Mercurial > repos > fgiacomoni > massbank_ws_searchspectrum

comparison t/lib/massbank_main_Test.pm @ 0:023c380900ef draft default tip

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Init repository with last massbank_ws_searchspectrum master version
author fgiacomoni
date Wed, 19 Apr 2017 11:31:58 -0400
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-1:000000000000 0:023c380900ef
1 package lib::massbank_main_Test ;
2
3 use diagnostics; # this gives you more debugging information
4 use warnings; # this warns you of bad practices
5 use strict; # this prevents silly errors
6 use Exporter ;
7 use Carp ;
8
9 use Data::Dumper ;
10
11 our $VERSION = "1.0";
12 our @ISA = qw(Exporter);
13 our @EXPORT = qw( run_main_massbank_pl);
14 our %EXPORT_TAGS = ( ALL => [qw(run_main_massbank_pl)] );
15
16 #use lib '/Users/fgiacomoni/Inra/labs/perl/galaxy_tools/massbank_ws_searchspectrum' ;
17 #use lib::mapper qw( :ALL ) ;
18
19 sub run_main_massbank_pl {
20
21 my ($input_file, $col_mz, $col_pcgroup, $col_int, $lineheader, $score_threshold, $mode, $instruments, $max, $unit, $tol, $cutoff, $server, $json, $csv, $xls) = @_ ;
22
23 my $msg = `perl /Users/fgiacomoni/Inra/labs/perl/galaxy_tools/massbank_ws_searchspectrum/massbank_ws_searchspectrum.pl -masses $input_file -col_mz $col_mz -col_pcgroup $col_pcgroup -col_int $col_int -lineheader $lineheader -mode $mode -score_threshold $score_threshold -instruments $instruments -max $max -unit $unit -tolerance $tol -cutoff $cutoff -server $server -json $json -csv $csv -xls $xls`;
24 print $msg ;
25 #-masses /Users/fgiacomoni/Inra/labs/tests/massbank_V02/pcgrp_annot.tsv
26 #-col_mz 1
27 #-col_pcgroup 14
28 #-col_int 7
29 #-lineheader 1
30 #-score_threshold 0.5
31 #-mode Positive
32 #-instruments all
33 #-max 2
34 #-unit unit
35 #-tolerance 0.3
36 #-cutoff 5
37 #-server JP
38 #-json /Users/fgiacomoni/Inra/labs/tests/massbank_V02/out.json
39 #-csv /Users/fgiacomoni/Inra/labs/tests/massbank_V02/out.csv
40 #-xls /Users/fgiacomoni/Inra/labs/tests/massbank_V02/out.xls
41
42 }
43
44
45 1 ;