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comparison flexbar_named_output.pl @ 14:570a7de9f151 draft

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read from bam; fix header issue
author rnateam
date Mon, 30 Nov 2015 07:53:36 -0500
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13:258b6f9e19ab 14:570a7de9f151
1 #!/usr/bin/env perl
2
3 # Flexbar wrapper for Galaxy tool definition, version 2.5
4 # Author: Johannes Roehr
5 # modified by Daniel Maticzka to include additional user-choosable output prefix
6
7 use warnings;
8 use strict;
9
10 # this parses the last 4 arguments
11 # what is id -> xml $output.id
12 # what is folder -> xml $__new_file_path__
13 # what is format? -> xml $reads.ext
14 my ($outFile, $id, $folder, $format, $output_prefix) = @ARGV[($#ARGV - 4) .. $#ARGV];
15
16 # this parses all but the last four arguments
17 # contains the call to the flexbar actual
18 my $call = join " ", @ARGV[0..($#ARGV - 5)];
19
20 # this calls flexbar and
21 # prefix for output files will be "FlexbarTargetFile"
22 system $call .' --target FlexbarTargetFile > '. $outFile and exit 1;
23
24 # now we parse all output files
25 foreach(<FlexbarTargetFile*>){
26
27 # determine filetype
28 my $fileType;
29
30 $fileType = $1 if /\.(\w+)$/;
31 $fileType = $format if /\.\w*fast\w$/;
32 $fileType = 'fasta' if /\.fasta$/;
33 $fileType = 'csfasta' if /\.csfasta$/;
34 $fileType = 'tabular' if /\.lengthdist$/;
35
36 # this is just the filename from the for loop
37 my $file = $_;
38
39 # replace underscores by minus in $_
40 s/_/-/g;
41
42 # set new name for output files
43 my $name = "primary_". $id ."_". $_ ."_visible_". $fileType;
44
45 # rename output file to a pattern recognized by flexbar?
46 rename $file, $name;
47 # best guess: this seems to move the file into a folder
48 # rename behavious is not specified by perl... or implementation differs.
49 rename $name, $folder;
50 }