Mercurial > repos > jvolkening > b2b_bam2consensus

annotate frag_lens @ 0:bfae6a56e5cf draft

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 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
author jvolkening
date Sat, 02 Mar 2024 07:43:22 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
1 #!/usr/bin/env perl
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
2
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
3 use strict;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
4 use warnings;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
5 use 5.012;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
6
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
7 use Cwd qw/abs_path/;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
8 use File::Temp qw/tempdir tempfile/;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
9 use IPC::Cmd qw/can_run/;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
10 use List::Util qw/sum/;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
11 use Getopt::Long;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
12 use Pod::Usage;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
13
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
14 my @good_codes = ( 0x0002, 0x0040 );
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
15 my @bad_codes = ( 0x0004, 0x0100, 0x0800 );
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
16
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
17 #-inputs---------------------------------------------------------------------#
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
18 my $fasta;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
19 my $forward;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
20 my $reverse;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
21 my $sam;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
22 #-knobs----------------------------------------------------------------------#
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
23 my $threads = 1;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
24 my $max_align = 10000;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
25
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
26 my $PROGRAM = 'frag_lens';
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
27 my $VERSION = 0.001;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
28
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
29 GetOptions(
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
30 #-inputs-----------------------------------------------------------------#
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
31 'sam=s' => \$sam,
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
32 'forward=s' => \$forward,
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
33 'reverse=s' => \$reverse,
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
34 'ref=s' => \$fasta,
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
35 #-knobs------------------------------------------------------------------#
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
36 'threads=i' => \$threads,
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
37 'max_aln=i' => \$max_align,
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
38 'help' => sub{ pod2usage(-verbose => 2); },
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
39 'version' => sub{ say "This is $PROGRAM v$VERSION";exit; },
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
40
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
41 ) or pod2usage( -verbose => 1);
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
42
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
43 my $fh_sam;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
44 my $tmp_fasta;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
45
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
46 if (defined $sam) {
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
47 open $fh_sam, '<', $sam or die "failed to open SAM\n";
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
48 }
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
49
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
50 else {
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
51
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
52 my $BWA = can_run('bwa')
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
53 // die "BWA is required but not found\n";
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
54
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
55 my ($tmp_dir) = tempdir( CLEANUP => 1);
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
56
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
57 die "specify forward and reverse read files and reference\n"
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
58 if (! defined $forward || ! defined $reverse || ! defined $fasta);
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
59
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
60 $fasta = abs_path($fasta);
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
61
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
62 my $res = system(
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
63 'ln',
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
64 '-s',
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
65 $fasta,
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
66 "$tmp_dir/tmp.fasta"
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
67 );
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
68 die "link failed" if ($res);
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
69 $res = system(
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
70 $BWA,
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
71 'index',
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
72 "$tmp_dir/tmp.fasta"
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
73 );
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
74 die "index failed" if ($res);
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
75 open $fh_sam, '-|', $BWA,
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
76 'mem',
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
77 '-t' => $threads,
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
78 '-v' => 1,
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
79 "$tmp_dir/tmp.fasta",
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
80 $forward,
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
81 $reverse
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
82 ;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
83 }
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
84
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
85 my $c = 0;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
86 while (my $line = <$fh_sam>) {
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
87 next if ($line =~ /^\@/);
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
88 chomp $line;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
89 my @parts = split "\t", $line;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
90 my $flags = $parts[1];
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
91 my $sum1 = sum map {$_ & $flags ? 1 : 0} @good_codes;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
92 my $sum2 = sum map {$_ & $flags ? 1 : 0} @bad_codes;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
93 if ($sum1 == scalar @good_codes && $sum2 == 0) {
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
94 say abs($parts[8]);
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
95 last if (++$c >= $max_align);
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
96 }
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
97 }
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
98 close $fh_sam;
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
99
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
100 __END__
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
101
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
102 =head1 NAME
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
103
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
104 frag_lens - Calculate paired end fragment lengths from read alignment
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
105
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
106 =head1 SYNOPSIS
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
107
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
108 frag_lens [--sam <in.sam>] OR [--ref <cons.fa> --forward <R1.fq> --reverse <R2.fq>] [options] > frag_lens.txt
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
109
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
110 =head1 DESCRIPTION
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
111
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
112 Calculates library fragment lengths based on paired-end read alignment.
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
113 Takes as input either a preprepared SAM alignment or a reference and read
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
114 files from which it produces an alignment. Outputs calculated fragment
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
115 lengths, one per line.
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
116
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
117 =head1 PREREQUISITES
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
118
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
119 Requires the following binaries:
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
120
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
121 =over 1
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
122
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
123 =item * bwa
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
124
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
125 =back
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
126
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
127 =head1 OPTIONS
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
128
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
129 =head2 Input option one
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
130
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
131 =over 4
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
132
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
133 =item B<--sam> I<filename>
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
134
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
135 Path to input SAM alignment.
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
136
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
137 =back
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
138
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
139 =head2 Input option two
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
140
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
141 =over 4
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
142
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
143 =item B<--ref> I<filename>
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
144
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
145 Path to reference sequence (e.g. assembly)
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
146
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
147 =item B<--forward> I<filename>
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
148
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
149 Forward reads in FASTQ format
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
150
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
151 =item B<--reverse> I<filename>
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
152
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
153 Reverse reads in FASTQ format
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
154
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
155 =back
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
156
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
157 =head2 Configuration
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
158
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
159 =over 4
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
160
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
161 =item B<--max_align>
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
162
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
163 Maximum number of alignment records to read as input. Used to limit run times.
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
164
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
165 =item B<--threads>
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
166
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
167 Number of threads to use for alignment (ignored if --sam is given)
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
168
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
169 =back
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
170
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
171 =head1 CAVEATS AND BUGS
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
172
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
173 Please submit bug reports to the issue tracker in the distribution repository.
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
174
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
175 =head1 AUTHOR
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
176
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
177 Jeremy Volkening (jdv@base2bio.com)
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
178
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
179 =head1 LICENSE AND COPYRIGHT
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
180
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
181 Copyright 2014-19 Jeremy Volkening
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
182
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
183 This program is free software: you can redistribute it and/or modify
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
184 it under the terms of the GNU General Public License as published by
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
185 the Free Software Foundation, either version 3 of the License, or
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
186 (at your option) any later version.
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
187
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
188 This program is distributed in the hope that it will be useful,
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
189 but WITHOUT ANY WARRANTY; without even the implied warranty of
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
190 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
191 GNU General Public License for more details.
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
192
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
193 You should have received a copy of the GNU General Public License
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
194 along with this program. If not, see <http://www.gnu.org/licenses/>.
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
195
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
196 =cut
bfae6a56e5cf planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
jvolkening
parents:
diff changeset
197