| Previous changeset 0:86296c048e46 (2019-06-05) Next changeset 2:23970530a518 (2023-01-17) |
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Commit message:
master branch Updating with tag :CI_COMMIT_TAG - - Fxx |
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modified:
HR2.xml README.txt conf_hr2.cfg hr2_manager.pl hr_out.tmpl lib/HR2_v1.04.cpp lib/hr.pm static/images/hr2.png t/hr2_managerTest.t t/lib/hrTest.pm test-data/out1.tabular test-data/out2.tabular |
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added:
Dockerfile test-data/out3.tabular |
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removed:
test-data/out1.html test-data/out2.html |
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| diff -r 86296c048e46 -r e2cbcf6fa22e Dockerfile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Dockerfile Sun Dec 11 17:16:43 2022 +0000 |
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| @@ -0,0 +1,41 @@ +#FROM pfem/perlfull +FROM python:3.8-buster + +# set author +LABEL maintainer="franck.giacomoni@inrae.fr" + +ENV PLANEMO_VENV_LOCATION /planemo-venv +ENV CONDA /tmp/conda + + +RUN apt-get update &&\ + apt-get upgrade -y &&\ + apt-get install --no-install-recommends --yes build-essential \ + git \ + libgl1-mesa-glx \ + libegl1-mesa \ + libxrandr2 \ + libxss1 \ + libxcursor1 \ + libxcomposite1 \ + libasound2 \ + libxi6 \ + libxtst6 \ +# python3 \ +# python3-pip \ + python-virtualenv && \ + pip install virtualenv && \ + python3 -m virtualenv "$PLANEMO_VENV_LOCATION" && \ + . "$PLANEMO_VENV_LOCATION"/bin/activate && \ + pip install --upgrade pip setuptools && \ + pip install planemo numpy && \ + pip install -U planemo && \ + #planemo conda_init --conda_prefix "$CONDA" && \ + apt-get autoremove -y && \ + apt-get clean && \ + rm -rf /var/lib/apt/lists/* && \ + rm -rf /tmp/* && \ + rm -rf /var/tmp/* && \ + rm -rf /usr/bin/X11 ; + +CMD [] \ No newline at end of file |
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| diff -r 86296c048e46 -r e2cbcf6fa22e HR2.xml --- a/HR2.xml Wed Jun 05 09:40:20 2019 -0400 +++ b/HR2.xml Sun Dec 11 17:16:43 2022 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="hr2" name="HR2 formula" version="1.1.1.7"> +<tool id="hr2" name="HR2 formula" version="1.1.2"> <description> find a chemical formula from a accurate mass </description> @@ -33,7 +33,7 @@ -charge "${mode_condition.qtCharge}" #end if - -regleOr "$regleOr" -atomes "$atomes_basic" -atomessup "$atomes_sup" + -regleOr "$regleOr" -atomes_basic "$atomes_basic" -atomes_sup "$atomes_sup" -output1 "$variableMetadata" -outputView "$hr2ResView" -verbose "$verbose" ]]></command> @@ -124,8 +124,7 @@ <param name="atomes_basic" value="C,O,N,H"/> <param name="regleOr" value="NO"/> <param name="verbose" value="3"/> - <output name="variableMetadata" file="out_test01.tabular"/> - <output name="hr2ResView" file="out_test01.html"/> + <output name="variableMetadata" file="out1.tabular"/> </test> <test> <param name="choice" value="NO"/> @@ -136,8 +135,19 @@ <param name="atomes_basic" value="C,O,H"/> <param name="regleOr" value="NO"/> <param name="verbose" value="3"/> - <output name="variableMetadata" file="out_test02.tabular"/> - <output name="hr2ResView" file="out_test02.html"/> + <output name="variableMetadata" file="out2.tabular"/> + </test> + <test> + <param name="choice" value="NO"/> + <param name="masse" value="427.019898895"/> + <param name="tolerance" 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="regleOr" value="NO"/> + <param name="verbose" value="3"/> + <output name="variableMetadata" file="out3.tabular"/> </test> </tests> |
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| diff -r 86296c048e46 -r e2cbcf6fa22e hr2_manager.pl --- a/hr2_manager.pl Wed Jun 05 09:40:20 2019 -0400 +++ b/hr2_manager.pl Sun Dec 11 17:16:43 2022 +0000 |
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| @@ -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 |
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| diff -r 86296c048e46 -r e2cbcf6fa22e lib/hr.pm --- a/lib/hr.pm Wed Jun 05 09:40:20 2019 -0400 +++ b/lib/hr.pm Sun Dec 11 17:16:43 2022 +0000 |
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| @@ -72,12 +72,15 @@ # basic atoms case: foreach my $atom ( (split(",", $atombasic )) ) { if ( exists $CONF->{$atom} ) { $atomsconfig->{$atom}{'max'} = $CONF->{$atom} ; } + else { print "*** $atom not recognized***\n" ; } } # suppl. atoms case foreach my $atom ( (split(",", $atomsupp )) ) { print "*** $atom***\n" ; - if ( exists $atomsconfig->{$atom} ) { $atomsconfig->{$atom} = $CONF->{'DEFAULT_MAX'} ; } + if ( exists $atomsconfig->{$atom} ) { $atomsconfig->{$atom}{'max'} = $CONF->{'DEFAULT_MAX'} ; } + else { print "*** $atom not recognized***\n" ; } + } # Create atoms and range parameters: |
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| diff -r 86296c048e46 -r e2cbcf6fa22e test-data/out1.html --- a/test-data/out1.html Wed Jun 05 09:40:20 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0" encoding="UTF-8" ?> -<!DOCTYPE html> -<html lang="en"> - <head><meta charset="utf-8"><meta name="viewport" content="width=device-width, initial-scale=1.0"><meta name="description" content=""><meta name="author" content="INRA de Clermont-Ferrand"><title>Galaxy HR2 queries - All results</title><link rel="stylesheet" href="css.php" media="all"><link rel="stylesheet" href="https://cdn.rawgit.com/fgiacomoni/galaxy_utils/master/style/simplePagination.css"/><script src="https://ajax.googleapis.com/ajax/libs/jquery/1.7.2/jquery.min.js"></script><script src="https://cdn.rawgit.com/fgiacomoni/galaxy_utils/master/scripts/jquery.simplePagination.js"></script><style>body{padding-top:70px} div.lm-table-warning{font-size:1.4em;font-weight:bold;padding-right:25px;color:#21536a;margin-left:3px;}tr.green td{background-color:#eaf2d3;color:black;} tr.blank td{background-color:#9999CC;color:black;} table{font-family:\"Trebuchet MS\", Arial, Helvetica, sans-serif;width:100%;border-collapse:collapse;}table.detail, table.detail tr.parent, table.detail td, table.detail th, table.detail tr.category {border-collapse:collapse;border:1px solid #98bf21;}table.detail th {font-size:1.2em;text-align:center;padding-top:5px;padding-bottom:10px;background-color:#a7c942;color:#ffffff;}td.ca {text-align:center;}footer{margin:50px 0;}</style><script>function test(pageNumber){var page="#page-id-"+pageNumber;$('.select').hide();$(page).show()}</script></head> - <body><div class="container"><div class="lm-table-warning">Results of HR elucidation queries - Mode used: negative / Charge: +1 / Mass tolerance: 1.0 / Composition: -C 0-100 -A 0-0 -1 0-0 -B 0-0 -K 0-0 -N 0-40 -P 0-0 -S 0-0 -O 0-70 -H 0-200 -F 0-0 -L 0-0</div><div id="detail_table_source" style="display:none"></div><p><div id="choose"></div><p><div id="ms_search_0" class="ms-search-table"></div><table id="detail_table" class="detail"><col style="width:20px;"><!-- Ids (m/z)--><col style="width:20px;"><!-- Mass (m/z)--><col style="width:20px;"><!-- Formula--><col style="width:60px;"><!-- cpd mw--><col style="width:50px;"><!-- delta--><col style="width:50px;"><!-- total--><thead><th>ID from input</th><th>Mass (m/z)</th><th>Formula</th><th>Compound MW (Da)</th><th>Delta</th><th>Total</th></thead><tbody class="select" id="page-id-1"><tr class="white"><td class="ca" >mass_01</td><td id="1" class="ca" >175.125</td><td class="ca" colspan="3"></td><td class="ca" >1</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">C11H16N2</td><td class="ca">176.1313485</td><td class="ca">0.93</td><td class="ca" colspan="1"></td></tr></tbody></table></div><div class="container"><hr><footer><div class="row"><div class="col-lg-12"><p><a href="http://jigsaw.w3.org/css-validator/check/referer" target="_blank"><img style="border:0;width:88px;height:31px" src="http://jigsaw.w3.org/css-validator/images/vcss-blue" alt="Valid CSS!" /></a></p><p>Copyright © INRA, N Paulhe, F Giacomoni 2014</a></p></div> </div></footer></div><script language="javascript">$(function() {$('#choose').pagination({items: 1,itemsOnPage: 1,currentPage: 1,onInit: function () { test(1); },cssStyle: 'light-theme',onPageClick: function(pageNumber){test(pageNumber)}}).pagination('redraw');});</script></body> -</html> \ No newline at end of file |
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| diff -r 86296c048e46 -r e2cbcf6fa22e test-data/out2.html --- a/test-data/out2.html Wed Jun 05 09:40:20 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0" encoding="UTF-8" ?> -<!DOCTYPE html> -<html lang="en"> - <head><meta charset="utf-8"><meta name="viewport" content="width=device-width, initial-scale=1.0"><meta name="description" content=""><meta name="author" content="INRA de Clermont-Ferrand"><title>Galaxy HR2 queries - All results</title><link rel="stylesheet" href="css.php" media="all"><link rel="stylesheet" href="https://cdn.rawgit.com/fgiacomoni/galaxy_utils/master/style/simplePagination.css"/><script src="https://ajax.googleapis.com/ajax/libs/jquery/1.7.2/jquery.min.js"></script><script src="https://cdn.rawgit.com/fgiacomoni/galaxy_utils/master/scripts/jquery.simplePagination.js"></script><style>body{padding-top:70px} div.lm-table-warning{font-size:1.4em;font-weight:bold;padding-right:25px;color:#21536a;margin-left:3px;}tr.green td{background-color:#eaf2d3;color:black;} tr.blank td{background-color:#9999CC;color:black;} table{font-family:\"Trebuchet MS\", Arial, Helvetica, sans-serif;width:100%;border-collapse:collapse;}table.detail, table.detail tr.parent, table.detail td, table.detail th, table.detail tr.category {border-collapse:collapse;border:1px solid #98bf21;}table.detail th {font-size:1.2em;text-align:center;padding-top:5px;padding-bottom:10px;background-color:#a7c942;color:#ffffff;}td.ca {text-align:center;}footer{margin:50px 0;}</style><script>function test(pageNumber){var page="#page-id-"+pageNumber;$('.select').hide();$(page).show()}</script></head> - <body><div class="container"><div class="lm-table-warning">Results of HR elucidation queries - Mode used: neutral / Charge: +1 / Mass tolerance: 1.0 / Composition: -K 0-0 -B 0-0 -F 0-0 -H 0-200 -L 0-0 -P 0-0 -C 0-100 -A 0-0 -1 0-0 -O 0-70 -S 0-0 -N 0-0</div><div id="detail_table_source" style="display:none"></div><p><div id="choose"></div><p><div id="ms_search_0" class="ms-search-table"></div><table id="detail_table" class="detail"><col style="width:20px;"><!-- Ids (m/z)--><col style="width:20px;"><!-- Mass (m/z)--><col style="width:20px;"><!-- Formula--><col style="width:60px;"><!-- cpd mw--><col style="width:50px;"><!-- delta--><col style="width:50px;"><!-- total--><thead><th>ID from input</th><th>Mass (m/z)</th><th>Formula</th><th>Compound MW (Da)</th><th>Delta</th><th>Total</th></thead><tbody class="select" id="page-id-1"><tr class="white"><td class="ca" >mass_01</td><td id="1" class="ca" >88.052</td><td class="ca" colspan="3"></td><td class="ca" >1</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">C4H8O2</td><td class="ca">88.0524295</td><td class="ca">-0.43</td><td class="ca" colspan="1"></td></tr></tbody></table></div><div class="container"><hr><footer><div class="row"><div class="col-lg-12"><p><a href="http://jigsaw.w3.org/css-validator/check/referer" target="_blank"><img style="border:0;width:88px;height:31px" src="http://jigsaw.w3.org/css-validator/images/vcss-blue" alt="Valid CSS!" /></a></p><p>Copyright © INRA, N Paulhe, F Giacomoni 2014</a></p></div> </div></footer></div><script language="javascript">$(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 |
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| diff -r 86296c048e46 -r e2cbcf6fa22e test-data/out3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out3.tabular Sun Dec 11 17:16:43 2022 +0000 |
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| @@ -0,0 +1,19 @@ +ID MASS_SUBMIT CPD_FORMULA CPD_MW DELTA +mass_01 427.019898895 C18H10N3O8P1 427.0205509 -0.65 +mass_01 427.019898895 C13H7N11O3P2 427.0208564 -0.96 +mass_01 427.019898895 C12H11N7O7P2 427.0195190 0.38 +mass_01 427.019898895 C22H12N3O1P3 427.0193219 0.58 +mass_01 427.019898895 C13H5N11O5S1 427.0195830 0.32 +mass_01 427.019898895 C10H14N5O10P1S1 427.0198990 -0.00 +mass_01 427.019898895 C20H15N1O4P2S1 427.0197019 0.20 +mass_01 427.019898895 C21H9N5O2S2 427.0197659 0.13 +mass_01 427.019898895 C13H15N7O2P2S2 427.0203874 -0.49 +mass_01 427.019898895 C12H19N3O6P2S2 427.0190500 0.85 +mass_01 427.019898895 C10H24N1O7P3S2 427.0207034 -0.80 +mass_01 427.019898895 C14H9N11S3 427.0204514 -0.55 +mass_01 427.019898895 C13H13N7O4S3 427.0191140 0.78 +mass_01 427.019898895 C11H18N5O5P1S3 427.0207674 -0.87 +mass_01 427.019898895 C10H22N1O9P1S3 427.0194300 0.47 +mass_01 427.019898895 C21H17N1O1S4 427.0192969 0.60 +mass_01 427.019898895 C13H23N3O1P2S4 427.0199184 -0.02 +mass_01 427.019898895 C11H26N1O4P1S5 427.0202984 -0.40 |
