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|
#!/usr/bin/env perl
# Flexbar wrapper for Galaxy tool definition, version 3.5.0
# Author: Johannes Roehr
use warnings;
use strict;
my $format;
my @inFiles;
my @outFiles;
my $compression = "";
foreach(0..$#ARGV){
my $arg = $ARGV[$_];
if($arg =~ /\.(fastq\w+)$/ || $arg =~ /\.(fastq\w+\.gz)$/ || $arg =~ /\.(fastq\w+\.bz2)$/){
if(defined $format && $format ne $1){
warn "Read files should have the same format.\n";
exit 1;
}
$format = $1;
my $file = $arg;
$arg =~ s/\.fastq\w+$/\.fastq/;
$arg =~ s/\.fastq\w+\.gz$/\.fastq\.gz/;
$arg =~ s/\.fastq\w+\.bz2$/\.fastq\.bz2/;
$compression = "GZ" if $arg =~ /\.fastq\.gz$/;
$compression = "BZ2" if $arg =~ /\.fastq\.bz2$/;
$ARGV[$_] = $arg;
if($arg =~ /\.dat_input\w\.fastq$/ || $arg =~ /\.dat_input\w\.fastq\.gz$/ || $arg =~ /\.dat_input\w\.fastq\.bz2$/){
push @inFiles, $arg;
rename $file, $arg;
}
push @outFiles, $arg if $arg =~ /\.dat\.fastq$/ || $arg =~ /\.dat\.fastq\.gz$/ || $arg =~ /\.dat\.fastq\.bz2$/;
}
}
my $barcoded = 0;
$barcoded = 1 if $ARGV[$#ARGV] =~ /barcoded$/;
my $call = join " ", @ARGV[0..($#ARGV - $barcoded)];
# $call = $call ." --zip-output ". $compression if $barcoded && $compression ne "";
system $call and exit 1;
unlink $_ or warn "Could not unlink $_: $!" foreach(@inFiles);
if($barcoded){
$format =~ s/\.gz//;
$format =~ s/\.bz2//;
foreach(<$ARGV[$#ARGV]/flexbarOut*.fastq*>){
my $file = $_;
s/fastq$/$format/;
# s/fastq\.gz$/$format/;
# s/fastq\.bz2$/$format/;
rename $file, $_;
}
}
else{
foreach(@outFiles){
my $file = $_;
s/\.fastq$//;
s/\.fastq\.gz$//;
s/\.fastq\.bz2$//;
rename $file, $_;
}
}
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