based 7 #set $gen_posClmn = int($input.metadata.rPos) - $zero_based
8 #set $gen_refClmn = int($input.metadata.pos) - $zero_based + 1 8 #set $gen_refClmn = int($input.metadata.pos) - $zero_based + 1
9 #set $gen_altrClmn = int($input.metadata.pos) - $zero_based + 2 9 #set $gen_altrClmn = int($input.metadata.pos) - $zero_based + 2
10 make_phylip.py '--altrClmn=$gen_altrClmn' '--chrClmn=$gen_chrClmn' '--gd_indivs=$indivs_input' '--input=$input' '--input_type=$input.ext' '--output=$output1' '--posClmn=$gen_posClmn' '--refClmn=$gen_refClmn' 10 make_phylip.py '--altrClmn=$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'
11 #if $input_type.choice == '0' 11 #if $input_type.choice == '0'
12 #set $cov_chrClmn = int($input_type.coverage_input.metadata.ref) - $zero_based 12 #set $cov_chrClmn = int($input_type.coverage_input.metadata.ref) - $zero_based
13 #set $cov_posClmn = int($input_type.coverage_input.metadata.rPos) - $zero_based 13 #set $cov_posClmn = int($input_type.coverage_input.metadata.rPos) - $zero_based
14 #set $cov_refClmn = int($input_type.coverage_input.metadata.pos) - $zero_based + 1 14 #set $cov_refClmn = int($input_type.coverage_input.metadata.pos) - $zero_based + 1
15 #set $cov_altrClmn = int($input_type.coverage_input.metadata.pos) - $zero_based + 2 15 #set $cov_altrClmn = int($input_type.coverage_input.metadata.pos) - $zero_based + 2