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annotate flexbar.pl @ 17:952389252467

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author jtilman
date Fri, 22 Feb 2013 05:31:55 -0500
parents 346a2b0979ea
children
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a8399cb4972b Uploaded Flexbar perl tool wrapper file flexbar.pl
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1 #!/usr/bin/env perl
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3 # Flexbar wrapper for Galaxy tool definition, version 2.32
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4 # Author: Johannes Roehr
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a8399cb4972b Uploaded Flexbar perl tool wrapper file flexbar.pl
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a8399cb4972b Uploaded Flexbar perl tool wrapper file flexbar.pl
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6 use warnings;
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7 use strict;
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9 my ($outFile, $id, $folder, $format) = @ARGV[($#ARGV - 3) .. $#ARGV];
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11 my $call = join " ", @ARGV[0..($#ARGV - 4)];
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13 system $call .' --target FlexbarTargetFile > '. $outFile and exit 1;
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16 foreach(<FlexbarTargetFile*>){
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18 my $fileType;
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20 $fileType = $1 if /\.(\w+)$/;
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4cbf6c6d2f2b Fixed issue where adapter removal can not be performed and further minor issues.
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21 $fileType = $format if /\.\w*fast\w$/;
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22 $fileType = 'fasta' if /\.fasta$/;
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23 $fileType = 'tabular' if $fileType eq 'lengthdist';
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25 my $file = $_;
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27 s/_//g;
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29 my $name = "primary_". $id ."_". $_ ."_visible_". $fileType;
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31 rename $file, $name;
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32 rename $name, $folder;
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a8399cb4972b Uploaded Flexbar perl tool wrapper file flexbar.pl
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33 }
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