Mercurial > repos > jvolkening > b2b_fq_deinterleave

annotate frag_lens @ 1:3cab918bc851 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit f66b297dfee0d16df8f185c075fe349b8c6b3203
author jvolkening
date Fri, 08 Mar 2024 01:49:12 +0000
parents b42eb9ff6a8c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
1 #!/usr/bin/env perl
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
2
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
3 use strict;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
4 use warnings;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
5 use 5.012;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
6
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
7 use Cwd qw/abs_path/;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
8 use File::Temp qw/tempdir tempfile/;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
9 use IPC::Cmd qw/can_run/;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
10 use List::Util qw/sum/;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
11 use Getopt::Long;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
12 use Pod::Usage;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
13
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
14 my @good_codes = ( 0x0002, 0x0040 );
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
15 my @bad_codes = ( 0x0004, 0x0100, 0x0800 );
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
16
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
17 #-inputs---------------------------------------------------------------------#
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
18 my $fasta;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
19 my $forward;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
20 my $reverse;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
21 my $sam;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
22 #-knobs----------------------------------------------------------------------#
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
23 my $threads = 1;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
24 my $max_align = 10000;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
25
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
26 my $PROGRAM = 'frag_lens';
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
27 my $VERSION = 0.001;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
28
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
29 GetOptions(
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
30 #-inputs-----------------------------------------------------------------#
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
31 'sam=s' => \$sam,
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
32 'forward=s' => \$forward,
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
33 'reverse=s' => \$reverse,
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
34 'ref=s' => \$fasta,
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
35 #-knobs------------------------------------------------------------------#
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
36 'threads=i' => \$threads,
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
37 'max_aln=i' => \$max_align,
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
38 'help' => sub{ pod2usage(-verbose => 2); },
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
39 'version' => sub{ say "This is $PROGRAM v$VERSION";exit; },
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
40
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
41 ) or pod2usage( -verbose => 1);
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
42
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
43 my $fh_sam;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
44 my $tmp_fasta;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
45
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
46 if (defined $sam) {
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
47 open $fh_sam, '<', $sam or die "failed to open SAM\n";
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
48 }
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
49
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
50 else {
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
51
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
52 my $BWA = can_run('bwa')
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
53 // die "BWA is required but not found\n";
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
54
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
55 my ($tmp_dir) = tempdir( CLEANUP => 1);
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
56
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
57 die "specify forward and reverse read files and reference\n"
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
58 if (! defined $forward || ! defined $reverse || ! defined $fasta);
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
59
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
60 $fasta = abs_path($fasta);
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
61
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
62 my $res = system(
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
63 'ln',
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
64 '-s',
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
65 $fasta,
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
66 "$tmp_dir/tmp.fasta"
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
67 );
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
68 die "link failed" if ($res);
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
69 $res = system(
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
70 $BWA,
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
71 'index',
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
72 "$tmp_dir/tmp.fasta"
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
73 );
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
74 die "index failed" if ($res);
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
75 open $fh_sam, '-|', $BWA,
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
76 'mem',
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
77 '-t' => $threads,
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
78 '-v' => 1,
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
79 "$tmp_dir/tmp.fasta",
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
80 $forward,
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
81 $reverse
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
82 ;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
83 }
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
84
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
85 my $c = 0;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
86 while (my $line = <$fh_sam>) {
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
87 next if ($line =~ /^\@/);
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
88 chomp $line;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
89 my @parts = split "\t", $line;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
90 my $flags = $parts[1];
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
91 my $sum1 = sum map {$_ & $flags ? 1 : 0} @good_codes;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
92 my $sum2 = sum map {$_ & $flags ? 1 : 0} @bad_codes;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
93 if ($sum1 == scalar @good_codes && $sum2 == 0) {
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
94 say abs($parts[8]);
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
95 last if (++$c >= $max_align);
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
96 }
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
97 }
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
98 close $fh_sam;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
99
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
100 __END__
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
101
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
102 =head1 NAME
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
103
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
104 frag_lens - Calculate paired end fragment lengths from read alignment
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
105
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
106 =head1 SYNOPSIS
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
107
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
108 frag_lens [--sam <in.sam>] OR [--ref <cons.fa> --forward <R1.fq> --reverse <R2.fq>] [options] > frag_lens.txt
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
109
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
110 =head1 DESCRIPTION
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
111
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
112 Calculates library fragment lengths based on paired-end read alignment.
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
113 Takes as input either a preprepared SAM alignment or a reference and read
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
114 files from which it produces an alignment. Outputs calculated fragment
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
115 lengths, one per line.
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
116
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
117 =head1 PREREQUISITES
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
118
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
119 Requires the following binaries:
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
120
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
121 =over 1
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
122
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
123 =item * bwa
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
124
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
125 =back
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
126
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
127 =head1 OPTIONS
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
128
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
129 =head2 Input option one
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
130
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
131 =over 4
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
132
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
133 =item B<--sam> I<filename>
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
134
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
135 Path to input SAM alignment.
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
136
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
137 =back
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
138
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
139 =head2 Input option two
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
140
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
141 =over 4
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
142
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
143 =item B<--ref> I<filename>
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
144
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
145 Path to reference sequence (e.g. assembly)
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
146
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
147 =item B<--forward> I<filename>
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
148
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
149 Forward reads in FASTQ format
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
150
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
151 =item B<--reverse> I<filename>
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
152
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
153 Reverse reads in FASTQ format
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
154
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
155 =back
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
156
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
157 =head2 Configuration
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
158
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
159 =over 4
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
160
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
161 =item B<--max_align>
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
162
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
163 Maximum number of alignment records to read as input. Used to limit run times.
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
164
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
165 =item B<--threads>
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
166
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
167 Number of threads to use for alignment (ignored if --sam is given)
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
168
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
169 =back
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
170
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
171 =head1 CAVEATS AND BUGS
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
172
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
173 Please submit bug reports to the issue tracker in the distribution repository.
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
174
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
175 =head1 AUTHOR
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
176
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
177 Jeremy Volkening (jdv@base2bio.com)
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
178
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
179 =head1 LICENSE AND COPYRIGHT
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
180
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
181 Copyright 2014-19 Jeremy Volkening
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
182
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
183 This program is free software: you can redistribute it and/or modify
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
184 it under the terms of the GNU General Public License as published by
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
185 the Free Software Foundation, either version 3 of the License, or
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
186 (at your option) any later version.
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
187
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
188 This program is distributed in the hope that it will be useful,
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
189 but WITHOUT ANY WARRANTY; without even the implied warranty of
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
190 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
191 GNU General Public License for more details.
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
192
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
193 You should have received a copy of the GNU General Public License
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
194 along with this program. If not, see <http://www.gnu.org/licenses/>.
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
195
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
196 =cut
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
parents:
diff changeset
197