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

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