Mercurial > repos > miller-lab > genome_diversity

comparison make_phylip.xml @ 36:51cd0307fb70

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Phylip's extra ouputs are now stored in the job working directory
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 20 Nov 2013 16:32:01 -0500
parents ea52b23f1141
children 884ccb07885b
comparison
equal deleted inserted replaced
35:ea52b23f1141 36:51cd0307fb70
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=$output1' '--output_id=$output1.id' '--output_dir=$__new_file_path__' '--posClmn=$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=$output1' '--posClmn=$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