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38
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1 #!/usr/bin/env perl
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2
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3 # Flexbar wrapper for Galaxy tool definition, version 3.4.2
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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 $format;
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10 my @inFiles;
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11 my @outFiles;
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12
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13 foreach(0..$#ARGV){
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14 my $arg = $ARGV[$_];
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15
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40
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16 if($arg =~ /\.(fastq\w+)$/ || $arg =~ /\.(fastq\w+\.gz)$/ || $arg =~ /\.(fastq\w+\.bz2)$/){
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38
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17
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40
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18 if(defined $format && $format ne $1){
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19 print STDERR "Paired read files should have the same format.\n";
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20 exit 1;
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21 }
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38
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22 $format = $1;
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40
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23
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38
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24 my $file = $arg;
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25
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26 $arg =~ s/\.fastq\w+$/\.fastq/;
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27 $arg =~ s/\.fastq\w+\.gz$/\.fastq\.gz/;
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40
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28 $arg =~ s/\.fastq\w+\.bz2$/\.fastq\.bz2/;
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29
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30 push @inFiles, $arg if $arg =~ /\.dat_input\.fastq$/ || $arg =~ /\.dat_input\.fastq\.gz$/ || $arg =~ /\.dat_input\.fastq\.bz2$/;
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31 push @outFiles, $arg if $arg =~ /\.dat\.fastq$/ || $arg =~ /\.dat\.fastq\.gz$/ || $arg =~ /\.dat\.fastq\.bz2$/;
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38
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32
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33 $ARGV[$_] = $arg;
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34 rename $file, $arg;
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35 }
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36 }
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37
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38 my $call = join " ", @ARGV;
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39
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40 system $call and exit 1;
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41
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42
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43 unlink $_ or warn "Could not unlink $_: $!" foreach(@inFiles);
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44
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45 foreach(@outFiles){
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46
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47 my $file = $_;
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48
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49 s/\.fastq$//;
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50 s/\.fastq\.gz$//;
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40
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51 s/\.fastq\.bz2$//;
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38
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52
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53 rename $file, $_;
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54 }
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55
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