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Changeset 21:63ba1cb240b7 (2019-02-14)

Previous changeset 20:b5a1d5e43685 (2019-01-23) Next changeset 22:453fbe98925a (2020-11-20)

Commit message:
Prod branch Updating - - Fxx

modified:
hmdb.tmpl
lib/hmdb.pm
test-data/out_test01.html
test-data/out_test02.html
test-data/out_test02.tabular
test-data/out_test02.txt
test-data/out_test03.html
test-data/out_test03.tabular
test-data/out_test03.txt
wsdl_hmdb.pl
wsdl_hmdb.xml

added:
test-data/out_test04.html
test-data/out_test04.tabular
test-data/out_test04.txt

diff -r b5a1d5e43685 -r 63ba1cb240b7 hmdb.tmpl
--- a/hmdb.tmpl Wed Jan 23 07:49:34 2019 -0500
+++ b/hmdb.tmpl Thu Feb 14 08:36:52 2019 -0500

b'@@ -1,1 +1,1 @@\n-<?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 HMDB queries - All results</title><link rel="stylesheet" type="text/css" href="css.php" media="all"><link rel="stylesheet" type="text/css" href="<TMPL_VAR NAME=CSS_GALAXY_PATH>/simplePagination.css"/><script src="https://ajax.googleapis.com/ajax/libs/jquery/1.7.2/jquery.min.js"></script><script src="<TMPL_VAR NAME=JS_GALAXY_PATH>/jquery.simplePagination.js"></script><style type="text/css">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 HMDB queries - <TMPL_VAR NAME=CONDITIONS></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:30px;"><col style="width:30px;"><col style="width:120px;"><col style="width:50px;"><col style="width:40px;"><col style="width:60px;"><col style="width:50px;"><col style="width:20px;"><col style="width:60px;"><col style="width:50px;"><col style="width:120px;"><col style="width:20;"><thead><th>ID from input</th><th>Mass (m/z)</th><th>Metabolite_Name</th><th>Compound_ID</th><th>Formula</th><th>Compound MW (Da)</th><th>Adduct</th><th>Adduct_Type</th><th>Adduct MW (Da)</th><th>Delta</th><th>InChI Identifier</th><th>Predicted LogP (ALOGPS)</th></thead><TMPL_LOOP NAME=PAGES><tbody class="select" id="page-id-<TMPL_VAR NAME=PAGE_NB>"><TMPL_LOOP NAME=MASSES><tr class="<TMPL_VAR NAME=MZ_COLOR>"><td class="ca" ><TMPL_VAR NAME=MASSES_ID_QUERY></td><td id="<TMPL_VAR NAME=MASSES_NB>" class="ca" ><TMPL_VAR NAME=MASSES_MZ_QUERY></td><td class="ca" colspan="10"></td></tr><TMPL_LOOP NAME=ENTRIES><tr class="<TMPL_VAR NAME=ENTRY_COLOR>"><td class="ca" colspan="2"></td><td class="ca"><TMPL_VAR NAME=ENTRY_ENTRY_NAME></td><td class="ca"><a href="http://www.hmdb.ca/metabolites/<TMPL_VAR NAME=ENTRY_ENTRY_ID2>" target="_blank" class="btn"><TMPL_VAR NAME=ENTRY_ENTRY_ID></a></td><td class="ca"><TMPL_VAR NAME=ENTRY_FORMULA></td><td class="ca"><TMPL_VAR NAME=ENTRY_CPD_MZ></td><td class="ca"><TMPL_VAR NAME=ENTRY_ADDUCT></td><td class="ca"><TMPL_VAR NAME=ENTRY_ADDUCT_TYPE></td><td class="ca"><TMPL_VAR NAME=ENTRY_ADDUCT_MZ></td><td class="ca"><TMPL_VAR NAME=ENTRY_DELTA></td><td class="ca"><TMPL_VAR NAME=ENTRY_ENTRY_INCHI></td><td class="ca"><TMPL_VAR NAME=ENTRY_ENTRY_LOGP></td></tr></TMPL_LOOP></TMPL_LOOP></tbody></TMPL_LOOP></table></div><div class="container"><hr><footer><div class="row"> <div class="col-lg-12"><p>Copyright © INRA, N Paulhe, F Giacomoni 2014 </p> </div> </div> </footer></div><script language="javascript">$(function() {$(\'#choose\').pagination({items: <TMPL_VAR NAME=PAGES_NB>,itemsOnPage: 1,currentPage: 1,onInit: function () { test(1); },cssStyle'..b'device-width, initial-scale=1.0"><meta name="description" content=""><meta name="author" content="INRA de Clermont-Ferrand"><title>Galaxy HMDB queries - All results</title><link rel="stylesheet" type="text/css" href="css.php" media="all"><link rel="stylesheet" type="text/css" href="<TMPL_VAR NAME=CSS_GALAXY_PATH>/simplePagination.css"/><script src="https://ajax.googleapis.com/ajax/libs/jquery/1.7.2/jquery.min.js"></script><script src="<TMPL_VAR NAME=JS_GALAXY_PATH>/jquery.simplePagination.js"></script><style type="text/css">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 HMDB queries - <TMPL_VAR NAME=CONDITIONS></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:30px;"><col style="width:30px;"><col style="width:120px;"><col style="width:50px;"><col style="width:40px;"><col style="width:60px;"><col style="width:50px;"><col style="width:20px;"><col style="width:60px;"><col style="width:50px;"><col style="width:120px;"><col style="width:20;"><thead><th>ID from input</th><th>Mass (m/z)</th><th>Metabolite_Name</th><th>Compound_ID</th><th>Formula</th><th>Compound MW (Da)</th><th>Adduct</th><th>Adduct type</th><th>Adduct MW (Da)</th><th>Delta (ppm)</th><th>InChI Identifier</th><th>Predicted LogP (ALOGPS)</th></thead><TMPL_LOOP NAME=PAGES><tbody class="select" id="page-id-<TMPL_VAR NAME=PAGE_NB>"><TMPL_LOOP NAME=MASSES><tr class="<TMPL_VAR NAME=MZ_COLOR>"><td class="ca" ><TMPL_VAR NAME=MASSES_ID_QUERY></td><td id="<TMPL_VAR NAME=MASSES_NB>" class="ca" ><TMPL_VAR NAME=MASSES_MZ_QUERY></td><td class="ca" colspan="10"></td></tr><TMPL_LOOP NAME=ENTRIES><tr class="<TMPL_VAR NAME=ENTRY_COLOR>"><td class="ca" colspan="2"></td><td class="ca"><TMPL_VAR NAME=ENTRY_ENTRY_NAME></td><td class="ca"><a href="http://www.hmdb.ca/metabolites/<TMPL_VAR NAME=ENTRY_ENTRY_ID2>" target="_blank" class="btn"><TMPL_VAR NAME=ENTRY_ENTRY_ID></a></td><td class="ca"><TMPL_VAR NAME=ENTRY_FORMULA></td><td class="ca"><TMPL_VAR NAME=ENTRY_CPD_MZ></td><td class="ca"><TMPL_VAR NAME=ENTRY_ADDUCT></td><td class="ca"><TMPL_VAR NAME=ENTRY_ADDUCT_TYPE></td><td class="ca"><TMPL_VAR NAME=ENTRY_ADDUCT_MZ></td><td class="ca"><TMPL_VAR NAME=ENTRY_DELTA></td><td class="ca"><TMPL_VAR NAME=ENTRY_ENTRY_INCHI></td><td class="ca"><TMPL_VAR NAME=ENTRY_ENTRY_LOGP></td></tr></TMPL_LOOP></TMPL_LOOP></tbody></TMPL_LOOP></table></div><div class="container"><hr><footer><div class="row"> <div class="col-lg-12"><p>Copyright © INRA, N Paulhe, F Giacomoni 2014 </p> </div> </div> </footer></div><script language="javascript">$(function() {$(\'#choose\').pagination({items: <TMPL_VAR NAME=PAGES_NB>,itemsOnPage: 1,currentPage: 1,onInit: function () { test(1); },cssStyle: \'light-theme\',onPageClick: function(pageNumber){test(pageNumber)}}).pagination(\'redraw\');});</script></body></html>\n\\ No newline at end of file\n'

diff -r b5a1d5e43685 -r 63ba1cb240b7 lib/hmdb.pm
--- a/lib/hmdb.pm Wed Jan 23 07:49:34 2019 -0500
+++ b/lib/hmdb.pm Thu Feb 14 08:36:52 2019 -0500

[

b'@@ -144,6 +144,45 @@\n }\r\n ## END of SUB\r\n \r\n+\r\n+=head2 METHOD prepareAdductListFormat\r\n+\r\n+\t## Description : prepare a adduct list well formatted for https queries\r\n+\t## Input : $adductString\r\n+\t## Output : $formattedAdductString\r\n+\t## Usage : my ( $formattedAdductString ) = prepareAdductListFormat ( $adductString ) ;\r\n+\t\r\n+=cut\r\n+## START of SUB\r\n+sub prepareAdductListFormat {\r\n+ ## Retrieve Values\r\n+ my $self = shift ;\r\n+ my ( $adductString ) = @_;\r\n+ my ( $formattedAdductString, $nbAdducts ) = ( undef, 0 ) ;\r\n+ \r\n+ ## Formatting is converting [+] in %2B, [-] as - and [,] in converted space as \'M%2BH%202M%2BH\' for \'M+H,2M+2H\'\r\n+# print "\\t$adductString ..." ;\r\n+\r\n+\tif (defined $adductString) {\r\n+\t\t\r\n+\t\t## counting selected adducts\r\n+\t\t$nbAdducts = scalar( my @adducts = ( split (/,/, $adductString) ) ) ;\r\n+\t\t\r\n+\t\t## Converting string into http post format\r\n+\t\t$adductString =~ s/\\+/%2B/g ;\r\n+\t\t$adductString =~ s/,/%20/g ;\r\n+\t\t$formattedAdductString = $adductString ;\r\n+\t}\r\n+\telse {\r\n+\t\twarn "\\t[WARN]the adduct type is not defined...It will set to \'Unknown\'\\n" ;\r\n+\t}\r\n+\t\r\n+#\tprint "->$formattedAdductString\\n" ;\r\n+\t\r\n+ return ($formattedAdductString, $nbAdducts) ;\r\n+}\r\n+### END of SUB\r\n+\r\n =head2 METHOD test_matches_from_hmdb_ua DEPRECATED\r\n \r\n \t## Description : [DEPRECATED]test a single query with tests parameters on hmdb - get the status of the complete server infra.\r\n@@ -232,10 +271,10 @@\n \t\t\tprint "\\tTesting HMDB server connexion ($top time(s) )...\\n" ;\r\n \t\t\t$mech->post(\r\n \t\t\t\t"http://specdb.wishartlab.com/ms/search.csv",\r\n-\t\t \tContent => \'utf8=TRUE&mode=positive&query_masses=420.159317&tolerance=0.000001&database=HMDB&commit=Download Results As CSV\'\r\n+\t\t \tContent => \'utf8=TRUE&mode=positive&adduct_type=M%2BH%202M%2BH&query_masses=125.0089&tolerance=0.001&database=HMDB&commit=Download Results As CSV\'\r\n \t\t\t);\r\n \t\t\t\r\n-\t\t#\tprint Dumper $mech ;\r\n+#\t\tprint Dumper $mech ;\r\n \t\t\t$statusPostLine = $mech->status() ;\r\n \t\t}\r\n \t\telse {\r\n@@ -243,7 +282,6 @@\n \t\t}\r\n \t\t$top++ ;\r\n \t}## End While\r\n-\t\r\n \treturn (\\$statusPostLine) ;\r\n }\r\n ## END of SUB\r\n@@ -278,7 +316,10 @@\n \t\t\tcroak "Internal Server Error $$status..." ;\r\n \t\t}\r\n \t}\r\n- \tif ( $$status == 200 ) { print "\\tThe HMDB server returns that your request (connexion test) was fulfilled\\n" ; }\r\n+ \tif ( $$status == 200 ) { \r\n+ \t\tprint "\\tThe HMDB server returns that your request (connexion test) was fulfilled\\n" ; \r\n+ \t\tprint "\\tAll searches should be sent successfully to HMDB...(Set verbose to \\"High\\" for more information!)\\n" ;\r\n+ \t}\r\n }\r\n \r\n return (1) ;\r\n@@ -342,7 +383,7 @@\n =head2 METHOD getMatchesFromHmdbWithUA\r\n \r\n \t## Description : HMDB querying via an user agent with parameters : mz, delta and molecular species (neutral, pos, neg)\r\n-\t## Input : $mass, $delta, $mode\r\n+\t## Input : $mass, $delta, $mode, adducts\r\n \t## Output : $results\r\n \t## Usage : my ( $results ) = getMatchesFromHmdbWithUA( $mass, $delta, $mode ) ;\r\n \t\r\n@@ -351,7 +392,7 @@\n sub getMatchesFromHmdbWithUA {\r\n \t## Retrieve Values\r\n my $self = shift ;\r\n- my ( $masses, $delta, $mode ) = @_ ;\r\n+ my ( $masses, $delta, $mode, $adducts ) = @_ ;\r\n \r\n my @page = () ;\r\n \r\n@@ -381,11 +422,17 @@\n \t\t$mech->add_header(\'Referer\', \'http://www.hmdb.ca/spectra/ms/search\');\r\n \t\t$mech->add_header(\'Accept\', \'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8\');\r\n \t}\r\n+\t## adduct format is adduct_type=M%2BH%202M%2BH\r\n \t\r\n+\tif ( (!defined $adducts) or ( $adducts eq \'\') ) {\r\n+\t\t$adducts = \'Unknown\' ;\r\n+\t}\r\n+\t\t\r\n \tmy $res = $mech->post(\r\n \t\t"http://specdb.wishartlab.com/ms/search.csv",\r\n \tContent => \'utf8=TRUE&mode=\'\r\n- \t\t.$mode.\'&query_masses=\'\r\n+ \t\t.$mode.\'&adduct_type=\'\r\n+ \t\t.$adducts.\'&query_masses=\'\r\n \t\t.$masses.\'&tolerance=\'\r\n \t\t.$delta.\'&database=HMDB&commit=Download Results As CSV\'\r\n \t);\r\n@@ -473,7 +520,7 @@\n foreach (@{$masses}) {\r\n \tif ($result_by_entry{$_}) { \r\n \t\r\n- \t\t## cut all entries > $ma'..b' IF defined ids\r\n else {\r\n \twarn "The HMDB ids list from HMDB is empty - No metabocard found\\n" ;\r\n }\r\n@@ -715,7 +761,7 @@\n \r\n =head2 METHOD map_suppl_data_on_hmdb_results\r\n \r\n-\t## Description : map supplementary data with already collected results with hmdb search\r\n+\t## Description : map supplementary data with already collected results with hmdb search - delete the entry if hmdb card doesn\'t exist...\r\n \t## Input : $results, $features\r\n \t## Output : $results\r\n \t## Usage : my ( $results ) = map_suppl_data_on_hmdb_results ( $results, $features ) ;\r\n@@ -726,52 +772,64 @@\n ## Retrieve Values\r\n my $self = shift ;\r\n my ( $results, $features ) = @_;\r\n- my ( @more_results ) = ( () ) ;\r\n+ my ( @moreResults ) = ( () ) ;\r\n \r\n- @more_results = @{$results} ; ## Dump array ref to map\r\n- \r\n- foreach my $result (@more_results) {\r\n+ foreach my $result (@{$results}) {\r\n+ \t\r\n+ \tmy @newResult = () ;\r\n \t\r\n- \tforeach my $entries (@{$result}) {\r\n+ \tforeach my $entry (@{$result}) {\r\n \t\t\r\n- \t\tif ( ($entries->{\'ENTRY_ENTRY_ID\'}) and ($entries->{\'ENTRY_ENTRY_ID\'} ne \'\' ) ) {\r\n- \t\t\t## check that we have a ID for mapping\r\n- \t\t\tmy $current_id = $entries->{\'ENTRY_ENTRY_ID\'} ;\r\n- \t\t\tif ($features->{"$current_id"}) {\r\n+ \t\tif ( ($entry->{\'ENTRY_ENTRY_ID\'}) and ($entry->{\'ENTRY_ENTRY_ID\'} ne \'\' ) ) {\r\n+ \t\t\t\r\n+ \t\t\tmy $current_id = $entry->{\'ENTRY_ENTRY_ID\'} ;\r\n+ \t\t\tmy $newCompletedEntry = $entry ;\r\n+ \t\t\t\r\n+ \t\t\t## If the id exists in feature hash and its status is not NOT_EXISTING\r\n+ \t\t\tif ( ($features->{"$current_id"} ) and ( $features->{"$current_id"}{STATUS} eq \'EXISTING\' ) ) {\r\n+ \t\t\t\t\r\n \t\t\t\t## Metabolite NAME\r\n \t\t\t\tif (defined $features->{"$current_id"}{\'metabolite_name\'} ) {\r\n- \t\t\t\t\t$entries->{\'ENTRY_ENTRY_NAME\'} = $features->{"$current_id"}{\'metabolite_name\'}\r\n+ \t\t\t\t\t$newCompletedEntry->{\'ENTRY_ENTRY_NAME\'} = $features->{"$current_id"}{\'metabolite_name\'}\r\n \t\t\t\t}\r\n \t\t\t\telse {\r\n- \t\t\t\t\t$entries->{\'ENTRY_ENTRY_NAME\'} = \'UNKNOWN\' ;\r\n+ \t\t\t\t\t$newCompletedEntry->{\'ENTRY_ENTRY_NAME\'} = \'UNKNOWN\' ;\r\n \t\t\t\t}\r\n \t\t\t\t## Metabolite INCHI\r\n \t\t\t\tif (defined $features->{"$current_id"}{\'metabolite_inchi\'} ) {\r\n- \t\t\t\t\t$entries->{\'ENTRY_ENTRY_INCHI\'} = $features->{"$current_id"}{\'metabolite_inchi\'}\r\n+ \t\t\t\t\t$newCompletedEntry->{\'ENTRY_ENTRY_INCHI\'} = $features->{"$current_id"}{\'metabolite_inchi\'}\r\n \t\t\t\t}\r\n \t\t\t\telse {\r\n- \t\t\t\t\t$entries->{\'ENTRY_ENTRY_INCHI\'} = \'NA\' ;\r\n+ \t\t\t\t\t$newCompletedEntry->{\'ENTRY_ENTRY_INCHI\'} = \'NA\' ;\r\n \t\t\t\t}\r\n \t\t\t\t## Metabolite LOGP\r\n \t\t\t\tif (defined $features->{"$current_id"}{\'metabolite_logp\'} ) {\r\n- \t\t\t\t\t$entries->{\'ENTRY_ENTRY_LOGP\'} = $features->{"$current_id"}{\'metabolite_logp\'}\r\n+ \t\t\t\t\t$newCompletedEntry->{\'ENTRY_ENTRY_LOGP\'} = $features->{"$current_id"}{\'metabolite_logp\'}\r\n \t\t\t\t}\r\n \t\t\t\telse {\r\n- \t\t\t\t\t$entries->{\'ENTRY_ENTRY_LOGP\'} = \'NA\' ;\r\n+ \t\t\t\t\t$newCompletedEntry->{\'ENTRY_ENTRY_LOGP\'} = \'NA\' ;\r\n \t\t\t\t}\r\n+ \t\t\t\tpush (@newResult, $newCompletedEntry) ;\r\n \t\t\t}\r\n+ \t\t\telsif ( ($features->{"$current_id"} ) and ( $features->{"$current_id"}{STATUS} eq \'NOT_EXISTING\' ) ) {\r\n+ \t\t\t\t$newCompletedEntry = undef ;\r\n+ \t\t\t\tnext ;\r\n+ \t\t\t\t\r\n+ \t\t\t}\r\n+ \t\t\t## In cas no features are given\r\n \t\t\telse {\r\n-# \t\t\t\tif ($features) {\r\n-# \t\t\t\t\twarn "This HMDB id doesn\'t match any collected ids\\n" ;\t\r\n-# \t\t\t\t}\r\n- \t\t\t\t$entries->{\'ENTRY_ENTRY_INCHI\'} = \'NONEDATA\' ;\r\n- \t\t\t\t$entries->{\'ENTRY_ENTRY_LOGP\'} = \'NONEDATA\' ;\r\n+ \t\t\t\t$newCompletedEntry->{\'ENTRY_ENTRY_INCHI\'} = \'NONEDATA\' ;\r\n+ \t\t\t\t$newCompletedEntry->{\'ENTRY_ENTRY_LOGP\'} = \'NONEDATA\' ;\r\n+ \t\t\t\tpush (@newResult, $newCompletedEntry) ;\r\n \t\t\t}\r\n \t\t}\r\n- \t}\r\n- }\r\n+ \t} ## END FOREACH ENTRIES\r\n+ \t\r\n+ \tpush (@moreResults, \\@newResult) ;\r\n+ \t\r\n+ } ## END FOREACH RESULT\r\n \r\n- return (\\@more_results) ;\r\n+ return (\\@moreResults) ;\r\n }\r\n ### END of SUB\r\n \r\n'

diff -r b5a1d5e43685 -r 63ba1cb240b7 test-data/out_test01.html
--- a/test-data/out_test01.html Wed Jan 23 07:49:34 2019 -0500
+++ b/test-data/out_test01.html Thu Feb 14 08:36:52 2019 -0500

b'@@ -1,1 +1,1 @@\n-<?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 HMDB queries - All results</title><link rel="stylesheet" type="text/css" href="css.php" media="all"><link rel="stylesheet" type="text/css" 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 type="text/css">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 HMDB queries - Search params : Molecular specie = neutral / delta (mass-to-charge ratio) = 0.001</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:30px;"><col style="width:30px;"><col style="width:120px;"><col style="width:50px;"><col style="width:40px;"><col style="width:60px;"><col style="width:50px;"><col style="width:20px;"><col style="width:60px;"><col style="width:50px;"><col style="width:120px;"><col style="width:20;"><thead><th>ID from input</th><th>Mass (m/z)</th><th>Metabolite_Name</th><th>Compound_ID</th><th>Formula</th><th>Compound MW (Da)</th><th>Adduct</th><th>Adduct_Type</th><th>Adduct MW (Da)</th><th>Delta</th><th>InChI Identifier</th><th>Predicted LogP (ALOGPS)</th></thead><tbody class="select" id="page-id-1"><tr class="white"><td class="ca" >mz_00001</td><td id="1" class="ca" >7.02080998</td><td class="ca" colspan="10"></td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/" target="_blank" class="btn">NONE</a></td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">0</td><td class="ca">n/a</td><td class="ca">n/a</td></tr><tr class="green"><td class="ca" >mz_00002</td><td id="2" class="ca" >75.05547146</td><td class="ca" colspan="10"></td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/" target="_blank" class="btn">NONE</a></td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">0</td><td class="ca">n/a</td><td class="ca">n/a</td></tr><tr class="white"><td class="ca" >mz_00003</td><td id="3" class="ca" >75.08059797</td><td class="ca" colspan="10"></td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/" target="_blank" class="btn">NONE</a></'..b' mw--><col style="width:50px;"><col style="width:20px;"><col style="width:60px;"><col style="width:50px;"><col style="width:120px;"><col style="width:20;"><thead><th>ID from input</th><th>Mass (m/z)</th><th>Metabolite_Name</th><th>Compound_ID</th><th>Formula</th><th>Compound MW (Da)</th><th>Adduct</th><th>Adduct type</th><th>Adduct MW (Da)</th><th>Delta (ppm)</th><th>InChI Identifier</th><th>Predicted LogP (ALOGPS)</th></thead><tbody class="select" id="page-id-1"><tr class="white"><td class="ca" >mz_00001</td><td id="1" class="ca" >7.02080998</td><td class="ca" colspan="10"></td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/" target="_blank" class="btn">NONE</a></td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">0</td><td class="ca">n/a</td><td class="ca">n/a</td></tr><tr class="green"><td class="ca" >mz_00002</td><td id="2" class="ca" >75.05547146</td><td class="ca" colspan="10"></td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/" target="_blank" class="btn">NONE</a></td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">0</td><td class="ca">n/a</td><td class="ca">n/a</td></tr><tr class="white"><td class="ca" >mz_00003</td><td id="3" class="ca" >75.08059797</td><td class="ca" colspan="10"></td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/" target="_blank" class="btn">NONE</a></td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">0</td><td class="ca">n/a</td><td class="ca">n/a</td></tr><tr class="green"><td class="ca" >mz_00004</td><td id="4" class="ca" >76.03942694</td><td class="ca" colspan="10"></td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/" target="_blank" class="btn">NONE</a></td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">0</td><td class="ca">n/a</td><td class="ca">n/a</td></tr></tbody><tbody class="select" id="page-id-2"><tr class="white"><td class="ca" >mz_00005</td><td id="5" class="ca" >76.07584477</td><td class="ca" colspan="10"></td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/" target="_blank" class="btn">NONE</a></td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">0</td><td class="ca">n/a</td><td class="ca">n/a</td></tr><tr class="green"><td class="ca" >mz_00006</td><td id="6" class="ca" >76.07593168</td><td class="ca" colspan="10"></td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/" target="_blank" class="btn">NONE</a></td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">0</td><td class="ca">n/a</td><td class="ca">n/a</td></tr></tbody></table></div><div class="container"><hr><footer><div class="row"> <div class="col-lg-12"><p>Copyright © INRA, N Paulhe, F Giacomoni 2014 </p> </div> </div> </footer></div><script language="javascript">$(function() {$(\'#choose\').pagination({items: 2,itemsOnPage: 1,currentPage: 1,onInit: function () { test(1); },cssStyle: \'light-theme\',onPageClick: function(pageNumber){test(pageNumber)}}).pagination(\'redraw\');});</script></body></html>\n\\ No newline at end of file\n'

diff -r b5a1d5e43685 -r 63ba1cb240b7 test-data/out_test02.html
--- a/test-data/out_test02.html Wed Jan 23 07:49:34 2019 -0500
+++ b/test-data/out_test02.html Thu Feb 14 08:36:52 2019 -0500

[

b'@@ -1,1 +1,1 @@\n-<?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 HMDB queries - All results</title><link rel="stylesheet" type="text/css" href="css.php" media="all"><link rel="stylesheet" type="text/css" 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 type="text/css">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 HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.001</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:30px;"><col style="width:30px;"><col style="width:120px;"><col style="width:50px;"><col style="width:40px;"><col style="width:60px;"><col style="width:50px;"><col style="width:20px;"><col style="width:60px;"><col style="width:50px;"><col style="width:120px;"><col style="width:20;"><thead><th>ID from input</th><th>Mass (m/z)</th><th>Metabolite_Name</th><th>Compound_ID</th><th>Formula</th><th>Compound MW (Da)</th><th>Adduct</th><th>Adduct_Type</th><th>Adduct MW (Da)</th><th>Delta</th><th>InChI Identifier</th><th>Predicted LogP (ALOGPS)</th></thead><tbody class="select" id="page-id-1"><tr class="white"><td class="ca" >mz_00001</td><td id="1" class="ca" >7.02080998</td><td class="ca" colspan="10"></td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Beryllium</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0002387" target="_blank" class="btn">HMDB0002387</a></td><td class="ca">Be</td><td class="ca">9.012182135</td><td class="ca">M+NH4-H2O</td><td class="ca">+</td><td class="ca">7.02033</td><td class="ca">68</td><td class="ca">InChI=1S/Be/q+2</td><td class="ca">NA</td></tr><tr class="green"><td class="ca" >mz_00002</td><td id="2" class="ca" >75.05547146</td><td class="ca" colspan="10"></td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">N-Nitrosodimethylamine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0031419" target="_blank" class="btn">HMDB0031419</a></td><td class="ca">C2H6N2O</td><td class="ca">74.048012824</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">75.055289</td><td class="ca">2</td><td class="ca">InChI=1S/C2H6N2O/c1-4(2)3-5/h1-2H3</td><td class="ca">-0.53</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Acetylhydrazine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0060428" target="_bla'..b'r class="white"><td class="ca" colspan="2"></td><td class="ca">Trimethylamine N-oxide</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0000925" target="_blank" class="btn">HMDB0000925</a></td><td class="ca">C3H9NO</td><td class="ca">75.068413915</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">76.07569</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">1-amino-propan-2-ol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0012136" target="_blank" class="btn">HMDB0012136</a></td><td class="ca">C3H9NO</td><td class="ca">75.068413915</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">76.07569</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">2-[ethyl(1-hydroxyethyl)amino]ethan-1-ol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0168716" target="_blank" class="btn">HMDB0168716</a></td><td class="ca">C6H15NO2</td><td class="ca">133.110278727</td><td class="ca">M+H+NH4</td><td class="ca">+</td><td class="ca">76.075689</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" >mz_00006</td><td id="6" class="ca" >76.07593168</td><td class="ca" colspan="10"></td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Propanolamine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0140038" target="_blank" class="btn">HMDB0140038</a></td><td class="ca">C3H9NO</td><td class="ca">75.068413915</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">76.07569</td><td class="ca">3</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">N-Methylethanolamine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0142449" target="_blank" class="btn">HMDB0142449</a></td><td class="ca">C3H9NO</td><td class="ca">75.068413914</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">76.07569</td><td class="ca">3</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Trimethylamine N-oxide</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0000925" target="_blank" class="btn">HMDB0000925</a></td><td class="ca">C3H9NO</td><td class="ca">75.068413915</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">76.07569</td><td class="ca">3</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">1-amino-propan-2-ol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0012136" target="_blank" class="btn">HMDB0012136</a></td><td class="ca">C3H9NO</td><td class="ca">75.068413915</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">76.07569</td><td class="ca">3</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">2-[ethyl(1-hydroxyethyl)amino]ethan-1-ol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0168716" target="_blank" class="btn">HMDB0168716</a></td><td class="ca">C6H15NO2</td><td class="ca">133.110278727</td><td class="ca">M+H+NH4</td><td class="ca">+</td><td class="ca">76.075689</td><td class="ca">3</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr></tbody></table></div><div class="container"><hr><footer><div class="row"> <div class="col-lg-12"><p>Copyright © INRA, N Paulhe, F Giacomoni 2014 </p> </div> </div> </footer></div><script language="javascript">$(function() {$(\'#choose\').pagination({items: 2,itemsOnPage: 1,currentPage: 1,onInit: function () { test(1); },cssStyle: \'light-theme\',onPageClick: function(pageNumber){test(pageNumber)}}).pagination(\'redraw\');});</script></body></html>\n\\ No newline at end of file\n'

diff -r b5a1d5e43685 -r 63ba1cb240b7 test-data/out_test02.tabular
--- a/test-data/out_test02.tabular Wed Jan 23 07:49:34 2019 -0500
+++ b/test-data/out_test02.tabular Thu Feb 14 08:36:52 2019 -0500

[

@@ -1,7 +1,7 @@
id mz rt hmdb(delta::name::mz::formula::adduct::id)
-1 7.02080998 49.38210915 68::[Beryllium]::9.012182135::Be::[M+NH4-H2O]::HMDB0002387
-2 75.05547146 0.658528069 "2::[N-Nitrosodimethylamine]::74.048012824::C2H6N2O::[M+H]::HMDB0031419 | 2::[Acetylhydrazine]::74.048012824::C2H6N2O::[M+H]::HMDB0060428 | 2::[glycinamide]::74.048012824::C2H6N2O::[M+H]::HMDB0062472 | 2::[Creatine]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB0000064 | 2::[Beta-Guanidinopropionic acid]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB0013222"
-3 75.08059797 1743.94267 "0::[Pyrophosphate]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0000250 | 0::[UNKNOWN]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0155221 | 2::[1-Butanol]::74.073164942::C4H10O::[M+H]::HMDB0004327 | 2::[2-Methylpropan-2-ol]::74.073164942::C4H10O::[M+H]::HMDB0031456 | 2::[Isobutanol]::74.073164942::C4H10O::[M+H]::HMDB0006006"
-4 76.03942694 51.23158899 "2::[L-Aspartic acid]::133.037507717::C4H7NO4::[M+H+NH4]::HMDB0000191 | 2::[UNKNOWN]::74.024751953::C2H4NO2::[M+H]::HMDB0161401 | 2::[Ethyl nitrite]::75.032028409::C2H5NO2::[M+H]::HMDB0031239 | 2::[1-deoxy-1-(N6-lysino)-D-fructose]::133.037507709::C4H7NO4::[M+H+NH4]::HMDB0062186 | 2::[N-acetyl-seryl-aspartate]::133.037507709::C4H7NO4::[M+H+NH4]::HMDB0062501"
-5 76.07584477 50.51249853 "2::[3-aminopropan-1-ol]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 2::[2-(methylamino)ethan-1-ol]::75.068413914::C3H9NO::[M+H]::HMDB0142449 | 2::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB0000925 | 2::[1-Amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB0012136 | 2::[UNKNOWN]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0168716"
-6 76.07593168 0.149308136 "3::[3-aminopropan-1-ol]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 3::[2-(methylamino)ethan-1-ol]::75.068413914::C3H9NO::[M+H]::HMDB0142449 | 3::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB0000925 | 3::[1-Amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB0012136 | 3::[UNKNOWN]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0168716"
+1 7.02080998 49.38210915 68::[Beryllium(2+)]::9.012182135::Be::[M+NH4-H2O]::HMDB0002387
+2 75.05547146 0.658528069 "2::[N-Nitrosodimethylamine]::74.048012824::C2H6N2O::[M+H]::HMDB0031419 | 2::[Acetohydrazide]::74.048012824::C2H6N2O::[M+H]::HMDB0060428 | 2::[Glycinamid]::74.048012824::C2H6N2O::[M+H]::HMDB0062472 | 2::[Creatine]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB0000064 | 2::[3-Guanidinopropanoic acid]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB0013222"
+3 75.08059797 1743.94267 "0::[Pyrophosphate]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0000250 | 0::[Pyrophosphate]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0155221 | 2::[1-Butanol]::74.073164942::C4H10O::[M+H]::HMDB0004327 | 2::[Tert-butanol]::74.073164942::C4H10O::[M+H]::HMDB0031456 | 2::[Isobutanol]::74.073164942::C4H10O::[M+H]::HMDB0006006"
+4 76.03942694 51.23158899 "2::[L-Aspartic acid]::133.037507717::C4H7NO4::[M+H+NH4]::HMDB0000191 | 2::[Glycinate]::74.024751953::C2H4NO2::[M+H]::HMDB0161401 | 2::[Ethyl nitrite]::75.032028409::C2H5NO2::[M+H]::HMDB0031239 | 2::[Aspartic acid]::133.037507709::C4H7NO4::[M+H+NH4]::HMDB0062186 | 2::[Aspartic acid]::133.037507709::C4H7NO4::[M+H+NH4]::HMDB0062501"
+5 76.07584477 50.51249853 "2::[Propanolamine]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 2::[N-Methylethanolamine]::75.068413914::C3H9NO::[M+H]::HMDB0142449 | 2::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB0000925 | 2::[1-amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB0012136 | 2::[2-[ethyl(1-hydroxyethyl)amino]ethan-1-ol]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0168716"
+6 76.07593168 0.149308136 "3::[Propanolamine]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 3::[N-Methylethanolamine]::75.068413914::C3H9NO::[M+H]::HMDB0142449 | 3::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB0000925 | 3::[1-amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB0012136 | 3::[2-[ethyl(1-hydroxyethyl)amino]ethan-1-ol]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0168716"

diff -r b5a1d5e43685 -r 63ba1cb240b7 test-data/out_test02.txt
--- a/test-data/out_test02.txt Wed Jan 23 07:49:34 2019 -0500
+++ b/test-data/out_test02.txt Thu Feb 14 08:36:52 2019 -0500

[

@@ -1,27 +1,27 @@
ID Query(Da) Delta(ppm) Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID
-mz_00001 7.02080998 68 [Beryllium] 9.012182135 Be [M+NH4-H2O] 7.02033 HMDB0002387
+mz_00001 7.02080998 68 [Beryllium(2+)] 9.012182135 Be [M+NH4-H2O] 7.02033 HMDB0002387
mz_00002 75.05547146 2 [N-Nitrosodimethylamine] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0031419
-mz_00002 75.05547146 2 [Acetylhydrazine] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0060428
-mz_00002 75.05547146 2 [glycinamide] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0062472
+mz_00002 75.05547146 2 [Acetohydrazide] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0060428
+mz_00002 75.05547146 2 [Glycinamid] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0062472
mz_00002 75.05547146 2 [Creatine] 131.069476547 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0000064
-mz_00002 75.05547146 2 [Beta-Guanidinopropionic acid] 131.069476547 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0013222
+mz_00002 75.05547146 2 [3-Guanidinopropanoic acid] 131.069476547 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0013222
mz_00003 75.08059797 0 [Pyrophosphate] 177.943225506 H4O7P2 [M+H+2Na] 75.080599 HMDB0000250
-mz_00003 75.08059797 0 [UNKNOWN] 177.943225506 H4O7P2 [M+H+2Na] 75.080599 HMDB0155221
+mz_00003 75.08059797 0 [Pyrophosphate] 177.943225506 H4O7P2 [M+H+2Na] 75.080599 HMDB0155221
mz_00003 75.08059797 2 [1-Butanol] 74.073164942 C4H10O [M+H] 75.080441 HMDB0004327
-mz_00003 75.08059797 2 [2-Methylpropan-2-ol] 74.073164942 C4H10O [M+H] 75.080441 HMDB0031456
+mz_00003 75.08059797 2 [Tert-butanol] 74.073164942 C4H10O [M+H] 75.080441 HMDB0031456
mz_00003 75.08059797 2 [Isobutanol] 74.073164942 C4H10O [M+H] 75.080441 HMDB0006006
mz_00004 76.03942694 2 [L-Aspartic acid] 133.037507717 C4H7NO4 [M+H+NH4] 76.039304 HMDB0000191
-mz_00004 76.03942694 2 [UNKNOWN] 74.024751953 C2H4NO2 [M+H] 76.039304 HMDB0161401
+mz_00004 76.03942694 2 [Glycinate] 74.024751953 C2H4NO2 [M+H] 76.039304 HMDB0161401
mz_00004 76.03942694 2 [Ethyl nitrite] 75.032028409 C2H5NO2 [M+H] 76.039304 HMDB0031239
-mz_00004 76.03942694 2 [1-deoxy-1-(N6-lysino)-D-fructose] 133.037507709 C4H7NO4 [M+H+NH4] 76.039304 HMDB0062186
-mz_00004 76.03942694 2 [N-acetyl-seryl-aspartate] 133.037507709 C4H7NO4 [M+H+NH4] 76.039304 HMDB0062501
-mz_00005 76.07584477 2 [3-aminopropan-1-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0140038
-mz_00005 76.07584477 2 [2-(methylamino)ethan-1-ol] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0142449
+mz_00004 76.03942694 2 [Aspartic acid] 133.037507709 C4H7NO4 [M+H+NH4] 76.039304 HMDB0062186
+mz_00004 76.03942694 2 [Aspartic acid] 133.037507709 C4H7NO4 [M+H+NH4] 76.039304 HMDB0062501
+mz_00005 76.07584477 2 [Propanolamine] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0140038
+mz_00005 76.07584477 2 [N-Methylethanolamine] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0142449
mz_00005 76.07584477 2 [Trimethylamine N-oxide] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0000925
-mz_00005 76.07584477 2 [1-Amino-propan-2-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0012136
-mz_00005 76.07584477 2 [UNKNOWN] 133.110278727 C6H15NO2 [M+H+NH4] 76.075689 HMDB0168716
-mz_00006 76.07593168 3 [3-aminopropan-1-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0140038
-mz_00006 76.07593168 3 [2-(methylamino)ethan-1-ol] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0142449
+mz_00005 76.07584477 2 [1-amino-propan-2-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0012136
+mz_00005 76.07584477 2 [2-[ethyl(1-hydroxyethyl)amino]ethan-1-ol] 133.110278727 C6H15NO2 [M+H+NH4] 76.075689 HMDB0168716
+mz_00006 76.07593168 3 [Propanolamine] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0140038
+mz_00006 76.07593168 3 [N-Methylethanolamine] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0142449
mz_00006 76.07593168 3 [Trimethylamine N-oxide] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0000925
-mz_00006 76.07593168 3 [1-Amino-propan-2-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0012136
-mz_00006 76.07593168 3 [UNKNOWN] 133.110278727 C6H15NO2 [M+H+NH4] 76.075689 HMDB0168716
+mz_00006 76.07593168 3 [1-amino-propan-2-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0012136
+mz_00006 76.07593168 3 [2-[ethyl(1-hydroxyethyl)amino]ethan-1-ol] 133.110278727 C6H15NO2 [M+H+NH4] 76.075689 HMDB0168716

diff -r b5a1d5e43685 -r 63ba1cb240b7 test-data/out_test03.html
--- a/test-data/out_test03.html Wed Jan 23 07:49:34 2019 -0500
+++ b/test-data/out_test03.html Thu Feb 14 08:36:52 2019 -0500

[

b'@@ -1,1 +1,1 @@\n-<?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 HMDB queries - All results</title><link rel="stylesheet" type="text/css" href="css.php" media="all"><link rel="stylesheet" type="text/css" 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 type="text/css">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 HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.05</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:30px;"><col style="width:30px;"><col style="width:120px;"><col style="width:50px;"><col style="width:40px;"><col style="width:60px;"><col style="width:50px;"><col style="width:20px;"><col style="width:60px;"><col style="width:50px;"><col style="width:120px;"><col style="width:20;"><thead><th>ID from input</th><th>Mass (m/z)</th><th>Metabolite_Name</th><th>Compound_ID</th><th>Formula</th><th>Compound MW (Da)</th><th>Adduct</th><th>Adduct_Type</th><th>Adduct MW (Da)</th><th>Delta</th><th>InChI Identifier</th><th>Predicted LogP (ALOGPS)</th></thead><tbody class="select" id="page-id-1"><tr class="white"><td class="ca" >mz_00001</td><td id="1" class="ca" >175.01</td><td class="ca" colspan="10"></td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0149376" target="_blank" class="btn">HMDB0149376</a></td><td class="ca">C19H16O14S</td><td class="ca">500.026076369</td><td class="ca">M+2H+Na</td><td class="ca">+</td><td class="ca">175.009949</td><td class="ca">0</td><td class="ca">NA</td><td class="ca">NA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0149375" target="_blank" class="btn">HMDB0149375</a></td><td class="ca">C19H16O14S</td><td class="ca">500.026076369</td><td class="ca">M+2H+Na</td><td class="ca">+</td><td class="ca">175.009949</td><td class="ca">0</td><td class="ca">NA</td><td class="ca">NA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0149391" target="_blank" class="btn">HMDB0149391</a></td><td class="ca">C19H16O14S</td><td class="ca">500.026076369</td><td class="ca">M+2H+Na</td><td class="ca">+</td><td class="ca">175.009949</td><td cl'..b'ass="btn">HMDB0138858</a></td><td class="ca">C25H20O9</td><td class="ca">464.110732224</td><td class="ca">2M+2H+3H2O</td><td class="ca">+</td><td class="ca">956.244584</td><td class="ca">6</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">"6-[(2,3-dioxo-4-phenyl-2,3-dihydro-1H-phenalen-1-yl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0168237" target="_blank" class="btn">HMDB0168237</a></td><td class="ca">C25H20O9</td><td class="ca">464.110732224</td><td class="ca">2M+2H+3H2O</td><td class="ca">+</td><td class="ca">956.244584</td><td class="ca">6</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" >mz_00006</td><td id="6" class="ca" >1100.45</td><td class="ca" colspan="10"></td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Npc</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0060499" target="_blank" class="btn">HMDB0060499</a></td><td class="ca">C28H30N4O6</td><td class="ca">518.216534712</td><td class="ca">2M+ACN+Na</td><td class="ca">+</td><td class="ca">1100.448834</td><td class="ca">1</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">"4-[(2S,15R)-3,9-dihydroxy-2-(hydroxymethyl)-15-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0\xc2\xb2,\xe2\x81\xb7.0\xc2\xb9\xc2\xb9,\xc2\xb9\xe2\x81\xb5]heptadecan-14-yl]pentanoic acid"</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0158990" target="_blank" class="btn">HMDB0158990</a></td><td class="ca">C24H38O10S</td><td class="ca">518.218568598</td><td class="ca">2M+ACN+Na</td><td class="ca">+</td><td class="ca">1100.452902</td><td class="ca">3</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">"4-[(2S,15R)-3,9-dihydroxy-15-(hydroxymethyl)-2-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0\xc2\xb2,\xe2\x81\xb7.0\xc2\xb9\xc2\xb9,\xc2\xb9\xe2\x81\xb5]heptadecan-14-yl]pentanoic acid"</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0158993" target="_blank" class="btn">HMDB0158993</a></td><td class="ca">C24H38O10S</td><td class="ca">518.218568598</td><td class="ca">2M+ACN+Na</td><td class="ca">+</td><td class="ca">1100.452902</td><td class="ca">3</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">"4-[(2S,15R)-8,9-dihydroxy-2-(hydroxymethyl)-15-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0\xc2\xb2,\xe2\x81\xb7.0\xc2\xb9\xc2\xb9,\xc2\xb9\xe2\x81\xb5]heptadecan-14-yl]pentanoic acid"</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0157972" target="_blank" class="btn">HMDB0157972</a></td><td class="ca">C24H38O10S</td><td class="ca">518.218568598</td><td class="ca">2M+ACN+Na</td><td class="ca">+</td><td class="ca">1100.452902</td><td class="ca">3</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">"4-[(2S,15R)-3,16-dihydroxy-15-(hydroxymethyl)-2-methyl-5-oxo-9-(sulfooxy)tetracyclo[8.7.0.0\xc2\xb2,\xe2\x81\xb7.0\xc2\xb9\xc2\xb9,\xc2\xb9\xe2\x81\xb5]heptadecan-14-yl]pentanoic acid"</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0158992" target="_blank" class="btn">HMDB0158992</a></td><td class="ca">C24H38O10S</td><td class="ca">518.218568598</td><td class="ca">2M+ACN+Na</td><td class="ca">+</td><td class="ca">1100.452902</td><td class="ca">3</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr></tbody></table></div><div class="container"><hr><footer><div class="row"> <div class="col-lg-12"><p>Copyright © INRA, N Paulhe, F Giacomoni 2014 </p> </div> </div> </footer></div><script language="javascript">$(function() {$(\'#choose\').pagination({items: 2,itemsOnPage: 1,currentPage: 1,onInit: function () { test(1); },cssStyle: \'light-theme\',onPageClick: function(pageNumber){test(pageNumber)}}).pagination(\'redraw\');});</script></body></html>\n\\ No newline at end of file\n'

diff -r b5a1d5e43685 -r 63ba1cb240b7 test-data/out_test03.tabular
--- a/test-data/out_test03.tabular Wed Jan 23 07:49:34 2019 -0500
+++ b/test-data/out_test03.tabular Thu Feb 14 08:36:52 2019 -0500

[

@@ -1,31 +1,31 @@
ID Query(Da) Delta(ppm) Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID
-mz_00001 175.01 0 [UNKNOWN] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149376
-mz_00001 175.01 0 [UNKNOWN] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149375
-mz_00001 175.01 0 [UNKNOWN] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149391
-mz_00001 175.01 0 [UNKNOWN] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149392
-mz_00001 175.01 0 [UNKNOWN] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149418
-mz_00002 238.19 4 [UNKNOWN] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0163116
-mz_00002 238.19 4 [UNKNOWN] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0187564
-mz_00002 238.19 4 [Alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0004043
+mz_00001 175.01 0 ["2-{[5,6-dihydroxy-3-(4-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149376
+mz_00001 175.01 0 ["2-({5,6-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149375
+mz_00001 175.01 0 ["2-hydroxy-3-({5-hydroxy-3-[4-hydroxy-3-(sulfooxy)phenyl]-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)butanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149391
+mz_00001 175.01 0 ["2-{[3-(3,4-dihydroxyphenyl)-5-hydroxy-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149392
+mz_00001 175.01 0 ["2-({5,8-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149418
+mz_00002 238.19 4 ["(4Z,7Z)-Deca-4,7-dien-1-ol"] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0163116
+mz_00002 238.19 4 [CTK8I1689] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0187564
+mz_00002 238.19 4 [(S)-alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0004043
mz_00002 238.19 4 [(S)-alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0036086
mz_00002 238.19 4 [Eucalyptol] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0004472
mz_00003 420.16 2 [N-Desmethyl-O-hydroxy rosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB0060836
mz_00003 420.16 2 [N-Desmethyl-p-hydroxyrosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB0060838
-mz_00003 420.16 2 [UNKNOWN] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0160148
-mz_00003 420.16 2 [UNKNOWN] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0160149
-mz_00003 420.16 2 [UNKNOWN] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0165020
-mz_00004 780.32 2 [UNKNOWN] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162081
-mz_00004 780.32 2 [Niazicinin A] 369.142366717 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0031947
-mz_00004 780.32 2 [UNKNOWN] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162078
-mz_00004 780.32 2 [UNKNOWN] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162083
-mz_00004 780.32 3 [UNKNOWN] 696.262935337 C33H44O16 [M+IsoProp+Na+H] 780.318045 HMDB0150342
-mz_00005 956.25 5 [PRE] 956.222252336 C44H44O24 [M+NH4-H2O] 956.244952 HMDB0041300
-mz_00005 956.25 6 [UNKNOWN] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168193
-mz_00005 956.25 6 [UNKNOWN] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168231
-mz_00005 956.25 6 [UNKNOWN] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0138858
-mz_00005 956.25 6 [UNKNOWN] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168237
-mz_00006 1100.45 1 [NPC] 518.216534712 C28H30N4O6 [2M+ACN+Na] 1100.448834 HMDB0060499
-mz_00006 1100.45 3 [UNKNOWN] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158990
-mz_00006 1100.45 3 [UNKNOWN] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158993
-mz_00006 1100.45 3 [UNKNOWN] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0157972
-mz_00006 1100.45 3 [UNKNOWN] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158992
+mz_00003 420.16 2 ["6-[(5-carboxy-3-methylpentanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0160148
+mz_00003 420.16 2 ["6-[(5-carboxy-4-methylpentanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0160149
+mz_00003 420.16 2 ["6-{[2-(acetyloxy)-3-methylbutanoyl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid"] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0165020
+mz_00004 780.32 2 ["3,4,5-trihydroxy-6-{[4-(methoxymethyl)-7-methyl-5H,6H,7H-cyclopenta[c]pyridin-5-yl]oxy}oxane-2-carboxylic acid"] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162081
+mz_00004 780.32 2 ["N-[(4-{[5-(acetyloxy)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}phenyl)methyl]methoxycarboximidic acid"] 369.142366717 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0031947
+mz_00004 780.32 2 ["3,4,5-trihydroxy-6-{[4-(methoxymethyl)-7-methyl-5H,6H,7H-cyclopenta[c]pyridin-7-yl]oxy}oxane-2-carboxylic acid"] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162078
+mz_00004 780.32 2 ["3,4,5-trihydroxy-6-{[4-(methoxymethyl)-5H,6H,7H-cyclopenta[c]pyridin-7-yl]methoxy}oxane-2-carboxylic acid"] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162083
+mz_00004 780.32 3 ["3,4,5-trihydroxy-6-[(9-hydroxy-16,17-dimethoxy-15-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tricyclo[12.3.1.1Â²,â¶]nonadeca-1(17),2,4,6(19),14(18),15-hexaen-3-yl)oxy]oxane-2-carboxylic acid"] 696.262935337 C33H44O16 [M+IsoProp+Na+H] 780.318045 HMDB0150342
+mz_00005 956.25 5 ["2-{2,3,6-trihydroxy-5-[(2Z)-3-(4-hydroxyphenyl)prop-2-enoyl]-4-oxo-3-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]cyclohexa-1,5-dien-1-yl}-2-{2,3,4-trihydroxy-5-[3-(4-hydroxyphenyl)prop-2-enoyl]-6-oxo-3-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]cyclohexa-1,4-dien-1-yl}acetic acid"] 956.222252336 C44H44O24 [M+NH4-H2O] 956.244952 HMDB0041300
+mz_00005 956.25 6 ["3,4,5-trihydroxy-6-[2-(2-hydroxy-1-oxo-1H-phenalen-9-yl)phenoxy]oxane-2-carboxylic acid"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168193
+mz_00005 956.25 6 ["6-[4-(2,3-dioxo-2,3-dihydro-1H-phenalen-4-yl)phenoxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168231
+mz_00005 956.25 6 ["5-(5,7-dihydroxy-4-oxo-3,4-dihydro-2H-1-benzopyran-2-yl)-7-hydroxy-2-(4-hydroxy-3-methoxyphenyl)-2,3-dihydro-1-benzofuran-3-carbaldehyde"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0138858
+mz_00005 956.25 6 ["6-[(2,3-dioxo-4-phenyl-2,3-dihydro-1H-phenalen-1-yl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168237
+mz_00006 1100.45 1 [Npc] 518.216534712 C28H30N4O6 [2M+ACN+Na] 1100.448834 HMDB0060499
+mz_00006 1100.45 3 ["4-[(2S,15R)-3,9-dihydroxy-2-(hydroxymethyl)-15-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0Â²,â·.0Â¹Â¹,Â¹âµ]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158990
+mz_00006 1100.45 3 ["4-[(2S,15R)-3,9-dihydroxy-15-(hydroxymethyl)-2-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0Â²,â·.0Â¹Â¹,Â¹âµ]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158993
+mz_00006 1100.45 3 ["4-[(2S,15R)-8,9-dihydroxy-2-(hydroxymethyl)-15-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0Â²,â·.0Â¹Â¹,Â¹âµ]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0157972
+mz_00006 1100.45 3 ["4-[(2S,15R)-3,16-dihydroxy-15-(hydroxymethyl)-2-methyl-5-oxo-9-(sulfooxy)tetracyclo[8.7.0.0Â²,â·.0Â¹Â¹,Â¹âµ]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158992

diff -r b5a1d5e43685 -r 63ba1cb240b7 test-data/out_test03.txt
--- a/test-data/out_test03.txt Wed Jan 23 07:49:34 2019 -0500
+++ b/test-data/out_test03.txt Thu Feb 14 08:36:52 2019 -0500

[

diff -r b5a1d5e43685 -r 63ba1cb240b7 test-data/out_test04.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_test04.html Thu Feb 14 08:36:52 2019 -0500

[

b'@@ -0,0 +1,1 @@\n+<?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 HMDB queries - All results</title><link rel="stylesheet" type="text/css" href="css.php" media="all"><link rel="stylesheet" type="text/css" 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 type="text/css">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 HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.05</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:30px;"><col style="width:30px;"><col style="width:120px;"><col style="width:50px;"><col style="width:40px;"><col style="width:60px;"><col style="width:50px;"><col style="width:20px;"><col style="width:60px;"><col style="width:50px;"><col style="width:120px;"><col style="width:20;"><thead><th>ID from input</th><th>Mass (m/z)</th><th>Metabolite_Name</th><th>Compound_ID</th><th>Formula</th><th>Compound MW (Da)</th><th>Adduct</th><th>Adduct type</th><th>Adduct MW (Da)</th><th>Delta (ppm)</th><th>InChI Identifier</th><th>Predicted LogP (ALOGPS)</th></thead><tbody class="select" id="page-id-1"><tr class="white"><td class="ca" >mz_00001</td><td id="1" class="ca" >175.01</td><td class="ca" colspan="10"></td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Mercaptopurine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0015167" target="_blank" class="btn">HMDB0015167</a></td><td class="ca">C5H4N4S</td><td class="ca">152.015666838</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">175.004885</td><td class="ca">29</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">SCHEMBL300353</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0171211" target="_blank" class="btn">HMDB0171211</a></td><td class="ca">C4H8O4S</td><td class="ca">152.014329912</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">175.003548</td><td class="ca">37</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">[(2Z)-but-2-en-1-yloxy]sulfonic acid</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0167141" target="_blank" class="btn">HMDB0167141</a></td><td class="ca">C4H8O4S</td><td class="ca">152.014329912</td><td class="ca">M+Na</td><'..b'<tr class="green"><td class="ca" colspan="2"></td><td class="ca">4-({[1-(2-{[2-amino-1-hydroxy-3-(4-hydroxyphenyl)propylidene]amino}acetyl)pyrrolidin-2-yl](hydroxy)methylidene}amino)-5-(2-{2-[(1-carboxy-2-methylpropyl)-C-hydroxycarbonimidoyl]pyrrolidine-1-carbonyl}pyrrolidin-1-yl)-5-oxopentanoic acid</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0164418" target="_blank" class="btn">HMDB0164418</a></td><td class="ca">C36H51N7O11</td><td class="ca">757.36465549</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">780.353873</td><td class="ca">43</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">2-{[hydroxy(1-{2-[(1-hydroxy-2-{[1-hydroxy-2-({hydroxy[1-(pyrrolidine-2-carbonyl)pyrrolidin-2-yl]methylidene}amino)-3-methylbutylidene]amino}-3-(4-hydroxyphenyl)propylidene)amino]acetyl}pyrrolidin-2-yl)methylidene]amino}pentanedioic acid</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0164423" target="_blank" class="btn">HMDB0164423</a></td><td class="ca">C36H51N7O11</td><td class="ca">757.36465549</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">780.353873</td><td class="ca">43</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">1-(4-carboxy-2-{[hydroxy({1-[2-({1-hydroxy-2-[(1-hydroxy-2-{[hydroxy(pyrrolidin-2-yl)methylidene]amino}-3-methylbutylidene)amino]-3-(4-hydroxyphenyl)propylidene}amino)acetyl]pyrrolidin-2-yl})methylidene]amino}butanoyl)pyrrolidine-2-carboxylic acid</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0164424" target="_blank" class="btn">HMDB0164424</a></td><td class="ca">C36H51N7O11</td><td class="ca">757.36465549</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">780.353873</td><td class="ca">43</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr></tbody><tbody class="select" id="page-id-2"><tr class="white"><td class="ca" >mz_00005</td><td id="5" class="ca" >956.25</td><td class="ca" colspan="10"></td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">\xce\x91-D-glcnac3S-(1\xe2\x86\x924)-\xce\xb2-D-glca(1\xe2\x86\x923)-\xce\xb2-D-gal(1\xe2\x86\x923)-\xce\xb2-D-gal(1\xe2\x86\x924)-D-xyl</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0062476" target="_blank" class="btn">HMDB0062476</a></td><td class="ca">C31H51NO29S</td><td class="ca">933.2267458</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">956.215964</td><td class="ca">36</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">(3S)-3-Isopropenyl-6-oxoheptanoyl-CoA</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0062370" target="_blank" class="btn">HMDB0062370</a></td><td class="ca">C31H50N7O18P3S</td><td class="ca">933.214589966</td><td class="ca">M+Na</td><td class="ca">+</td><td class="ca">956.203808</td><td class="ca">48</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" >mz_00006</td><td id="6" class="ca" >1100.45</td><td class="ca" colspan="10"></td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/" target="_blank" class="btn">NONE</a></td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">0</td><td class="ca">n/a</td><td class="ca">n/a</td></tr></tbody></table></div><div class="container"><hr><footer><div class="row"> <div class="col-lg-12"><p>Copyright © INRA, N Paulhe, F Giacomoni 2014 </p> </div> </div> </footer></div><script language="javascript">$(function() {$(\'#choose\').pagination({items: 2,itemsOnPage: 1,currentPage: 1,onInit: function () { test(1); },cssStyle: \'light-theme\',onPageClick: function(pageNumber){test(pageNumber)}}).pagination(\'redraw\');});</script></body></html>\n\\ No newline at end of file\n'

diff -r b5a1d5e43685 -r 63ba1cb240b7 test-data/out_test04.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_test04.tabular Thu Feb 14 08:36:52 2019 -0500

[

@@ -0,0 +1,24 @@
+ID Query(Da) Delta(ppm) Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID
+mz_00001 175.01 29 [Mercaptopurine] 152.015666838 C5H4N4S [M+Na] 175.004885 HMDB0015167
+mz_00001 175.01 37 [SCHEMBL300353] 152.014329912 C4H8O4S [M+Na] 175.003548 HMDB0171211
+mz_00001 175.01 37 [[(2Z)-but-2-en-1-yloxy]sulfonic acid] 152.014329912 C4H8O4S [M+Na] 175.003548 HMDB0167141
+mz_00001 175.01 50 [(Methylsulfanyl)(phenyl)methanone] 152.029585568 C8H8OS [M+Na] 175.018804 HMDB0029694
+mz_00001 175.01 72 ["9H-Purine-6,8-diol"] 152.033425392 C5H4N4O2 [M+Na] 175.022643 HMDB0001182
+mz_00002 238.19 49 [[2-(Heptanoyloxy)ethyl]trimethylazanium] 216.196354081 C12H26NO2 [M+Na] 238.178296 HMDB0013239
+mz_00002 238.19 140 [Fencamfamin] 215.167399677 C15H21N [M+Na] 238.156618 HMDB0015508
+mz_00002 238.19 148 [(4-{[4-(dimethylamino)butyl]amino}butyl)dimethylamine] 215.236147943 C12H29N3 [M+Na] 238.225366 HMDB0031202
+mz_00002 238.19 157 [Diethylcarbamazine N-oxide] 215.163376931 C10H21N3O2 [M+Na] 238.152595 HMDB0060817
+mz_00002 238.19 204 [N-Nonanoylglycine] 215.152143543 C11H21NO3 [M+Na] 238.141362 HMDB0013279
+mz_00003 420.16 35 ["(2E,8E)-9-[4-hydroxy-3-(sulfooxy)phenyl]-N-(2-methylpropyl)nona-2,8-dienimidic acid"] 397.155908767 C19H27NO6S [M+Na] 420.145127 HMDB0161604
+mz_00003 420.16 35 ["(4E,8E)-9-[4-hydroxy-3-(sulfooxy)phenyl]-N-(2-methylpropyl)nona-4,8-dienimidic acid"] 397.155908767 C19H27NO6S [M+Na] 420.145127 HMDB0161565
+mz_00003 420.16 43 ["N-[2-(2-Hydroxy-3,4-dimethoxyphenyl)-6,7-dimethoxynaphthalen-1-yl]-N-methylformamide"] 397.152537473 C22H23NO6 [M+Na] 420.141755 HMDB0030435
+mz_00003 420.16 80 ["6-[(6-carboxy-3,4-dihydroxyoxan-2-yl)oxy]-4-methoxy-6-methyl-2H,5H,6H,7H,8H-[1,3]dioxolo[4,5-g]isoquinolin-6-ium"] 398.144557777 C18H24NO9 [M+Na] 420.1265 HMDB0165501
+mz_00003 420.16 113 ["3,4,5-trihydroxy-6-[(4-hydroxy-6-propanoyl-7,8-dihydropteridin-2-yl)amino]oxane-2-carboxylic acid"] 397.123362592 C15H19N5O8 [M+Na] 420.112581 HMDB0158327
+mz_00004 780.32 43 [5-[2-(2-{[1-({1-[(carboxymethyl)-C-hydroxycarbonimidoyl]-2-(4-hydroxyphenyl)ethyl}-C-hydroxycarbonimidoyl)-2-methylpropyl]-C-hydroxycarbonimidoyl}pyrrolidine-1-carbonyl)pyrrolidin-1-yl]-4-{[hydroxy(pyrrolidin-2-yl)methylidene]amino}-5-oxopentanoic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164422
+mz_00004 780.32 43 [1-(1-{2-[({1-[2-({2-[(2-amino-1-hydroxy-3-methylbutylidene)amino]-1-hydroxy-3-(4-hydroxyphenyl)propylidene}amino)acetyl]pyrrolidin-2-yl}(hydroxy)methylidene)amino]-4-carboxybutanoyl}pyrrolidine-2-carbonyl)pyrrolidine-2-carboxylic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164421
+mz_00004 780.32 43 [4-({[1-(2-{[2-amino-1-hydroxy-3-(4-hydroxyphenyl)propylidene]amino}acetyl)pyrrolidin-2-yl](hydroxy)methylidene}amino)-5-(2-{2-[(1-carboxy-2-methylpropyl)-C-hydroxycarbonimidoyl]pyrrolidine-1-carbonyl}pyrrolidin-1-yl)-5-oxopentanoic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164418
+mz_00004 780.32 43 [2-{[hydroxy(1-{2-[(1-hydroxy-2-{[1-hydroxy-2-({hydroxy[1-(pyrrolidine-2-carbonyl)pyrrolidin-2-yl]methylidene}amino)-3-methylbutylidene]amino}-3-(4-hydroxyphenyl)propylidene)amino]acetyl}pyrrolidin-2-yl)methylidene]amino}pentanedioic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164423
+mz_00004 780.32 43 [1-(4-carboxy-2-{[hydroxy({1-[2-({1-hydroxy-2-[(1-hydroxy-2-{[hydroxy(pyrrolidin-2-yl)methylidene]amino}-3-methylbutylidene)amino]-3-(4-hydroxyphenyl)propylidene}amino)acetyl]pyrrolidin-2-yl})methylidene]amino}butanoyl)pyrrolidine-2-carboxylic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164424
+mz_00005 956.25 36 [Î-D-glcnac3S-(1â4)-Î²-D-glca(1â3)-Î²-D-gal(1â3)-Î²-D-gal(1â4)-D-xyl] 933.2267458 C31H51NO29S [M+Na] 956.215964 HMDB0062476
+mz_00005 956.25 48 [(3S)-3-Isopropenyl-6-oxoheptanoyl-CoA] 933.214589966 C31H50N7O18P3S [M+Na] 956.203808 HMDB0062370
+mz_00006 1100.45 0 UNKNOWN N/A N/A N/A N/A N/A

diff -r b5a1d5e43685 -r 63ba1cb240b7 test-data/out_test04.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_test04.txt Thu Feb 14 08:36:52 2019 -0500

[

diff -r b5a1d5e43685 -r 63ba1cb240b7 wsdl_hmdb.pl
--- a/wsdl_hmdb.pl Wed Jan 23 07:49:34 2019 -0500
+++ b/wsdl_hmdb.pl Thu Feb 14 08:36:52 2019 -0500

[

@@ -27,7 +27,7 @@
my ( $mass ) = undef ;
my ( $masses_file, $col_id, $col_mass, $header_choice, $nbline_header ) = ( undef, undef, undef, undef, undef ) ;
my $max_query = undef ;
-my ( $delta, $molecular_species, $out_tab, $out_html, $out_xls ) = ( undef, undef, undef, undef, undef ) ;
+my ( $adductType, $delta, $molecular_species, $out_tab, $out_html, $out_xls ) = ( undef, undef, undef, undef, undef, undef ) ;
my $advancedFeatures = 0 ;
my $VERBOSE = ( 3 ) ;

@@ -42,13 +42,14 @@
"header_choice:s" => \$header_choice, ## Presence or not of header in tabular file
"nblineheader:i" => \$nbline_header, ## numbre of header line present in file
"colfactor:i" => \$col_mass, ## Column id for retrieve formula list in tabular file
+ "adduct_type:s" => \$adductType, ## A list of selected adducts
"delta:f" => \$delta,
"mode:s" => \$molecular_species, ## Molecular species (positive/negative/neutral)
"maxquery:i" => \$max_query, ## Maximum query return (default is 20 entries by query // min 1 & max 50 )
"output_tabular:s" => \$out_tab, ## option : path to the ouput (tabular : input+results )
"output_html|v:s" => \$out_html, ## option : path to the results view (output2)
"output_xlsx:s" => \$out_xls, ## option : path to the xls-like format output
- "advancedFeatures:s"=> \$advancedFeatures, ## option : set to 1 to get advanced options or 0 to get first level only.
+ "advancedFeatures:i"=> \$advancedFeatures, ## option : set to 1 to get advanced options or 0 to get first level only.
"verbose:i" => \$VERBOSE, ## VERBOSE Of the tool
) ;

@@ -84,7 +85,13 @@
my $metabocard_features = undef ;
my $search_condition = "Search params : Molecular specie = $molecular_species / delta (mass-to-charge ratio) = $delta" ;

-print "\t with $search_condition\n" if ($VERBOSE>1) ;
+print "\twith $search_condition\n" if ($VERBOSE>1) ;
+
+## $adductType
+if (defined $adductType ) {
+ print "\twith Adducts: $adductType\n" if ($VERBOSE>1) ;
+}
+

## --------------- retrieve input data -------------- :

@@ -122,12 +129,12 @@
my $oHmdb = lib::hmdb::new() ;
my $hmdb_pages = undef ;
my $status = undef ;
- my $hmdb_ids = undef ;
+ my ($hmdb_ids, $idsNumber) = (undef, 0) ;

$results = [] ; # prepare arrays ref
my $submasses = $oHmdb->extract_sub_mz_lists($masses, $CONF->{HMDB_LIMITS} ) ;

- print "\t and ".scalar(@$masses)." masses are submitted as ".scalar(@$submasses)." queries to HMDB \n\n" if ($VERBOSE>1) ;
+ print "\tand ".scalar(@$masses)." masses are submitted as ".scalar(@$submasses)." queries to HMDB \n\n" if ($VERBOSE>1) ;

## get the hmdb server status by a test query - continuous queries or kill script.
$status = $oHmdb->testMatchesFromHmdbWithUA() ;
@@ -139,10 +146,11 @@
my $result = undef ;

my ( $hmdb_masses, $nb_masses_to_submit ) = $oHmdb->prepare_multi_masses_query($mzs) ;
+ my ($hmdb_adducts, $nb_selected_adducts) = $oHmdb->prepareAdductListFormat($adductType) ;

print "\n\tSubmission of m/z cluster ".sprintf '%04s',$cluster."" if ($VERBOSE>1) ;

- ($hmdb_pages, $status) = $oHmdb->getMatchesFromHmdbWithUA($hmdb_masses, $delta, $molecular_species) ;
+ ($hmdb_pages, $status) = $oHmdb->getMatchesFromHmdbWithUA($hmdb_masses, $delta, $molecular_species, $hmdb_adducts) ;
print "...HMDB reply results with status: $status\n" if ($VERBOSE>1) ;

# print Dumper $hmdb_pages ;
@@ -161,15 +169,15 @@
if ($advancedFeatures > 0) {

## foreach metabolite get its own metabocard
- $hmdb_ids = $oHmdb->get_unik_ids_from_results($results) ;
+ ($hmdb_ids, $idsNumber) = $oHmdb->get_unik_ids_from_results($results) ;

- print "\tComplementary annotation: asking for ".scalar(@$results)." metabocards\n" if ($VERBOSE>1) ;
+ print "\tComplementary annotation: asking for $idsNumber metabocards\n" if ($VERBOSE>1) ;

# $hmdb_ids->{'HMDB03125'} = 1 ,
$metabocard_features = $oHmdb->get_hmdb_metabocard_from_id($hmdb_ids, $CONF->{'HMDB_METABOCARD_URL'}) ; ## Try to multithread the querying
- # print Dumper $results ;
+# print Dumper $results ;
# print Dumper $hmdb_ids ;
- # print Dumper $metabocard_features ;
+# print Dumper $metabocard_features ;
## Map metabocards with results (add supplementary data)
if ( ( defined $results ) and ( defined $metabocard_features ) ) {
$results = $oHmdb->map_suppl_data_on_hmdb_results($results, $metabocard_features) ;
@@ -180,8 +188,6 @@
## Fill with msg not asked advanced annotation
$results = $oHmdb->map_suppl_data_on_hmdb_results($results, undef) ;
}
-
-

## Uses N mz and theirs entries per page (see config file).
# how many pages you need with your input mz list?
@@ -327,4 +333,6 @@

version 1.6 : 23 / 01 / 2019 - Manage UA http error and advanced feature from hmdb.

+version 1.6.1 : 30 / 01 / 2019 - Adding adducts and fixxing minors bugs and requirements
+
=cut
\ No newline at end of file

diff -r b5a1d5e43685 -r 63ba1cb240b7 wsdl_hmdb.xml
--- a/wsdl_hmdb.xml Wed Jan 23 07:49:34 2019 -0500
+++ b/wsdl_hmdb.xml Thu Feb 14 08:36:52 2019 -0500

@@ -1,4 +1,4 @@
-<tool id="wsdl_hmdb" name="HMDB MS search" version="1.6.0">
+<tool id="wsdl_hmdb" name="HMDB MS search" version="1.6.1">
   <description>
         search by masses on HMDB online LCMS bank
   </description>
@@ -8,10 +8,11 @@
       <requirement type="package" version="2.97">perl-html-template</requirement>
       <requirement type="package" version="1.19">perl-soap-lite</requirement>
       <requirement type="package" version="6.15">perl-lwp-simple</requirement>
-   <requirement type="package" version="6.15">perl-libwww-perl</requirement>
+      <requirement type="package" version="6.15">perl-libwww-perl</requirement>
       <requirement type="package" version="1.74">perl-uri</requirement>
       <requirement type="package" version="1.97">perl-text-csv</requirement>
       <requirement type="package" version="3.52">perl-xml-twig</requirement>
+      <requirement type="package" version="1.91">perl-www-mechanize</requirement>
   </requirements>

   <stdio>
@@ -33,7 +34,18 @@
             -mass "${input_type.mass}"
             -output_tabular "$variableMetadata2" -output_html "$HmdbOutWeb2" -output_xls "$HmdbOutXlsx2"
         #end if
-        -delta "$delta" -mode "$mode" -maxquery "$maxquery"
+
+        -mode "${mode_type.mode}"
+
+        #if str($mode_type.mode) == "positive":
+         -adduct_type "${mode_type.data_positive_adducts}"
+        #elif str($mode_type.mode) == "negative":
+         -adduct_type "${mode_type.data_negative_adducts}"
+        #elif str($mode_type.mode) == "neutral":
+         -adduct_type "${mode_type.data_neutral_adducts}"
+        #end if
+
+        -delta "$delta" -maxquery "$maxquery"
         -advancedFeatures "$advancedFeatures"
         -verbose "$verbose"

@@ -64,12 +76,91 @@
     </conditional>

     <param name="delta" label="Mass-to-charge ratio " type="float" value="0.05" min="0" max="10" size="10" help="Default value is 0.05 for HMDB (mass-to-charge ratio)"/>
-    <param name="maxquery" label="Number of maximum entries returned by the query " type="integer" value="20" min="1" max="50" size="10" help="Default value is 20 for each queried mz / max is 50"/>
-    <param name="mode" label="Molecular Species " type="select" display="radio" help="">
-      <option value="positive">Positif Mode</option>
-      <option value="negative">Negatif Mode</option>
-      <option value="neutral" selected="True">Neutral Mass</option>
-    </param>
+    <param name="maxquery" label="Number of maximum entries returned by the query " type="integer" value="10" min="1" max="50" size="10" help="Default value is 10 for each queried mz / max is 50"/>
+
+    <conditional name="mode_type">
+     <param name="mode" label="Molecular Species " type="select" display="radio" help="">
+       <option value="positive">Positif Mode</option>
+       <option value="negative">Negatif Mode</option>
+       <option value="neutral" selected="True">Neutral Mass</option>
+     </param>
+     <when value="positive">
+     <param name="data_positive_adducts" label="Select multiple adducts" type="select" display="checkboxes" multiple="True" help="">
+     <option value="Unknown">Unknown</option>
+     <option value="M+H" selected="True">M+H</option>
+     <option value="M+H-2H2O">M+H-2H2O</option>
+     <option value="M+H-H2O">M+H-H2O</option>
+     <option value="M+NH4-H2O">M+NH4-H2O</option>
+     <option value="M+Li">M+Li</option>
+     <option value="M+NH4">M+NH4</option>
+     <option value="M+Na">M+Na</option>
+     <option value="M+CH3OH+H">M+CH3OH+H</option>
+     <option value="M+K">M+K</option>
+     <option value="M+ACN+H">M+ACN+H</option>
+     <option value="M+2Na-H">M+2Na-H</option>
+     <option value="M+IsoProp+H">M+IsoProp+H</option>
+     <option value="M+ACN+Na">M+ACN+Na</option>
+     <option value="M+2K-H">M+2K-H</option>
+     <option value="M+DMSO+H">M+DMSO+H</option>
+     <option value="M+2ACN+H">M+2ACN+H</option>
+     <option value="M+IsoProp+Na+H">M+IsoProp+Na+H</option>
+     <option value="M+H+HCOONa">M+H+HCOONa</option>
+     <option value="2M+H">2M+H</option>
+     <option value="2M+NH4">2M+NH4</option>
+     <option value="2M+Na">2M+Na</option>
+     <option value="2M+2H+3H2O">2M+2H+3H2O</option>
+     <option value="2M+K">2M+K</option>
+     <option value="2M+ACN+H">2M+ACN+H</option>
+     <option value="2M+ACN+Na">2M+ACN+Na</option>
+     <option value="2M+H-H2O">2M+H-H2O</option>
+     <option value="M+2H">M+2H</option>
+     <option value="M+H+NH4">M+H+NH4</option>
+     <option value="M+H+Na">M+H+Na</option>
+     <option value="M+H+K">M+H+K</option>
+     <option value="M+ACN+2H">M+ACN+2H</option>
+     <option value="M+2Na">M+2Na</option>
+     <option value="M+2ACN+2H">M+2ACN+2H</option>
+     <option value="M+3ACN+2H">M+3ACN+2H</option>
+     <option value="M+3H">M+3H</option>
+     <option value="M+2H+Na">M+2H+Na</option>
+     <option value="M+H+2Na">M+H+2Na</option>
+     <option value="M+3Na">M+3Na</option>
+     <option value="M+H+2K">M+H+2K</option>
+     </param>
+     </when>
+     <when value="negative">
+     <param name="data_negative_adducts" label="Select multiple adducts" type="select" display="checkboxes" multiple="True" help="">
+     <option value="Unknown">Unknown</option>
+     <option value="M-H" selected="True">M-H</option>
+     <option value="M-H20-H">M-H20-H</option>
+     <option value="M+F">M+F</option>
+     <option value="M+Na-2H">M+Na-2H</option>
+     <option value="M+Cl">M+Cl</option>
+     <option value="M+K-2H">M+K-2H</option>
+     <option value="M+FA-H">M+FA-H</option>
+     <option value="M+Hac-H">M+Hac-H</option>
+     <option value="M+Br">M+Br</option>
+     <option value="M+TFA-H">M+TFA-H</option>
+     <option value="M-H+HCOONa">M-H+HCOONa</option>
+     <option value="2M-H">2M-H</option>
+     <option value="2M+FA-H">2M+FA-H</option>
+     <option value="2M+Hac-H">2M+Hac-H</option>
+     <option value="3M-H">3M-H</option>
+     <option value="M-2H">M-2H</option>
+     <option value="M-3H">M-3H</option>
+     </param>
+     </when>
+     <when value="neutral">
+     <param name="data_neutral_adducts" label="Select multiple adducts" type="select" display="checkboxes" multiple="True" help="">
+     <option value="Unknown">Unknown</option>
+     <option value="M" selected="True">M</option>
+     </param>
+     </when>
+    </conditional>
+
+
+
+
     <param name="advancedFeatures" label="Performing advanced annotation " type="select" display="radio" help="Getting more information from HMDB (Inchi, logP, ...) but increase time of tool execution">
       <option value="1">Advanced mode</option>
       <option value="0" selected="True">Default mode</option>