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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 2.5
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4 # Author: Johannes Roehr
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5 # modified by Daniel Maticzka to include additional user-choosable output prefix
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6
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7 use warnings;
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8 use strict;
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9
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10 # this parses the last 4 arguments
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11 # what is id -> xml $output.id
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12 # what is folder -> xml $__new_file_path__
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13 # what is format? -> xml $reads.ext
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14 my ($outFile, $id, $folder, $format, $output_prefix) = @ARGV[($#ARGV - 4) .. $#ARGV];
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15
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16 # this parses all but the last four arguments
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17 # contains the call to the flexbar actual
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18 my $call = join " ", @ARGV[0..($#ARGV - 5)];
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19
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20 # this calls flexbar and
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21 # prefix for output files will be "FlexbarTargetFile"
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22 system $call .' --target FlexbarTargetFile > '. $outFile and exit 1;
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23
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24 # now we parse all output files
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25 foreach(<FlexbarTargetFile*>){
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26
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27 # determine filetype
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28 my $fileType;
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29
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30 $fileType = $1 if /\.(\w+)$/;
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31 $fileType = $format if /\.\w*fast\w$/;
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32 $fileType = 'fasta' if /\.fasta$/;
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33 $fileType = 'csfasta' if /\.csfasta$/;
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34 $fileType = 'tabular' if /\.lengthdist$/;
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35
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36 # this is just the filename from the for loop
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37 my $file = $_;
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38
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39 # replace underscores by minus in $_
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40 s/_/-/g;
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41
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42 # set new name for output files
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43 my $name = "primary_". $id ."_". $_ ."_visible_". $fileType;
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44
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45 # rename output file to a pattern recognized by flexbar?
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46 rename $file, $name;
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47 # best guess: this seems to move the file into a folder
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48 # rename behavious is not specified by perl... or implementation differs.
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49 rename $name, $folder;
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50 }
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