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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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16 if($arg =~ /\.(fastq\w+)$/ || $arg =~ /\.(fastq\w+\.gz)$/){
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17
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18 $format = $1;
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19 my $file = $arg;
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20
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21 $arg =~ s/\.fastq\w+$/\.fastq/;
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22 $arg =~ s/\.fastq\w+\.gz$/\.fastq\.gz/;
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23
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24 $ARGV[$_] = $arg;
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25 rename $file, $arg;
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26
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27 push @inFiles, $arg if $arg =~ /\.dat_input\.fastq$/ || $arg =~ /\.dat_input\.fastq\.gz$/;
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28 push @outFiles, $arg if $arg =~ /\.dat\.fastq$/ || $arg =~ /\.dat\.fastq\.gz$/;
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29 }
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30 }
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31
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32 my $call = join " ", @ARGV;
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33
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34 system $call and exit 1;
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35
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36
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37 unlink $_ or warn "Could not unlink $_: $!" foreach(@inFiles);
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38
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39 foreach(@outFiles){
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40
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41 my $file = $_;
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42
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43 s/\.fastq$//;
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44 s/\.fastq\.gz$//;
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45
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46 rename $file, $_;
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47 }
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48
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