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comparison flexbar.pl @ 13:258b6f9e19ab draft

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author rnateam
date Fri, 27 Nov 2015 04:33:02 -0500
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12:55b539a509f0 13:258b6f9e19ab
1 #!/usr/bin/env perl
2
3 # Flexbar wrapper for Galaxy tool definition, version 2.5
4 # Author: Johannes Roehr
5
6 use warnings;
7 use strict;
8
9 # this parses the last 4 arguments
10 # what is id -> xml $output.id
11 # what is folder -> xml $__new_file_path__
12 # what is format? -> xml $reads.ext
13 my ($outFile, $id, $folder, $format) = @ARGV[($#ARGV - 3) .. $#ARGV];
14
15 # this parses all but the last four arguments
16 # contains the call to the flexbar actual
17 my $call = join " ", @ARGV[0..($#ARGV - 4)];
18
19 # this calls flexbar and
20 # prefix for output files will be "FlexbarTargetFile"
21 system $call .' --target FlexbarTargetFile > '. $outFile and exit 1;
22
23 # now we parse all output files
24 foreach(<FlexbarTargetFile*>){
25
26 # determine filetype
27 my $fileType;
28
29 $fileType = $1 if /\.(\w+)$/;
30 $fileType = $format if /\.\w*fast\w$/;
31 $fileType = 'fasta' if /\.fasta$/;
32 $fileType = 'csfasta' if /\.csfasta$/;
33 $fileType = 'tabular' if /\.lengthdist$/;
34
35 # this is just the filename from the for loop
36 my $file = $_;
37
38 # replace underscores by minus in $_
39 s/_/-/g;
40
41 # set new name for output files
42 my $name = "primary_". $id ."_". $_ ."_visible_". $fileType;
43
44 # rename output file to a pattern recognized by flexbar?
45 rename $file, $name;
46 # best guess: this seems to move the file into a folder
47 # rename behavious is not specified by perl... or implementation differs.
48 rename $name, $folder;
49 }