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comparison srst2.pl @ 1:599a4dc309aa draft

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planemo upload commit 1ea98fb88a93a571beda5bbd56449c946860a258
author nml
date Wed, 01 Mar 2017 12:39:11 -0500
parents 6f870ed59b6e
children
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0:6f870ed59b6e 1:599a4dc309aa
4 use strict; 4 use strict;
5 use warnings; 5 use warnings;
6 use Cwd; 6 use Cwd;
7 use File::Copy; 7 use File::Copy;
8 8
9 #The first 4 arguments should be in this format: 9 #The first 3 arguments should be in this format:
10 # /path/to/srst2.py bam_output scores_output pileup_output ... 10 # bam_output scores_output pileup_output ...
11 11
12 my $binary = $ARGV[0];
13 shift;
14 12
15 my ($bam_results, $scores, $pileup, $job_type, $txt_results, $genes_results, $fullgenes_results, $name, $databases); 13 my ($bam_results, $scores, $pileup, $job_type, $txt_results, $genes_results, $fullgenes_results, $name, $databases);
16 my ($allele_results,$allele_type); 14 my ($allele_results,$allele_type);
17 15
18 16
152 } 150 }
153 } 151 }
154 152
155 153
156 154
157 my $command = "python $binary @ARGV"; 155 my $command = "srst2 @ARGV";
158 156
159 my $exit_code = system($command); 157 my $exit_code = system($command);
160 158
161 my $cur_dir = getcwd(); 159 my $cur_dir = getcwd();
162 # make arrays for using multiple custom databases (creates multiple output files - need to be concatenated) 160 # make arrays for using multiple custom databases (creates multiple output files - need to be concatenated)