Mercurial > repos > fgiacomoni > hr2
diff hr2_manager.pl @ 1:e2cbcf6fa22e draft
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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--- a/hr2_manager.pl Wed Jun 05 09:40:20 2019 -0400 +++ b/hr2_manager.pl Sun Dec 11 17:16:43 2022 +0000 @@ -3,6 +3,7 @@ ## script : hr2_manager.pl ## VERSIONS : # - 01/03/2019 : Fix P issue, permit more flexible atom settings and add requirements for conda auto managing. +# - 09/12/2022 : Fix "Additional atomes not taken into account" - Ticket issue #7 #============================================================================= # Included modules and versions @@ -47,8 +48,8 @@ "mode:s" => \$mode, "charge:i" => \$charge, "regleOr:s" => \$has_golden_rules, - "atomes:s" => \$atomes_basic, # [basic atoms like CNOHP] - "atomessup:s" => \$atomes, + "atomes_basic:s"=> \$atomes_basic, # [basic atoms like CNOHP] + "atomes_sup:s" => \$atomes, "output1:s" => \$output_csv, "outputView:s" => \$output_html, "verbose:i" => \$verbose, @@ -190,6 +191,9 @@ my ($tbody_object) = $oHtml->set_html_tbody_object( $nb_pages_for_html_out, $CONF->{HTML_ENTRIES_PER_PAGE} ) ; ($tbody_object) = $oHtml->add_mz_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $ids, $parsed_results ) ; ($tbody_object) = $oHtml->add_entries_to_tbody_object($tbody_object, $parsed_results) ; + + print Dumper $tbody_object ; + my $html_file = $binPath.'/'.$CONF->{'HTML_TEMPLATE'} ; 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'}) ; @@ -270,15 +274,15 @@ # hr2_manager is a script to elucide chemical formula by their accurate masses. The HiRes program is integrate in this package # Input : a accurate mass or a file of masses -# Author : Franck Giacomoni and Marion Landi -# Email : fgiacomoni\@clermont.inra.fr or mlandi\@clermont.inra.fr -# Version : 1.1 +# Authors : Lain Pavot, Marion Landi and Franck Giacomoni +# Email : franck.giacomoni\@inrae.fr +# Version : 1.1.2 # Created : 01/12/2011 -# Last Update : 09032014 +# Last Update : 06/12/2022 USAGE : hr2_manager.pl -h or 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] - 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] + 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] " ; exit(1); } @@ -294,8 +298,8 @@ =head1 USAGE hr2_manager.pl -h or - 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] - 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] + 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] + 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] =head1 SYNOPSIS @@ -315,8 +319,9 @@ =head1 AUTHOR -Franck Giacomoni E<lt>franck.giacomoni@clermont.inra.frE<gt> -Marion Landi E<lt>marion.landi@clermont.inra.frE<gt> +Franck Giacomoni E<lt>franck.giacomoni@inrae.frE<gt> +Marion Landi E<lt>marion.landi@inrae.frE<gt> +Lain Pavot E<lt>lain.pavot@inrae.frE<gt> =head1 LICENSE @@ -332,4 +337,6 @@ version 4 : 01/03/2019 +version 5 : 09/12/2022 + =cut \ No newline at end of file