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38
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1 #!/usr/bin/env perl
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2
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44
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3 # Flexbar wrapper for Galaxy tool definition, version 3.5.0
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38
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4 # Author: Johannes Roehr
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5
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6 use warnings;
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7 use strict;
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8
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9 my $format;
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10 my @inFiles;
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11 my @outFiles;
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12
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13 my $compression = "";
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14
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15 foreach(0..$#ARGV){
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16 my $arg = $ARGV[$_];
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17
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40
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18 if($arg =~ /\.(fastq\w+)$/ || $arg =~ /\.(fastq\w+\.gz)$/ || $arg =~ /\.(fastq\w+\.bz2)$/){
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19
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20 if(defined $format && $format ne $1){
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21 warn "Read files should have the same format.\n";
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22 exit 1;
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23 }
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24 $format = $1;
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25
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26 my $file = $arg;
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27
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28 $arg =~ s/\.fastq\w+$/\.fastq/;
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29 $arg =~ s/\.fastq\w+\.gz$/\.fastq\.gz/;
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30 $arg =~ s/\.fastq\w+\.bz2$/\.fastq\.bz2/;
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31
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32 $compression = "GZ" if $arg =~ /\.fastq\.gz$/;
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33 $compression = "BZ2" if $arg =~ /\.fastq\.bz2$/;
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34
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35 $ARGV[$_] = $arg;
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36
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37 if($arg =~ /\.dat_input\w\.fastq$/ || $arg =~ /\.dat_input\w\.fastq\.gz$/ || $arg =~ /\.dat_input\w\.fastq\.bz2$/){
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38 push @inFiles, $arg;
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39 rename $file, $arg;
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40 }
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41
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42 push @outFiles, $arg if $arg =~ /\.dat\.fastq$/ || $arg =~ /\.dat\.fastq\.gz$/ || $arg =~ /\.dat\.fastq\.bz2$/;
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38
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43 }
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44 }
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45
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46 my $barcoded = 0;
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47
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48 $barcoded = 1 if $ARGV[$#ARGV] =~ /barcoded$/;
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49
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50 my $call = join " ", @ARGV[0..($#ARGV - $barcoded)];
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51
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52 # $call = $call ." --zip-output ". $compression if $barcoded && $compression ne "";
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53
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54 system $call and exit 1;
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55
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56
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57 unlink $_ or warn "Could not unlink $_: $!" foreach(@inFiles);
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58
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59 if($barcoded){
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60 $format =~ s/\.gz//;
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61 $format =~ s/\.bz2//;
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62
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63 foreach(<$ARGV[$#ARGV]/flexbarOut*.fastq*>){
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64
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65 my $file = $_;
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66
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67 s/fastq$/$format/;
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68 # s/fastq\.gz$/$format/;
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69 # s/fastq\.bz2$/$format/;
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70
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71 rename $file, $_;
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72 }
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73 }
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74 else{
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75 foreach(@outFiles){
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76
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77 my $file = $_;
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78
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79 s/\.fastq$//;
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80 s/\.fastq\.gz$//;
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81 s/\.fastq\.bz2$//;
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82
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83 rename $file, $_;
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84 }
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85 }
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86
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