Mercurial > repos > jdv > b2b_count_mapped_reads

annotate summarize_assembly @ 1:20d941ecc1bb draft default tip

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"planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
author jdv
date Tue, 28 Sep 2021 06:11:32 +0000
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20d941ecc1bb "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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1 #!/usr/bin/env perl
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3 use strict;
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4 use warnings;
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5 use 5.012;
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7 use Getopt::Long;
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8 use Pod::Usage;
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9 use List::Util qw/sum max min/;
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10 use List::MoreUtils qw/uniq/;
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11 use BioX::Seq::Stream;
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13 my $PROGRAM = 'summarize_assembly';
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14 my $VERSION = 0.002;
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16 my $fn_fasta;
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17 my @cutoffs;
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18 my $strip = 0;
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19 my $split = 0;
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21 # Collect command-line parameters
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22 my $err_msg = 'Syntax error: please check your syntax';
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23 GetOptions(
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24 'fasta=s' => \$fn_fasta,
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25 'cutoffs:i{,}' => \@cutoffs,
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26 'strip_N' => \$strip,
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27 'split_N' => \$split,
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28 'help' => sub{ pod2usage( -verbose => 2 ) },
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29 'version' => sub{ print "This is $PROGRAM v$VERSION\n";exit; },
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30 ) or pod2usage( -msg => $err_msg, -verbose => 1 );
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32 # Set default cutoffs if necessary and sort
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33 if (! scalar @cutoffs) {
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34 warn "No cutoff supplied, defaulting to N50\n";
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35 push @cutoffs, 50;
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36 }
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37 @cutoffs = sort {$a <=> $b} uniq @cutoffs;
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39 # Only one of 'strip_N' or 'split_N' is valid
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40 if ($strip && $split) {
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41 warn "Only one of --strip_N or --split_N is valid, ignoring --strip_N\n";
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42 $strip = 0;
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43 }
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45 # Check for a few necessary conditions
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46 die "Can't open FASTA file for reading"
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47 if (defined $fn_fasta && ! -r $fn_fasta);
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48 die "One or more cutoffs outside valid range (1-99)"
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49 if (grep {$_ < 1 || $_ > 99} @cutoffs);
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50 die "Cutoffs must be integer values"
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51 if (grep {$_ ne int($_)} @cutoffs);
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52 my @lens;
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53 my $N_sum = 0;
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54 my $GC_sum = 0;
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55
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56 # Read in sequences and calculate descriptive stats
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57 my $stream = BioX::Seq::Stream->new( $fn_fasta ); #STDIN if undefined
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58
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59 SEQ:
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60 while (my $seq = $stream->next_seq) {
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61 my @parts = ($seq);
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62 @parts = split(/n+/i, $seq) if $split;
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63 for (@parts) {
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64 my $Ns = ($_ =~ tr/Nn//);
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65 $N_sum += $Ns;
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66 $GC_sum += ($_ =~ tr/GCgc//);
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67 push @lens, length($_) - $Ns * $strip;
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68 }
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69 }
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70 @lens = sort {$b <=> $a} @lens;
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71
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72 # Calculate basic stats
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73 my $scaffold_count = scalar @lens;
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74 my $total_len = sum @lens;
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75 my $N_fraction = round( $N_sum/($total_len + $N_sum*$strip), 2 )*100;
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76 my $max_length = max @lens;
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77 my $min_length = min @lens;
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78 my $mean_length = round($total_len/$scaffold_count, 0);
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79
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80 # GC percentage calculated from non-ambiguous bases only
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81 my $GC_fraction = round( $GC_sum/($total_len + ($strip - 1)*$N_sum), 2 )*100;
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82
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83 # Calculate Nx (N50, N80, etc) values
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84 # For example, N50 is the size of the smallest contig for which it and all
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85 # larger contigs contain 50% of the total nucleotides in the database
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86 my $cum_length = 0;
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87 my @fractions = map {$_/100} @cutoffs;
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88 my @Nx;
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89
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90 LEN:
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91 for (@lens) {
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92 $cum_length += $_;
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93 if ($cum_length/$total_len >= $fractions[0]) {
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94 push @Nx, $_;
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95 shift @fractions;
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96 last LEN if (@fractions < 1);
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97 }
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98 }
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99
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100 # Print summary
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101 print '-' x 40 . "\n"
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102 . "Summary\n"
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103 . '-' x 40 . "\n"
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104 . "number of scaffolds: $scaffold_count\n"
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105 . "total length: $total_len\n"
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106 . "average length: $mean_length\n"
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107 . "G/C content: $GC_fraction\%\n"
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108 . "ambiguous content: $N_fraction\%\n"
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109 . "longest scaffold: $max_length\n";
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110 for (0..$#Nx) {
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111 my $label = sprintf "N%02d", $cutoffs[$_];
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112 print "$label: $Nx[$_]\n";
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113 }
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114 print "shortest scaffold: $min_length\n";
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115 print "NOTE: Ns were stripped for above calculations\n" if ($strip);
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116 print "NOTE: Scaffolds were split on Ns for above calculations\n" if ($split);
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117 print '-' x 40 . "\n";
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118
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119 exit;
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120
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121 sub round {
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122
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123 my ($val,$places) = @_;
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124 return int($val*10**$places+0.5)/10**$places;
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125
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126 }
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127
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128
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129 __END__
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130
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131 =head1 NAME
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132
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133 summarize_assembly - print basic summary info for a file of assembly scaffolds
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134
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135 =head1 SYNOPSIS
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136
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137 summarize_assembly [--cutoffs I<cutoff_1> I<cutoff_2> .. I<cutoff_N> --strip_N --split_N ] --fasta I<input_file>]
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138
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139 =head1 DESCRIPTION
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140
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141 This program takes a FASTA file and optionally a list of cutoff values as
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142 input and prints out summary information about the contigs/scaffolds contained
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143 in the file. You can, of course, supply a FASTA file of any sort of nucleic
20d941ecc1bb "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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144 acid sequences, but the summary information makes most sense for contigs from
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145 genomic sequencing assemblies.
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146
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147 =head1 OPTIONS
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148
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149 =over
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150
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151 =item B<--fasta> I<filename>
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152
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153 Specify contig/scaffold file from which to read input (default: STDIN)
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154
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155 =item B<--cutoffs>
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156
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157 Space-separated integer list of cutoffs to calculate (e.g. '--cutoffs 50 90'
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158 will output N50 and N90 values) (default: 50)
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159
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160 =item B<--strip_N>
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161
20d941ecc1bb "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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162 If specified, Ns will be stripped from scaffold sequences before statistics
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163 are calculated (default: FALSE)
20d941ecc1bb "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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164
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165 =item B<--split_N>
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166
20d941ecc1bb "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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167 If specified, scaffold sequences will be split at regions of one or more Ns
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168 before statistics are calculated (e.g. to get contig-level stats from a
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169 scaffold file). Note that if this flag is specified, the value of '--strip_N'
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170 will be ignored. (default: FALSE)
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171
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172 =item B<--help>
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173
20d941ecc1bb "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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174 Display this usage page
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175
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176 =item B<--version>
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177
20d941ecc1bb "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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178 Print version information
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179
20d941ecc1bb "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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180 =back
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181
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182 =head1 CAVEATS AND BUGS
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183
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184 Please submit bug reports to the issue tracker in the distribution repository.
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185
20d941ecc1bb "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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186 =head1 AUTHOR
20d941ecc1bb "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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187
20d941ecc1bb "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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188 Jeremy Volkening (jdv@base2bio.com)
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189
20d941ecc1bb "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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190 =head1 LICENSE AND COPYRIGHT
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191
20d941ecc1bb "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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192 Copyright 2014-16 Jeremy Volkening
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193
20d941ecc1bb "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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194 This program is free software: you can redistribute it and/or modify
20d941ecc1bb "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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195 it under the terms of the GNU General Public License as published by
20d941ecc1bb "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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196 the Free Software Foundation, either version 3 of the License, or
20d941ecc1bb "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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197 (at your option) any later version.
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198
20d941ecc1bb "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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199 This program is distributed in the hope that it will be useful,
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200 but WITHOUT ANY WARRANTY; without even the implied warranty of
20d941ecc1bb "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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201 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
20d941ecc1bb "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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202 GNU General Public License for more details.
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203
20d941ecc1bb "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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204 You should have received a copy of the GNU General Public License
20d941ecc1bb "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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205 along with this program. If not, see <http://www.gnu.org/licenses/>.
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206
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207 =cut
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208