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comparison flexbar.pl @ 13:346a2b0979ea

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Adjusted tool definition and wrapper to Flexbar 2.31 release.
author jtilman
date Thu, 17 Jan 2013 18:26:14 +0100
parents 4cbf6c6d2f2b
children 952389252467
comparison
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12:4cbf6c6d2f2b 13:346a2b0979ea
1 #!/usr/bin/env perl 1 #!/usr/bin/env perl
2 2
3 # Author: Johannes T. Roehr 3 # Flexbar wrapper for Galaxy tool definition, version 2.31
4 # Author: Johannes Roehr
4 5
5 use warnings; 6 use warnings;
6 use strict; 7 use strict;
7
8 8
9 my ($outFile, $id, $folder, $format) = @ARGV[($#ARGV - 3) .. $#ARGV]; 9 my ($outFile, $id, $folder, $format) = @ARGV[($#ARGV - 3) .. $#ARGV];
10 10
11 my $call = join " ", @ARGV[0..($#ARGV - 4)]; 11 my $call = join " ", @ARGV[0..($#ARGV - 4)];
12 12
13 system $call .' --target reads > '. $outFile and exit 1; 13 system $call .' --target FlexbarTargetFile > '. $outFile and exit 1;
14 14
15 15
16 foreach(<reads*>){ 16 foreach(<FlexbarTargetFile*>){
17 17
18 my $fileType; 18 my $fileType;
19 19
20 $fileType = $1 if /\.(\w+)$/; 20 $fileType = $1 if /\.(\w+)$/;
21 $fileType = $format if /\.\w*fast\w$/; 21 $fileType = $format if /\.\w*fast\w$/;
22 $fileType = 'fasta' if /\.fasta$/;
22 $fileType = 'tabular' if $fileType eq 'lengthdist'; 23 $fileType = 'tabular' if $fileType eq 'lengthdist';
23 24
24 my $file = $_; 25 my $file = $_;
25 26
26 s/_//g; 27 s/_//g;