Mercurial > repos > fgiacomoni > hr2
changeset 3:78afd7f439f3 draft default tip
master branch Updating with tag :CI_COMMIT_TAG - - Fxx
author | fgiacomoni |
---|---|
date | Wed, 15 Feb 2023 15:57:49 +0000 |
parents | 23970530a518 |
children | |
files | HR2.xml hr2_manager.pl lib/hr.pm test-data/input06.tabular test-data/out6.html test-data/out6.tabular |
diffstat | 6 files changed, 186 insertions(+), 101 deletions(-) [+] |
line wrap: on
line diff
--- a/HR2.xml Tue Jan 17 10:31:32 2023 +0000 +++ b/HR2.xml Wed Feb 15 15:57:49 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="hr2" name="HR2 formula" version="1.1.3"> +<tool id="hr2" name="HR2 formula" version="1.2.0"> <description> find a chemical formula from a accurate mass </description> @@ -34,9 +34,27 @@ #end if -regleOr "$regleOr" -atomes_basic "$atomes_basic" -atomes_sup "$atomes_sup" + + #if str($max_custom_atom_condition.max_custom_atom_choice) == "YES": + -C12_max_value "${max_custom_atom_condition.C12_max_value}" + -C13_max_value "${max_custom_atom_condition.C13_max_value}" + -H_max_value "${max_custom_atom_condition.H_max_value}" + -N_max_value "${max_custom_atom_condition.N_max_value}" + -O_max_value "${max_custom_atom_condition.O_max_value}" + -P_max_value "${max_custom_atom_condition.P_max_value}" + -S_max_value "${max_custom_atom_condition.S_max_value}" + -F_max_value "${max_custom_atom_condition.F_max_value}" + -Cl_max_value "${max_custom_atom_condition.Cl_max_value}" + -K_max_value "${max_custom_atom_condition.K_max_value}" + -Br_max_value "${max_custom_atom_condition.Br_max_value}" + -Na_max_value "${max_custom_atom_condition.Na_max_value}" + + #end if + -output1 "$variableMetadata" -outputView "$hr2ResView" -verbose "$verbose" ]]></command> + <!-- -customAtomValues "-C 0-${max_custom_atom_condition.C12_max_value} -1 0-${max_custom_atom_condition.C13_max_value} -H 0-${max_custom_atom_condition.H_max_value} -N 0-${max_custom_atom_condition.N_max_value} -O 0-${max_custom_atom_condition.O_max_value} -P 0-${max_custom_atom_condition.P_max_value} -S 0-${max_custom_atom_condition.S_max_value} -F 0-${max_custom_atom_condition.F_max_value} -L 0-${max_custom_atom_condition.Cl_max_value} -K 0-${max_custom_atom_condition.K_max_value} -B 0-${max_custom_atom_condition.Br_max_value} -A 0-${max_custom_atom_condition.Na_max_value}" --> <inputs> <conditional name="input_type"> @@ -104,6 +122,28 @@ <option value="A">Na</option> <option value="1">13C</option> </param> + <conditional name="max_custom_atom_condition"> + <param name="max_custom_atom_choice" label="Do you want to manage custom maximum number atoms?" type="select" display="radio" help="To work only with [13]C isotopes for example, use YES - ()Don't forget to select wanted atoms below)"> + <option value="NO" selected="true">NO</option> + <option value="YES">YES</option> + </param> + <when value="YES"> + <param name="C12_max_value" label="[12]C atom max number " type="integer" value="0" min="0" max="100" help="The maximum of [12]C you need to (should be between 0 and 100 atoms per structure). Default value is 0"/> + <param name="C13_max_value" label="[13]C atom max number " type="integer" value="40" min="0" max="100" help="The maximum of [13]C you need to (should be between 0 and 100 atoms per structure). Default value is 40"/> + <param name="H_max_value" label="[1]H atom max number " type="integer" value="200" min="0" max="200" help="The maximum of H you need to (should be between 0 and 200 atoms per structure). Default value is 200"/> + <param name="N_max_value" label="[15]N atom max number " type="integer" value="40" min="0" max="100" help="The maximum of N you need to (should be between 0 and 100 atoms per structure). Default value is 40"/> + <param name="O_max_value" label="[16]O atom max number " type="integer" value="70" min="0" max="100" help="The maximum of O you need to (should be between 0 and 100 atoms per structure). Default value is 70"/> + <param name="P_max_value" label="[31]P atom max number " type="integer" value="10" min="0" max="100" help="The maximum of P you need to (should be between 0 and 100 atoms per structure). Default value is 10"/> + <param name="S_max_value" label="[32]S atom max number " type="integer" value="10" min="0" max="100" help="The maximum of S you need to (should be between 0 and 100 atoms per structure). Default value is 10"/> + <param name="F_max_value" label="[19]F atom max number " type="integer" value="10" min="0" max="100" help="The maximum of F you need to (should be between 0 and 100 atoms per structure). Default value is 10"/> + <param name="Cl_max_value" label="[35]Cl atom max number " type="integer" value="10" min="0" max="100" help="The maximum of Cl you need to (should be between 0 and 100 atoms per structure). Default value is 10"/> + <param name="K_max_value" label="[13]K atom max number " type="integer" value="10" min="0" max="100" help="The maximum of K you need to (should be between 0 and 100 atoms per structure). Default value is 10"/> + <param name="Br_max_value" label="[80]Br atom max number " type="integer" value="10" min="0" max="100" help="The maximum of Br you need to (should be between 0 and 100 atoms per structure). Default value is 10"/> + <param name="Na_max_value" label="[23]Na atom max number " type="integer" value="10" min="0" max="100" help="The maximum of Na you need to (should be between 0 and 40 atoms per structure). Default value is 10"/> + </when> + <when value="NO"> + </when> + </conditional> <param name="verbose" type="select" label="Verbose level" display="radio" help=""> <option value="1" selected="true">Low</option> <option value="3" >High</option> @@ -118,7 +158,7 @@ <test> <param name="choice" value="NO"/> <param name="masse" value="175.125"/> - <param name="tolerance" value="1.0"/> + <param name="tol" value="1.0"/> <param name="mode" value="negative"/> <param name="qtCharge" value="1"/> <param name="atomes_basic" value="C,O,N,H"/> @@ -129,7 +169,7 @@ <test> <param name="choice" value="NO"/> <param name="masse" value="88.052"/> - <param name="tolerance" value="1.0"/> + <param name="tol" value="1.0"/> <param name="mode" value="neutral"/> <param name="qtCharge" value="1"/> <param name="atomes_basic" value="C,O,H"/> @@ -140,11 +180,12 @@ <test> <param name="choice" value="NO"/> <param name="masse" value="427.019898895"/> - <param name="tolerance" value="1.0"/> + <param name="tol" value="1.0"/> <param name="mode" value="neutral"/> <param name="qtCharge" value="1"/> <param name="atomes_basic" value="C,O,N,H,P"/> <param name="atomes_sup" value="S"/> + <param name="S_max_value" value="40"/> <param name="regleOr" value="NO"/> <param name="verbose" value="3"/> <output name="variableMetadata" file="out3.tabular"/>
--- a/hr2_manager.pl Tue Jan 17 10:31:32 2023 +0000 +++ b/hr2_manager.pl Wed Feb 15 15:57:49 2023 +0000 @@ -4,6 +4,7 @@ ## 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 +# - 15/02/2023 : New feature - optionnal managing max atom value #============================================================================= # Included modules and versions @@ -32,6 +33,8 @@ my ( $input_file, $line_header, $col_id, $col_mass ) = ( undef, undef, undef, undef ) ; # manage input option file of masses my ( $mass ) = ( undef ) ; # manage input option masses list my ( $tolerance, $mode, $charge, $has_golden_rules, $atomes, $atomes_basic ) = ( undef, undef, undef, undef, undef, undef ) ; # manage params +my ( $C13_max_value, $C12_max_value, $H_max_value, $N_max_value, $O_max_value, $P_max_value, $S_max_value, $F_max_value, $Cl_max_value, $K_max_value, $Br_max_value, $Na_max_value) = (undef, undef,undef,undef,undef,undef,undef,undef,undef,undef,undef,undef) ; +my ($customAtomValues) = (undef) ; my ( $output_csv, $output_html ) = ( undef, undef) ; # manage ouputs my $verbose = 2 ; @@ -50,6 +53,21 @@ "regleOr:s" => \$has_golden_rules, "atomes_basic:s"=> \$atomes_basic, # [basic atoms like CNOHP] "atomes_sup:s" => \$atomes, + #"customAtomValues:s"=> \$customAtomValues, + + "C12_max_value:i" => \$C12_max_value, # OPTIONNAL + "C13_max_value:i" => \$C13_max_value, + "H_max_value:i" => \$H_max_value, + "N_max_value:i" => \$N_max_value, + "O_max_value:i" => \$O_max_value, + "P_max_value:i" => \$P_max_value, + "S_max_value:i" => \$S_max_value, + "F_max_value:i" => \$F_max_value, + "Cl_max_value:i" => \$Cl_max_value, + "K_max_value:i" => \$K_max_value, + "Br_max_value:i" => \$Br_max_value, + "Na_max_value:i" => \$Na_max_value, + "output1:s" => \$output_csv, "outputView:s" => \$output_html, "verbose:i" => \$verbose, @@ -63,19 +81,19 @@ #============================================================================= # MAIN SCRIPT #============================================================================= -my %atomsConf = () ; -$atomsConf{'C'} = {'min' => 0, 'max' => 0} ; -$atomsConf{ 'H'} = {'min' => 0, 'max' => 0} ; -$atomsConf{ 'N'} = {'min' => 0, 'max' => 0} ; -$atomsConf{ 'O'} = {'min' => 0, 'max' => 0} ; -$atomsConf{ 'P'} = {'min' => 0, 'max' => 0} ; -$atomsConf{ 'S'} = {'min' => 0, 'max' => 0} ; -$atomsConf{ 'F'} = {'min' => 0, 'max' => 0} ; -$atomsConf{ 'L'} = {'min' => 0, 'max' => 0} ; -$atomsConf{ 'K'} = {'min' => 0, 'max' => 0} ; -$atomsConf{ 'B'} = {'min' => 0, 'max' => 0} ; -$atomsConf{ 'A'} = {'min' => 0, 'max' => 0} ; -$atomsConf{ '1'} = {'min' => 0, 'max' => 0} ; + +#print "CUSTOM C12: $C12_max_value\n" if (defined $C12_max_value) ; +#print "CUSTOM H: $H_max_value if (defined $H_max_value) ; +#print "CUSTOM N: $N_max_value if (defined $N_max_value) ; +#print "CUSTOM O: $O_max_value if (defined $O_max_value) ; +#print "CUSTOM P: $P_max_value if (defined $P_max_value) ; +#print "CUSTOM S: $S_max_value if (defined $S_max_value) ; +#print "CUSTOM F: $F_max_value if (defined $F_max_value) ; +#print "CUSTOM Cl: $Cl_max_value if (defined $Cl_max_value) ; +#print "CUSTOM K: $K_max_value if (defined $K_max_value) ; +#print "CUSTOM Br: $Br_max_value if (defined $Br_max_value) ; +#print "CUSTOM Na: $Na_max_value if (defined $Na_max_value) ; +#print "CUSTOM C13: $C13_max_value if (defined $C13_max_value) ; ## -------------- Conf file and verbose ------------------------ : my ( $CONF ) = ( undef ) ; ## verbose level is 3 for debugg @@ -104,18 +122,10 @@ #$hr_atoms_list = $ohr->manage_atoms(\$atomes, \$CONF->{'DEFAULT_ATOMS'}) ; ## DEPRECATED # manage atoms and their ranges with a hash structure -my $atomsCurrentConf = $ohr->manage_atoms_and_ranges(\%atomsConf, $CONF, $atomes_basic, $atomes) ; -#if ( defined $hr_atoms_list ) { -# ## implements range foreach atom -# foreach my $atom ( (split(",", $$hr_atoms_list )) ) { -# my $range_max = $CONF->{'DEFAULT_MAX'} ; # manage max value in case of -# if ( exists $CONF->{$atom} ) { $range_max = $CONF->{$atom} ; } -# my $ref_range = $ohr->manage_atom_and_range(\$atom, \$CONF->{'DEFAULT_MIN'}, \$range_max ) ; -# $hr_atoms_and_ranges .= $$ref_range ; ## concat ranges -# } -#} -#else { croak "No atom detected with input params\n" ; } +my $AtomsFullConf = $ohr->manageAtomsConf($CONF, $C12_max_value, $C13_max_value, $H_max_value, $N_max_value, $O_max_value, $P_max_value, $S_max_value, $F_max_value, $Cl_max_value, $K_max_value, $Br_max_value, $Na_max_value ) ; + +my $atomsCurrentConf = $ohr->manage_atoms_and_ranges($AtomsFullConf, $atomes_basic, $atomes) ; ## Parsing input file with masses/ids or unik mass : ## manage only one mass @@ -155,12 +165,11 @@ ## computes mass my $ohr_mode = lib::hr->new() ; my ( $exact_mass ) = $ohr_mode->manage_mode( \$mode, \$charge, \$CONF->{'electron'}, \$CONF->{'proton'}, \$mz ) ; - print "Current MZ send to HR\n" if $verbose == 3 ; - print Dumper $exact_mass if $verbose == 3 ; + print "Current MZ $$exact_mass send to HR\n" if $verbose == 3 ; ## build exe line my $ohr_exe = lib::hr->new() ; my $hr_cmd = $ohr_exe->config_hr_exe( \$CONF->{'HR2_EXE'}, \$tolerance, $exact_mass, \$has_golden_rules, \$atomsCurrentConf ) ; - print "$$hr_cmd\n" if $verbose == 3 ; + print "\t$$hr_cmd\n" if $verbose == 3 ; push(@{$hr_cmds}, $$hr_cmd) ; } @@ -225,7 +234,7 @@ ### VERBOSE OUTPUTs if ( $verbose == 3 ) { - print "-- Conf file contains :\n" ; + print "\n\n-- Conf file contains :\n" ; print Dumper $CONF ; print "-- Atoms input list :\n" ; print Dumper $atomes_basic ; @@ -340,4 +349,6 @@ version 5 : 09/12/2022 +version 6 : 15/02/2023 + =cut \ No newline at end of file
--- a/lib/hr.pm Tue Jan 17 10:31:32 2023 +0000 +++ b/lib/hr.pm Wed Feb 15 15:57:49 2023 +0000 @@ -14,8 +14,8 @@ our $VERSION = "1.0"; our @ISA = qw(Exporter); -our @EXPORT = qw( manage_atoms_and_ranges manage_atoms check_hr_exe manage_atom_and_range manage_tolerance manage_mode config_hr_exe ); -our %EXPORT_TAGS = ( ALL => [qw(manage_atoms_and_ranges manage_atoms check_hr_exe manage_atom_and_range manage_tolerance manage_mode config_hr_exe )] ); +our @EXPORT = qw( manageAtomsConf manage_atoms_and_ranges check_hr_exe manage_tolerance manage_mode config_hr_exe ); +our %EXPORT_TAGS = ( ALL => [qw(manageAtomsConf manage_atoms_and_ranges check_hr_exe manage_tolerance manage_mode config_hr_exe )] ); =head1 NAME @@ -54,6 +54,75 @@ } ### END of SUB + +=head2 METHOD manageAtomsConf + + ## Description : take all max atom values from CONF file and personal choice + ## Input : $confFile, $C12_max_value, $C13_max_value, $H_max_value, $N_max_value, $O_max_value, $P_max_value, $S_max_value, $F_max_value, $Cl_max_value, $K_max_value, $Br_max_value, $Na_max_value + ## Output : $atomFullConfig + ## Usage : my ( $atomFullConfig ) = manageAtomsConf ( $confFile, $C12_max_value, $C13_max_value, $H_max_value, $N_max_value, $O_max_value, $P_max_value, $S_max_value, $F_max_value, $Cl_max_value, $K_max_value, $Br_max_value, $Na_max_value ) ; + +=cut +## START of SUB +sub manageAtomsConf{ + ## Retrieve Values + my $self = shift ; + my ($confFile, $C12_max_value, $C13_max_value, $H_max_value, $N_max_value, $O_max_value, $P_max_value, $S_max_value, $F_max_value, $Cl_max_value, $K_max_value, $Br_max_value, $Na_max_value) = @_ ; + + my %atomFullConfig = () ; + $atomFullConfig{'C'} = {'min' => 0, 'max' => 0} ; + $atomFullConfig{'H'} = {'min' => 0, 'max' => 0} ; + $atomFullConfig{'N'} = {'min' => 0, 'max' => 0} ; + $atomFullConfig{'O'} = {'min' => 0, 'max' => 0} ; + $atomFullConfig{'P'} = {'min' => 0, 'max' => 0} ; + $atomFullConfig{'S'} = {'min' => 0, 'max' => 0} ; + $atomFullConfig{'F'} = {'min' => 0, 'max' => 0} ; + $atomFullConfig{'L'} = {'min' => 0, 'max' => 0} ; + $atomFullConfig{'K'} = {'min' => 0, 'max' => 0} ; + $atomFullConfig{'B'} = {'min' => 0, 'max' => 0} ; + $atomFullConfig{'A'} = {'min' => 0, 'max' => 0} ; + $atomFullConfig{'1'} = {'min' => 0, 'max' => 0} ; + + if (defined $C12_max_value) { $atomFullConfig{'C'}{'max'} = $C12_max_value ; } + else { $atomFullConfig{'C'}{'max'} = $confFile->{'C'} } + + if (defined $H_max_value) { $atomFullConfig{'H'}{'max'} = $H_max_value ; } + else { $atomFullConfig{'H'}{'max'} = $confFile->{'H'} } + + if (defined $N_max_value) { $atomFullConfig{'N'}{'max'} = $N_max_value ; } + else { $atomFullConfig{'N'}{'max'} = $confFile->{'N'} } + + if (defined $O_max_value) { $atomFullConfig{'O'}{'max'} = $O_max_value ; } + else { $atomFullConfig{'O'}{'max'} = $confFile->{'O'} } + + if (defined $P_max_value) { $atomFullConfig{'P'}{'max'} = $P_max_value ; } + else { $atomFullConfig{'P'}{'max'} = $confFile->{'DEFAULT_MAX'} } + + if (defined $S_max_value) { $atomFullConfig{'S'}{'max'} = $S_max_value ; } + else { $atomFullConfig{'S'}{'max'} = $confFile->{'DEFAULT_MAX'} } + + if (defined $F_max_value) { $atomFullConfig{'F'}{'max'} = $F_max_value ; } + else { $atomFullConfig{'F'}{'max'} = $confFile->{'DEFAULT_MAX'} } + + if (defined $Cl_max_value) { $atomFullConfig{'L'}{'max'} = $Cl_max_value ; } + else { $atomFullConfig{'L'}{'max'} = $confFile->{'DEFAULT_MAX'} } + + if (defined $K_max_value) { $atomFullConfig{'K'}{'max'} = $K_max_value ; } + else { $atomFullConfig{'K'}{'max'} = $confFile->{'DEFAULT_MAX'} } + + if (defined $Br_max_value) { $atomFullConfig{'B'}{'max'} = $Br_max_value ; } + else { $atomFullConfig{'B'}{'max'} = $confFile->{'DEFAULT_MAX'} } + + if (defined $Na_max_value) { $atomFullConfig{'A'}{'max'} = $Na_max_value ; } + else { $atomFullConfig{'A'}{'max'} = $confFile->{'DEFAULT_MAX'} } + + if (defined $C13_max_value) { $atomFullConfig{'1'}{'max'} = $C13_max_value ; } + else { $atomFullConfig{'1'}{'max'} = $confFile->{'DEFAULT_MAX'} } + + return (\%atomFullConfig) ; +} +### END of SUB + =head2 METHOD manage_atoms_and_ranges ## Description : allow from an initial config to add or delete atoms and their range @@ -66,90 +135,45 @@ sub manage_atoms_and_ranges { ## Retrieve Values my $self = shift ; - my ( $atomsconfig, $CONF, $atombasic, $atomsupp ) = @_; - my ( $atomcleanconfig ) = ( undef ) ; + my ( $atomFullconfig, $atombasic, $atomsupp ) = @_; + my ( $atomConfigCmd ) = ( undef ) ; + my %atomCurrentConfig = () ; + $atomCurrentConfig{'C'} = {'min' => 0, 'max' => 0} ; + $atomCurrentConfig{'H'} = {'min' => 0, 'max' => 0} ; + $atomCurrentConfig{'N'} = {'min' => 0, 'max' => 0} ; + $atomCurrentConfig{'O'} = {'min' => 0, 'max' => 0} ; + $atomCurrentConfig{'P'} = {'min' => 0, 'max' => 0} ; + $atomCurrentConfig{'S'} = {'min' => 0, 'max' => 0} ; + $atomCurrentConfig{'F'} = {'min' => 0, 'max' => 0} ; + $atomCurrentConfig{'L'} = {'min' => 0, 'max' => 0} ; + $atomCurrentConfig{'K'} = {'min' => 0, 'max' => 0} ; + $atomCurrentConfig{'B'} = {'min' => 0, 'max' => 0} ; + $atomCurrentConfig{'A'} = {'min' => 0, 'max' => 0} ; + $atomCurrentConfig{'1'} = {'min' => 0, 'max' => 0} ; # basic atoms case: foreach my $atom ( (split(",", $atombasic )) ) { - if ( exists $CONF->{$atom} ) { $atomsconfig->{$atom}{'max'} = $CONF->{$atom} ; } + if ( exists $atomFullconfig->{$atom}{'max'} ) { $atomCurrentConfig{$atom}{'max'} = $atomFullconfig->{$atom}{'max'} ; } else { print "*** $atom not recognized***\n" ; } } # suppl. atoms case foreach my $atom ( (split(",", $atomsupp )) ) { #print "*** $atom***\n" ; - if ( exists $atomsconfig->{$atom} ) { $atomsconfig->{$atom}{'max'} = $CONF->{'DEFAULT_MAX'} ; } + if ( exists $atomFullconfig->{$atom}{'max'} ) { $atomCurrentConfig{$atom}{'max'} = $atomFullconfig->{$atom}{'max'} ; } else { print "*** $atom not recognized***\n" ; } } # Create atoms and range parameters: - foreach my $selectedAtom ( keys %{$atomsconfig} ) { - $atomcleanconfig .= ' -'.$selectedAtom.' '.$atomsconfig->{$selectedAtom}{'min'}.'-'.$atomsconfig->{$selectedAtom}{'max'} ; + foreach my $selectedAtom ( keys %atomCurrentConfig ) { + $atomConfigCmd .= ' -'.$selectedAtom.' '.$atomCurrentConfig{$selectedAtom}{'min'}.'-'.$atomCurrentConfig{$selectedAtom}{'max'} ; } - return ($atomcleanconfig) ; + return ($atomConfigCmd) ; } ### END of SUB - - -=head2 METHOD manage_atoms ### DEPRECATED - - ## Description : controles atoms input list and prepare it like hr binary parameter - ## Input : $input_atoms, $conf_atoms - ## Output : $hr_atoms_param - ## Usage : my ( $hr_atoms_param ) = manage_atoms( $input_atoms, $conf_atoms ) ; - ### DEPRECATED - -=cut -## START of SUB -sub manage_atoms { ### DEPRECATED - ## Retrieve Values - my $self = shift ; - my ( $input_atoms, $conf_atoms ) = @_ ; - my $hr_atoms_param = undef ; - - if ( ( defined $$input_atoms ) and ( defined $$conf_atoms ) ) { - if ( ( $$input_atoms eq 'None' ) or ( $$input_atoms eq '' ) or ( $$input_atoms eq ' ' ) ) { $hr_atoms_param = $$conf_atoms ; } - elsif ( $$input_atoms =~ /[P|S|F|L|K|B|A|1|,]+/ ) { $hr_atoms_param = $$conf_atoms.','.$$input_atoms ; } - else { $hr_atoms_param = $$conf_atoms ; } - } ## END IF - elsif ( !defined $$input_atoms ) { $hr_atoms_param = $$conf_atoms ; } - elsif ( !defined $$conf_atoms ) { warn "hr module can't manage any atom list (undef values in conf)\n" ; } - else { warn "hr module musn't manage any atom list\n" ; } - - return(\$hr_atoms_param) ; -} -## END of SUB - -=head2 METHOD manage_atom_and_range ### DEPRECATED - - ## Description : build atom range with defined value in conf file - ## Input : $atom, $min, $max - ## Output : $hr_range - ## Usage : my ( ) = manage_atom_and_range( $atom, $min, $max ) ; - ### DEPRECATED - -=cut -## START of SUB -sub manage_atom_and_range { ### DEPRECATED - ## Retrieve Values - my $self = shift ; - my ( $atom, $min, $max ) = @_ ; - my $hr_range = undef ; - - if ( ( defined $$atom ) and ( defined $$min ) and ( defined $$max ) ) { - ## manage ragne like "-C 0-200" - $hr_range = ' -'.$$atom.' '.$$min.'-'.$$max ; - } ## END IF - else { - warn "Some argvts are missing to build the current atom range line\n" ; - } - return(\$hr_range) ; -} -## END of SUB - =head2 METHOD manage_tolerance ## Description : check range and format of tolerance @@ -757,7 +781,7 @@ =over 4 -=item :ALL is manage_atoms, check_hr_exe, manage_tolerance +=item :ALL is manageAtomsConf manage_atoms_and_ranges check_hr_exe manage_tolerance manage_mode config_hr_exe =back @@ -773,6 +797,6 @@ version 1 : 02 / 20 / 2014 -version 2 : ?? +version 2 : 02/ 15 / 2023 - Add personal max value for each atom manager methods, remove deprecated methods =cut \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input06.tabular Wed Feb 15 15:57:49 2023 +0000 @@ -0,0 +1,4 @@ +id mz formula +01 257.1704 [13]C11 H20 O5 N +02 305.1373 [13]C11 H20 O6 N S +03 344.2046 [13]C13 H23 O6 N4 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out6.html Wed Feb 15 15:57:49 2023 +0000 @@ -0,0 +1,1 @@ +<?xml version="1.0" encoding="UTF-8" ?><!DOCTYPE html><html lang="en"><head><meta charset="utf-8"><meta name="viewport" content="width=device-width, initial-scale=1.0"><meta name="description" content=""><meta name="author" content="INRAE Clermont-Ferrand"><title>Galaxy HR2 queries - All results</title><link rel="stylesheet" href="css.php" media="all"><link rel="stylesheet" href="https://cdn.rawgit.com/fgiacomoni/galaxy_utils/master/style/simplePagination.css"/><script src="https://ajax.googleapis.com/ajax/libs/jquery/1.7.2/jquery.min.js"></script><script src="https://cdn.rawgit.com/fgiacomoni/galaxy_utils/master/scripts/jquery.simplePagination.js"></script><style>body{padding-top:70px} div.lm-table-warning{font-size:1.4em;font-weight:bold;padding-right:25px;color:#21536a;margin-left:3px;}tr.green td{background-color:#eaf2d3;color:black;} tr.blank td{background-color:#9999CC;color:black;} table{font-family:\"Trebuchet MS\", Arial, Helvetica, sans-serif;width:100%;border-collapse:collapse;}table.detail, table.detail tr.parent, table.detail td, table.detail th, table.detail tr.category {border-collapse:collapse;border:1px solid #98bf21;}table.detail th {font-size:1.2em;text-align:center;padding-top:5px;padding-bottom:10px;background-color:#a7c942;color:#ffffff;}td {text-align:center;}footer{margin:50px 0;}</style><script>function test(pageNumber){var page="#page-id-"+pageNumber;$('.select').hide();$(page).show()}</script></head><body><div class="container"><div class="lm-table-warning">Results of HR elucidation queries - Mode used: positive / Charge: +1 / Mass tolerance: 1.0 / Composition: -S 0-10 -O 0-70 -L 0-0 -K 0-0 -P 0-10 -F 0-0 -N 0-40 -B 0-0 -A 0-0 -1 0-40 -C 0-0 -H 0-200</div><div id="detail_table_source" style="display:none"></div><p><div id="choose"></div><p><div id="ms_search_0" class="ms-search-table"></div><table id="detail_table" class="detail"><col style="width:20px;"><!-- Ids (m/z)--><col style="width:20px;"><!-- Mass (m/z)--><col style="width:20px;"><!-- Formula--><col style="width:60px;"><!-- cpd mw--><col style="width:50px;"><!-- delta--><col style="width:50px;"><!-- total--><thead><th>ID from input</th><th>Mass (m/z)</th><th>Formula</th><th>Compound MW (Da)</th><th>Delta</th><th>Total</th></thead><tbody class="select" id="page-id-1"><tr class="white"><td>01</td><td id="1">257.1704</td><td colspan="3"></td><td>2</td></tr><tr class="white"><td colspan="2"></td><td >iC11H19N1O5</td><td >256.1632259</td><td >-0.10</td><td colspan="1"></td></tr><tr class="white"><td colspan="2"></td><td >iC12H21O3P1</td><td >256.1630892</td><td >0.03</td><td colspan="1"></td></tr><tr class="green"><td>02</td><td id="2">305.1373</td><td colspan="3"></td><td>3</td></tr><tr class="green"><td colspan="2"></td><td >iC13H13N3O5</td><td >304.1291334</td><td >0.89</td><td colspan="1"></td></tr><tr class="green"><td colspan="2"></td><td >iC11H19N1O6S1</td><td >304.1302113</td><td >-0.19</td><td colspan="1"></td></tr><tr class="green"><td colspan="2"></td><td >iC12H21O4P1S1</td><td >304.1300745</td><td >-0.05</td><td colspan="1"></td></tr><tr class="white"><td>03</td><td id="3">344.2046</td><td colspan="3"></td><td>7</td></tr><tr class="white"><td colspan="2"></td><td >iC7H20N12O4</td><td >343.1965311</td><td >0.79</td><td colspan="1"></td></tr><tr class="white"><td colspan="2"></td><td >iC13H22N4O6</td><td >343.1975474</td><td >-0.22</td><td colspan="1"></td></tr><tr class="white"><td colspan="2"></td><td >iC8H22N11O2P1</td><td >343.1963943</td><td >0.93</td><td colspan="1"></td></tr><tr class="white"><td colspan="2"></td><td >iC14H24N3O4P1</td><td >343.1974106</td><td >-0.09</td><td colspan="1"></td></tr><tr class="white"><td colspan="2"></td><td >iC15H26N2O2P2</td><td >343.1972739</td><td >0.05</td><td colspan="1"></td></tr><tr class="white"><td colspan="2"></td><td >iC16H28N1P3</td><td >343.1971372</td><td >0.19</td><td colspan="1"></td></tr><tr class="white"><td colspan="2"></td><td >iC13H30O5S2</td><td >343.1970783</td><td >0.25</td><td colspan="1"></td></tr></tbody></table></div><div class="container"><hr><footer><div class="row"><div class="col-lg-12"><p><a href="http://jigsaw.w3.org/css-validator/check/referer" target="_blank"><img style="border:0;width:88px;height:31px" src="http://jigsaw.w3.org/css-validator/images/vcss-blue" alt="Valid CSS!" /></a></p><p>Copyright © INRAE, N Paulhe, L Pavot, F Giacomoni 2023</a></p></div> </div></footer></div><script language="javascript">$(function() {$('#choose').pagination({items: 1,itemsOnPage: 1,currentPage: 1,onInit: function () { test(1); },cssStyle: 'light-theme',onPageClick: function(pageNumber){test(pageNumber)}}).pagination('redraw');});</script></body></html> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out6.tabular Wed Feb 15 15:57:49 2023 +0000 @@ -0,0 +1,4 @@ +id mz formula hr2 +01 257.1704 "[13]C11 H20 O5 N" -0.10::(iC11H19N1O5)::256.1632259|0.03::(iC12H21O3P1)::256.1630892 +02 305.1373 "[13]C11 H20 O6 N S" 0.89::(iC13H13N3O5)::304.1291334|-0.19::(iC11H19N1O6S1)::304.1302113|-0.05::(iC12H21O4P1S1)::304.1300745 +03 344.2046 "[13]C13 H23 O6 N4" 0.79::(iC7H20N12O4)::343.1965311|-0.22::(iC13H22N4O6)::343.1975474|0.93::(iC8H22N11O2P1)::343.1963943|-0.09::(iC14H24N3O4P1)::343.1974106|0.05::(iC15H26N2O2P2)::343.1972739|0.19::(iC16H28N1P3)::343.1971372|0.25::(iC13H30O5S2)::343.1970783