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comparison hr2_manager.pl @ 1:e2cbcf6fa22e draft

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master branch Updating with tag :CI_COMMIT_TAG - - Fxx
author fgiacomoni
date Sun, 11 Dec 2022 17:16:43 +0000
parents 86296c048e46
children 23970530a518
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0:86296c048e46 1:e2cbcf6fa22e
1 #!perl 1 #!perl
2 2
3 ## script : hr2_manager.pl 3 ## script : hr2_manager.pl
4 ## VERSIONS : 4 ## VERSIONS :
5 # - 01/03/2019 : Fix P issue, permit more flexible atom settings and add requirements for conda auto managing. 5 # - 01/03/2019 : Fix P issue, permit more flexible atom settings and add requirements for conda auto managing.
6 # - 09/12/2022 : Fix "Additional atomes not taken into account" - Ticket issue #7
6 7
7 #============================================================================= 8 #=============================================================================
8 # Included modules and versions 9 # Included modules and versions
9 #============================================================================= 10 #=============================================================================
10 ## Perl modules 11 ## Perl modules
45 "masse:s" => \$mass, 46 "masse:s" => \$mass,
46 "tolerance:f" => \$tolerance, 47 "tolerance:f" => \$tolerance,
47 "mode:s" => \$mode, 48 "mode:s" => \$mode,
48 "charge:i" => \$charge, 49 "charge:i" => \$charge,
49 "regleOr:s" => \$has_golden_rules, 50 "regleOr:s" => \$has_golden_rules,
50 "atomes:s" => \$atomes_basic, # [basic atoms like CNOHP] 51 "atomes_basic:s"=> \$atomes_basic, # [basic atoms like CNOHP]
51 "atomessup:s" => \$atomes, 52 "atomes_sup:s" => \$atomes,
52 "output1:s" => \$output_csv, 53 "output1:s" => \$output_csv,
53 "outputView:s" => \$output_html, 54 "outputView:s" => \$output_html,
54 "verbose:i" => \$verbose, 55 "verbose:i" => \$verbose,
55 ) ; 56 ) ;
56 57
188 if ( ( defined $output_html ) and ( defined $parsed_results ) ) { 189 if ( ( defined $output_html ) and ( defined $parsed_results ) ) {
189 my $oHtml = lib::hr::new() ; 190 my $oHtml = lib::hr::new() ;
190 my ($tbody_object) = $oHtml->set_html_tbody_object( $nb_pages_for_html_out, $CONF->{HTML_ENTRIES_PER_PAGE} ) ; 191 my ($tbody_object) = $oHtml->set_html_tbody_object( $nb_pages_for_html_out, $CONF->{HTML_ENTRIES_PER_PAGE} ) ;
191 ($tbody_object) = $oHtml->add_mz_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $ids, $parsed_results ) ; 192 ($tbody_object) = $oHtml->add_mz_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $ids, $parsed_results ) ;
192 ($tbody_object) = $oHtml->add_entries_to_tbody_object($tbody_object, $parsed_results) ; 193 ($tbody_object) = $oHtml->add_entries_to_tbody_object($tbody_object, $parsed_results) ;
194
195 print Dumper $tbody_object ;
196
193 my $html_file = $binPath.'/'.$CONF->{'HTML_TEMPLATE'} ; 197 my $html_file = $binPath.'/'.$CONF->{'HTML_TEMPLATE'} ;
194 my $output = $oHtml->write_html_skel(\$output_html, $tbody_object, $nb_pages_for_html_out, $search_condition, $html_file, $CONF->{'JS_GALAXY_PATH'}, $CONF->{'CSS_GALAXY_PATH'}) ; 198 my $output = $oHtml->write_html_skel(\$output_html, $tbody_object, $nb_pages_for_html_out, $search_condition, $html_file, $CONF->{'JS_GALAXY_PATH'}, $CONF->{'CSS_GALAXY_PATH'}) ;
195 199
196 } ## END IF 200 } ## END IF
197 else { 201 else {
268 print STDERR " 272 print STDERR "
269 hr2_manager.pl 273 hr2_manager.pl
270 274
271 # hr2_manager is a script to elucide chemical formula by their accurate masses. The HiRes program is integrate in this package 275 # hr2_manager is a script to elucide chemical formula by their accurate masses. The HiRes program is integrate in this package
272 # Input : a accurate mass or a file of masses 276 # Input : a accurate mass or a file of masses
273 # Author : Franck Giacomoni and Marion Landi 277 # Authors : Lain Pavot, Marion Landi and Franck Giacomoni
274 # Email : fgiacomoni\@clermont.inra.fr or mlandi\@clermont.inra.fr 278 # Email : franck.giacomoni\@inrae.fr
275 # Version : 1.1 279 # Version : 1.1.2
276 # Created : 01/12/2011 280 # Created : 01/12/2011
277 # Last Update : 09032014 281 # Last Update : 06/12/2022
278 USAGE : 282 USAGE :
279 hr2_manager.pl -h or 283 hr2_manager.pl -h or
280 hr2_manager.pl -input [cvs file of masses] -colId [int] -colmass [int] -nbHeader [int] -tolerance [float] -mode [positive, neutral or negative] -charge [int] -regleOr [yes or no] -atome [P, S, F, Cl, K, B, A, 1 ] -output1 [csv file] -outputView [html file] 284 hr2_manager.pl -input [cvs file of masses] -colId [int] -colmass [int] -nbHeader [int] -tolerance [float] -mode [positive, neutral or negative] -charge [int] -regleOr [yes or no] -atome [P, S, F, Cl, K, B, A, 1 ] -output1 [csv file] -outputView [html file]
281 hr2_manager.pl -masse [double] -tolerance [float] -mode [positive, neutral or negative] -charge [int] -regleOr [yes or no] -atome [P, S, F, Cl, K, B, A, 1 ] -output1 [csv file] -outputView [html file] 285 hr2_manager.pl -masse [double] -tolerance [float] -mode [positive, neutral or negative] -charge [int] -regleOr [yes or no] -atomes_basic [C, N, O, P, H ] -atomes_sup [S, F, Cl, K, B, A, 1 ] -output1 [csv file] -outputView [html file]
282 " ; 286 " ;
283 exit(1); 287 exit(1);
284 } 288 }
285 289
286 ## END of script - F Giacomoni 290 ## END of script - F Giacomoni
292 hr2_manager.pl -- script for launch / manage hr2 binary 296 hr2_manager.pl -- script for launch / manage hr2 binary
293 297
294 =head1 USAGE 298 =head1 USAGE
295 299
296 hr2_manager.pl -h or 300 hr2_manager.pl -h or
297 hr2_manager.pl -input [cvs file of masses] -colId [int] -colmass [int] -nbHeader [int] -tolerance [float] -mode [positive, neutral or negative] -charge [int] -regleOr [yes or no] -atome [P, S, F, Cl, K, B, A, 1 ] -output1 [csv file] -outputView [html file] 301 hr2_manager.pl -input [cvs file of masses] -colId [int] -colmass [int] -nbHeader [int] -tolerance [float] -mode [positive, neutral or negative] -charge [int] -regleOr [yes or no] -atomes_basic [C, N, O, P, H ] -atomes_sup [S, F, Cl, K, B, A, 1 ] -output1 [csv file] -outputView [html file]
298 hr2_manager.pl -masse [double] -tolerance [float] -mode [positive, neutral or negative] -charge [int] -regleOr [yes or no] -atome [P, S, F, Cl, K, B, A, 1 ] -output1 [csv file] -outputView [html file] 302 hr2_manager.pl -masse [double] -tolerance [float] -mode [positive, neutral or negative] -charge [int] -regleOr [yes or no] -atomes_basic [C, N, O, P, H ] -atomes_sup [S, F, Cl, K, B, A, 1 ] -output1 [csv file] -outputView [html file]
299 303
300 =head1 SYNOPSIS 304 =head1 SYNOPSIS
301 305
302 This script manages hr2 binary which elucids raw formula with exact masses. 306 This script manages hr2 binary which elucids raw formula with exact masses.
303 307
313 317
314 =back 318 =back
315 319
316 =head1 AUTHOR 320 =head1 AUTHOR
317 321
318 Franck Giacomoni E<lt>franck.giacomoni@clermont.inra.frE<gt> 322 Franck Giacomoni E<lt>franck.giacomoni@inrae.frE<gt>
319 Marion Landi E<lt>marion.landi@clermont.inra.frE<gt> 323 Marion Landi E<lt>marion.landi@inrae.frE<gt>
324 Lain Pavot E<lt>lain.pavot@inrae.frE<gt>
320 325
321 =head1 LICENSE 326 =head1 LICENSE
322 327
323 This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. 328 This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
324 329
330 335
331 version 3 : 20/02/2014 336 version 3 : 20/02/2014
332 337
333 version 4 : 01/03/2019 338 version 4 : 01/03/2019
334 339
340 version 5 : 09/12/2022
341
335 =cut 342 =cut