| Next changeset 1:2744d20c830a (2020-11-27) |
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Commit message:
Init repository for bih4maconda |
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added:
Dockerfile LICENSE README README.md _template.tabular bih4maconda.pl bih4maconda.xml conf.cfg test-data/in_test01_pos.tabular test-data/in_test02_pos.tabular test-data/in_test03_neg.tabular test-data/outFull_test01.tabular test-data/outFull_test02.tabular test-data/outFull_test03.tabular test-data/outTab_test01.tabular test-data/outTab_test02.tabular test-data/outTab_test03.tabular |
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| diff -r 000000000000 -r de13e2c45971 Dockerfile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Dockerfile Tue Jan 21 15:49:00 2020 -0500 |
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| @@ -0,0 +1,51 @@ +FROM ubuntu:18.04 + +# set author +MAINTAINER Franck Giacomoni <franck.giacomoni.fr> + +### +### [CONTAINER CORE FUNCTIONS]: +### xxxx +### xxxx +### [NOTES] +### xxxx + +ENV PATH /opt/conda/bin:$PATH + +RUN apt-get -y update &&\ + apt-get -y install build-essential \ + cpanminus \ + gzip \ + wget \ + bzip2 \ + ca-certificates \ + libglib2.0-0 \ + libxext6 \ + libsm6 \ + libxrender1 \ + libtext-csv-perl \ + libxml-twig-perl \ + libfile-share-perl + +RUN wget --quiet https://repo.anaconda.com/archive/Anaconda3-5.3.0-Linux-x86_64.sh -O ~/anaconda.sh && \ + /bin/bash ~/anaconda.sh -b -p /opt/conda && \ + rm ~/anaconda.sh && \ + ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \ + echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \ + echo "conda activate base" >> ~/.bashrc + +RUN cpan install ExtUtils::MakeMaker && \ + cpan install File::ShareDir::Install && \ + cpan install Module::Release &&\ + cpan install Archive::Zip &&\ + + apt -y install git &&\ + apt -y install python2.7 python-pip &&\ + apt -y install virtualenv &&\ + pip install "pip>=7" &&\ + pip install -U git+git://github.com/galaxyproject/planemo.git &&\ + + apt-get autoremove -y && \ + apt-get clean && \ + rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* + |
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| diff -r 000000000000 -r de13e2c45971 LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Tue Jan 21 15:49:00 2020 -0500 |
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| b'@@ -0,0 +1,519 @@\n+The BiH4MaConDa module is licensed under the CeCILL 2.1 license.\n+\n+ CeCILL FREE SOFTWARE LICENSE AGREEMENT\n+\n+Version 2.1 dated 2013-06-21\n+\n+\n+ Notice\n+\n+This Agreement is a Free Software license agreement that is the result\n+of discussions between its authors in order to ensure compliance with\n+the two main principles guiding its drafting:\n+\n+ * firstly, compliance with the principles governing the distribution\n+ of Free Software: access to source code, broad rights granted to users,\n+ * secondly, the election of a governing law, French law, with which it\n+ is conformant, both as regards the law of torts and intellectual\n+ property law, and the protection that it offers to both authors and\n+ holders of the economic rights over software.\n+\n+The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre]) \n+license are: \n+\n+Commissariat \xc3\xa0 l\'\xc3\xa9nergie atomique et aux \xc3\xa9nergies alternatives - CEA, a\n+public scientific, technical and industrial research establishment,\n+having its principal place of business at 25 rue Leblanc, immeuble Le\n+Ponant D, 75015 Paris, France.\n+\n+Centre National de la Recherche Scientifique - CNRS, a public scientific\n+and technological establishment, having its principal place of business\n+at 3 rue Michel-Ange, 75794 Paris cedex 16, France.\n+\n+Institut National de Recherche en Informatique et en Automatique -\n+Inria, a public scientific and technological establishment, having its\n+principal place of business at Domaine de Voluceau, Rocquencourt, BP\n+105, 78153 Le Chesnay cedex, France.\n+\n+\n+ Preamble\n+\n+The purpose of this Free Software license agreement is to grant users\n+the right to modify and redistribute the software governed by this\n+license within the framework of an open source distribution model.\n+\n+The exercising of this right is conditional upon certain obligations for\n+users so as to preserve this status for all subsequent redistributions.\n+\n+In consideration of access to the source code and the rights to copy,\n+modify and redistribute granted by the license, users are provided only\n+with a limited warranty and the software\'s author, the holder of the\n+economic rights, and the successive licensors only have limited liability.\n+\n+In this respect, the risks associated with loading, using, modifying\n+and/or developing or reproducing the software by the user are brought to\n+the user\'s attention, given its Free Software status, which may make it\n+complicated to use, with the result that its use is reserved for\n+developers and experienced professionals having in-depth computer\n+knowledge. Users are therefore encouraged to load and test the\n+suitability of the software as regards their requirements in conditions\n+enabling the security of their systems and/or data to be ensured and,\n+more generally, to use and operate it in the same conditions of\n+security. This Agreement may be freely reproduced and published,\n+provided it is not altered, and that no provisions are either added or\n+removed herefrom.\n+\n+This Agreement may apply to any or all software for which the holder of\n+the economic rights decides to submit the use thereof to its provisions.\n+\n+Frequently asked questions can be found on the official website of the\n+CeCILL licenses family (http://www.cecill.info/index.en.html) for any \n+necessary clarification.\n+\n+\n+ Article 1 - DEFINITIONS\n+\n+For the purpose of this Agreement, when the following expressions\n+commence with a capital letter, they shall have the following meaning:\n+\n+Agreement: means this license agreement, and its possible subsequent\n+versions and annexes.\n+\n+Software: means the software in its Object Code and/or Source Code form\n+and, where applicable, its documentation, "as is" when the Licensee\n+accepts the Agreement.\n+\n+Initial Software: means the Software in its Source Code and possibly its\n+Object Code form and, where applicable, its documentation, "as is" when\n+it is first distributed under the terms and conditions of the'..b"ase basis between the relevant Licensor and the\n+Licensee pursuant to a memorandum of understanding. The Licensor\n+disclaims any and all liability as regards the Licensee's use of the\n+name of the Software. No warranty is given as regards the existence of\n+prior rights over the name of the Software or as regards the existence\n+of a trademark.\n+\n+\n+ Article 10 - TERMINATION\n+\n+10.1 In the event of a breach by the Licensee of its obligations\n+hereunder, the Licensor may automatically terminate this Agreement\n+thirty (30) days after notice has been sent to the Licensee and has\n+remained ineffective.\n+\n+10.2 A Licensee whose Agreement is terminated shall no longer be\n+authorized to use, modify or distribute the Software. However, any\n+licenses that it may have granted prior to termination of the Agreement\n+shall remain valid subject to their having been granted in compliance\n+with the terms and conditions hereof.\n+\n+\n+ Article 11 - MISCELLANEOUS\n+\n+\n+ 11.1 EXCUSABLE EVENTS\n+\n+Neither Party shall be liable for any or all delay, or failure to\n+perform the Agreement, that may be attributable to an event of force\n+majeure, an act of God or an outside cause, such as defective\n+functioning or interruptions of the electricity or telecommunications\n+networks, network paralysis following a virus attack, intervention by\n+government authorities, natural disasters, water damage, earthquakes,\n+fire, explosions, strikes and labor unrest, war, etc.\n+\n+11.2 Any failure by either Party, on one or more occasions, to invoke\n+one or more of the provisions hereof, shall under no circumstances be\n+interpreted as being a waiver by the interested Party of its right to\n+invoke said provision(s) subsequently.\n+\n+11.3 The Agreement cancels and replaces any or all previous agreements,\n+whether written or oral, between the Parties and having the same\n+purpose, and constitutes the entirety of the agreement between said\n+Parties concerning said purpose. No supplement or modification to the\n+terms and conditions hereof shall be effective as between the Parties\n+unless it is made in writing and signed by their duly authorized\n+representatives.\n+\n+11.4 In the event that one or more of the provisions hereof were to\n+conflict with a current or future applicable act or legislative text,\n+said act or legislative text shall prevail, and the Parties shall make\n+the necessary amendments so as to comply with said act or legislative\n+text. All other provisions shall remain effective. Similarly, invalidity\n+of a provision of the Agreement, for any reason whatsoever, shall not\n+cause the Agreement as a whole to be invalid.\n+\n+\n+ 11.5 LANGUAGE\n+\n+The Agreement is drafted in both French and English and both versions\n+are deemed authentic.\n+\n+\n+ Article 12 - NEW VERSIONS OF THE AGREEMENT\n+\n+12.1 Any person is authorized to duplicate and distribute copies of this\n+Agreement.\n+\n+12.2 So as to ensure coherence, the wording of this Agreement is\n+protected and may only be modified by the authors of the License, who\n+reserve the right to periodically publish updates or new versions of the\n+Agreement, each with a separate number. These subsequent versions may\n+address new issues encountered by Free Software.\n+\n+12.3 Any Software distributed under a given version of the Agreement may\n+only be subsequently distributed under the same version of the Agreement\n+or a subsequent version, subject to the provisions of Article 5.3.4\n+<#compatibility>.\n+\n+\n+ Article 13 - GOVERNING LAW AND JURISDICTION\n+\n+13.1 The Agreement is governed by French law. The Parties agree to\n+endeavor to seek an amicable solution to any disagreements or disputes\n+that may arise during the performance of the Agreement.\n+\n+13.2 Failing an amicable solution within two (2) months as from their\n+occurrence, and unless emergency proceedings are necessary, the\n+disagreements or disputes shall be referred to the Paris Courts having\n+jurisdiction, by the more diligent Party.\n\\ No newline at end of file\n" |
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| diff -r 000000000000 -r de13e2c45971 README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Tue Jan 21 15:49:00 2020 -0500 |
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| @@ -0,0 +1,41 @@ +## ****** MON_MODULE environnemnt : ****** ## +# version 0.1 2019 F Giacomoni + +## --- PERL compilator / libraries : --- ## +$ perl -v +This is perl, v5.10.1 (*) built for x86_64-linux-thread-multi + +# libs CORE PERL : +use strict ; +use warnings ; +use Carp qw (cluck croak carp) ; +use Exporter ; +use Data::Dumper ; +use Getopt::Long ; +use FindBin ; + +# libs CPAN PERL : +$ perl -e 'use XX::XX' +$ sudo perl -MCPAN -e shell +cpan> install XX::XX + +-- + +## --- Binary dependencies --- ## +Install folowing binaries : +-- + +## --- Config : --- ## +Edit the config file : /path/*.conf + +-- + +## --- XML HELP PART --- ## +Copy the following images in ~/static/images/metabolomics : +-- + +## --- DATASETS --- ## +-- + +## --- ??? COMMENTS ??? --- ## +-- \ No newline at end of file |
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| diff -r 000000000000 -r de13e2c45971 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Tue Jan 21 15:49:00 2020 -0500 |
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| @@ -0,0 +1,4 @@ + +# BiH4MaConDa + +MS Contaminants Annotation package with MaConDa database. \ No newline at end of file |
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| diff -r 000000000000 -r de13e2c45971 _template.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/_template.tabular Tue Jan 21 15:49:00 2020 -0500 |
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| @@ -0,0 +1,1 @@ +_MESURED_MONOISOTOPIC_MASS_ _PPM_ERROR_ _COMPUTED_MONOISOTOPIC_MASS_ _ANNOTATION_NAME_ _ANNOTATION_TYPE_ _ANNOTATION_IN_NEG_MODE_ _ANNOTATION_IN_POS_MODE_ _ANNOTATION_FORMULA_ \ No newline at end of file |
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| diff -r 000000000000 -r de13e2c45971 bih4maconda.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bih4maconda.pl Tue Jan 21 15:49:00 2020 -0500 |
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| b'@@ -0,0 +1,244 @@\n+#!c:\\Perl\\bin\\perl.exe -w\r\n+\r\n+=head1 NAME\r\n+\r\n+bih4maconda.pl - Utility to detect potential contaminants in your peak list based on MaConDa database\r\n+\r\n+=head1 USAGE\r\n+\r\n+\r\n+=head1 SYNOPSIS\r\n+\r\n+=head1 DESCRIPTION\r\n+\r\n+=over 4\r\n+\r\n+=item B<function01>\r\n+\r\n+=item B<function02>\r\n+\r\n+=back\r\n+\r\n+=head1 AUTHOR\r\n+\r\n+Prenom Nom E<lt>franck.giacomoni@inra.frE<gt>\r\n+\r\n+=head1 SUPPORT\r\n+\r\n+You can find documentation for this module with the perldoc command.\r\n+\r\n+ perldoc bih4maconda.pl\r\n+\r\n+=head1 LICENSE\r\n+\r\n+This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.\r\n+\r\n+=head1 VERSION\r\n+\r\n+version 1 : 2019/07/24\r\n+\r\n+version 2 : ??\r\n+\r\n+=cut\r\n+#=============================================================================\r\n+# Included modules and versions\r\n+#=============================================================================\r\n+## Perl modules\r\n+use strict ;\r\n+use warnings ;\r\n+use diagnostics ;\r\n+use Carp qw (cluck croak carp) ;\r\n+\r\n+use Data::Dumper ;\r\n+use Getopt::Long ;\r\n+use File::Basename ;\r\n+use FindBin ; ## Allows you to locate the directory of original perl script\r\n+\r\n+## Specific Perl Modules (PFEM)\r\n+use lib $FindBin::Bin ;\r\n+my $binPath = $FindBin::Bin ;\r\n+\r\n+## Dedicate Perl Modules (Home made...)\r\n+use Metabolomics::Fragment::Annotation qw( :all ) ;\r\n+use Metabolomics::Banks qw( :all ) ;\r\n+use Metabolomics::Banks::BloodExposome qw( :all ) ;\r\n+use Metabolomics::Banks::MaConDa qw( :all ) ;\r\n+use Metabolomics::Banks::AbInitioFragments qw( :all ) ;\r\n+use Metabolomics::Utils qw( :all ) ;\r\n+\r\n+## Initialized values\r\n+my $ProgramName = basename($0) ;\r\n+my $OptionHelp = undef ;\r\n+my $VERBOSE = undef ;\r\n+\r\n+my ($inputFile, $mzCol, $asHeader, $ppmError, $mode, $instruments, $instrumentTypes) = (undef, undef, undef, undef, undef, undef, undef ) ;\r\n+my ($outputTabular, $outputXls, $outputHTML, $outputFull) = (undef, undef, undef, undef) ;\r\n+\r\n+my $QueryMode = undef ; # depending of the input data the query mode can be ION|NEUTRAL\r\n+\r\n+#=============================================================================\r\n+# Manage EXCEPTIONS\r\n+#=============================================================================\r\n+&GetOptions ( \t"h|help" => \\$OptionHelp, # HELP\r\n+\t\t\t\t"v|verbose=i"\t=> \\$VERBOSE,\t\t# Level of verbose (0 to 2)\r\n+\t\t\t\t"i|input=s"\t\t=> \\$inputFile, \t\t# Input file containing a peak list (mz)\r\n+\t\t\t\t"mzCol=i"\t\t=> \\$mzCol,\t\t\t\t# Column in CSV file for MZ\r\n+\t\t\t\t"header=i"\t\t=> \\$asHeader,\t\t\t\t# CSV file as header (1=true, 0=false)\r\n+\t\t\t\t"ppmError=f"\t=> \\$ppmError,\t\t\t\t# ppm error\r\n+\t\t\t\t"m|mode=s"\t\t=> \\$mode,\t\t\t\t# indicate the ionisation mode (POS|NEG|NEUTRAL)\r\n+\t\t\t\t"filterInstrument=s"\t=> \\$instruments,\t# instruments listing to apply filter\r\n+\t\t\t\t"filterInstrumentType=s"\t=> \\$instrumentTypes,\t# instrumentTypes listing to apply filter\r\n+\t\t\t\t"outputTab=s"\t\t=> \\$outputTabular,\t\t\t# output file in tabular format\r\n+\t\t\t\t"outputXls=s"\t\t=> \\$outputXls,\t\t\t# output file in Xls format\r\n+\t\t\t\t"outputHtml=s"\t\t=> \\$outputHTML,\t\t\t# output file in html format\r\n+\t\t\t\t"outputFull=s"\t\t=> \\$outputFull,\t\t\t# output file in full format\r\n+\t\t\t\t\r\n+ ) ;\r\n+ \r\n+## if you put the option -help or -h function help is started\r\n+if ( defined($OptionHelp) ){ &help ; }\r\n+\r\n+#=============================================================================\r\n+# MAIN SCRIPT\r\n+#=============================================================================\r\n+\r\n+if ($VERBOSE == 3) {\r\n+\tprint "The $ProgramName program is launched as:\\n";\r\n+\tprint "./$ProgramName " ;\r\n+\tprint "--h " if (defined $OptionHelp) ;\r\n+\tprint "--input $inputFile " if (defined $inputFile) ;\r\n+\tprint "--mzCol $mzCol " if (defined $mzCol) ;\r\n+\tprint "--header $asHeader " if (defined $asHeader) ;\r\n+\tprint "--ppmError $ppmError " if (defined $ppmError) ;\r\n+\tprint "--mode $mode " if (defined $mode) ;\r\n+\tprint "--fil'..b'pty bank object\r\n+\tmy $oBank = Metabolomics::Banks::MaConDa->new() ;\r\n+\t\r\n+\t# get contaminants bank\r\n+\tmy ($oFilteredContaminants, $totalEntryNum, $fiteredEntryNum) = (undef, 0, 0) ;\r\n+\t\r\n+\t$oBank->getContaminantsExtensiveFromSource() ;\r\n+\t\r\n+\t# Applying filters\r\n+\t\r\n+\t## Instrument #Filter01 (ALL|...)\r\n+\tif ( defined $instruments ) {\r\n+\t\tmy @instruments = split(/,/, $instruments) ;\r\n+\t\t($oFilteredContaminants, $totalEntryNum, $fiteredEntryNum) = $oBank->filterContaminantInstruments(\\@instruments) ;\r\n+\t\tprint "Only few instruments were selected: $fiteredEntryNum/$totalEntryNum entries were filtered.\\n" ;\r\n+\t}\r\n+\t## Instrument type #Filter02 (ALL|...)\r\n+\tif ( defined $instrumentTypes ) {\r\n+\t\t\r\n+\t\tmy @instrumentTypes = split(/,/, $instrumentTypes) ;\r\n+\t\tif (!defined $oFilteredContaminants){\t($oFilteredContaminants, $totalEntryNum, $fiteredEntryNum) = $oBank->filterContaminantInstrumentTypes(\\@instrumentTypes) ; \t\t}\r\n+\t\telse \t\t\t\t\t\t\t\t{\t($oFilteredContaminants, $totalEntryNum, $fiteredEntryNum) = $oFilteredContaminants->filterContaminantInstrumentTypes(\\@instrumentTypes) ; }\r\n+\t\t\r\n+\t\tprint "Only few instrument types were selected: $fiteredEntryNum/$totalEntryNum entries were filtered.\\n" ;\r\n+\t}\r\n+\t## Ion mode #Filter03 (POS|NEG|BOTH)\r\n+\tif ( defined $mode) {\r\n+\t\t\r\n+\t\tprint "Mode selected is $mode..." ;\r\n+\t\t\r\n+\t\tif (!defined $oFilteredContaminants){\t$oFilteredContaminants = $oBank->filterContaminantIonMode($mode) ; \t}\r\n+\t\telse \t\t\t\t\t\t\t\t{\t$oFilteredContaminants = $oFilteredContaminants->filterContaminantIonMode($mode) ; }\r\n+\t\t\r\n+\t\tif ( ($mode eq \'POSITIVE\') or ($mode eq \'NEGATIVE\') or ($mode eq \'BOTH\') ) {\r\n+\t\t\t$QueryMode = \'ION\' ;\r\n+\t\t}\r\n+\t\telsif ($mode eq \'NEUTRAL\') {\r\n+\t\t\t$QueryMode = \'NEUTRAL\' ;\r\n+\t\t}\r\n+\t\telse {\r\n+\t\t\tcroak "[ERROR] mode $mode is not recognize...Please defined a acceptable one\\n" ;\r\n+\t\t}\r\n+\t\tprint "and detected query mode is $QueryMode...\\n" ;\r\n+\t}\r\n+\t# in case no filter is defined beforr\r\n+\tif ( ( !defined $mode) and ( !defined $instruments) and ( !defined $instrumentTypes) ) {\r\n+\t\t$oFilteredContaminants = $oBank ;\r\n+\t}\r\n+\r\n+\t# build the query object\r\n+\t$oFilteredContaminants->buildTheoPeakBankFromContaminants($QueryMode) ;\r\n+\t\r\n+\t# get experimental masses\r\n+\tif ( (defined $mzCol) and (defined $asHeader) ) {\r\n+\t\t$oFilteredContaminants->parsingMsFragments($inputFile, $asHeader, $mzCol) ;\r\n+\t}\r\n+\t\r\n+\t## Analysis :\r\n+\tmy $oAnalysis = Metabolomics::Fragment::Annotation->new($oFilteredContaminants) ;\r\n+\t\r\n+\t\r\n+\t# Compare peaklists:\r\n+\t$oAnalysis->compareExpMzToTheoMzList(\'PPM\', $ppmError) ;\r\n+\t\r\n+#\tprint Dumper $oBank ;\r\n+\t\r\n+\t\r\n+\t\r\n+\t# complete initial input tabular file\r\n+\tif ( (defined $outputFull) and (defined $inputFile) ) {\r\n+\t\tmy $tabularfile = $oAnalysis->writeFullTabularWithPeakBankObject($inputFile, $oTEMPLATE, $outputFull)\r\n+\t}\r\n+\t# write a simple tabular output\r\n+\tif ( (defined $outputTabular) and (defined $inputFile) ) {\r\n+\t\tmy $tabularfile = $oAnalysis->writeTabularWithPeakBankObject($oTEMPLATE, $outputTabular) ;\r\n+\t}\r\n+}\r\n+else {\r\n+\tcroak "Input file is not defined or is not exist.\\n" ;\r\n+}\r\n+\r\n+\r\n+\r\n+\r\n+\r\n+#====================================================================================\r\n+# Help subroutine called with -h option\r\n+# number of arguments : 0\r\n+# Argument(s) :\r\n+# Return : 1\r\n+#====================================================================================\r\n+sub help {\r\n+\r\n+\r\n+print STDERR <<EOF ;\r\n+### $ProgramName ###\r\n+#\r\n+# AUTHOR: Franck Giacomoni\r\n+# VERSION: 1.0\r\n+# CREATED: 2019/08/21\r\n+# LAST MODIF: \r\n+# PURPOSE: This program annotates any known contaminants from ms analysis depending some filters as instruments, ionisation mode from MaConDa database \r\n+# USAGE: $ProgramName or $ProgramName --input *.tabular --mzCol INT --header INT --ppmError 5 --mode POSITIVE|NEGATIVE|NEUTRAL --outputTab outTab.tabular --outputFull outFull.tabular --verbose 3 \r\n+EOF\r\n+exit(1) ;\r\n+}\r\n+\r\n+## END of script - F Giacomoni \r\n+\r\n+__END__\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r de13e2c45971 bih4maconda.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bih4maconda.xml Tue Jan 21 15:49:00 2020 -0500 |
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| @@ -0,0 +1,179 @@ +<tool id="bih4maconda" name="Bih4MaConDa" version="0.1.3"> + <description> + : Utility to detect potential contaminants in your peak list based on MaConDa database + </description> + <requirements> + <requirement type="package" version="0.2.0">perl-metabolomics-fragment-annotation</requirement> + </requirements> + <stdio> + <exit_code range="1" level="fatal" /> + </stdio> + + <command><![CDATA[ + perl $__tool_directory__/bih4maconda.pl + -input $variableMetadata_in + -mzCol $colmass + + #if str($has_header.header_choice) == "YES": + -header "${has_header.header}" + #end if + + -ppmError $ppm_error + -mode $mode + -outputTab $outputTab + -outputFull $outFull + -verbose $verbose + ]]></command> + <inputs> + <param name="variableMetadata_in" type="data" label="Input file containing a list of mzs (format: tabular)" help="Generally variable metadata file" format="tabular" /> + + <conditional name="has_header"> + <param name="header_choice" type="boolean" checked="true" truevalue="YES" falsevalue="NO" label="Do you have a header?" help="if 'YES' is selected then enter your number of header lines" /> + <when value="YES"> + <param name="header" type="integer" label="Number of header lines" value="1" min="1" max="10" help="number of lines not containing masses"/> + </when> + <when value="NO"/> + </conditional> + + <param name="colmass" label="Column of masses (MZ)" type="data_column" data_ref="variableMetadata_in" accept_default="true" /> + + <param name="verbose" type="select" label="Verbose level" display="radio" help=""> + <option value="1" selected="true">Low</option> + <option value="3" >High</option> + </param> + + + <param name="ppm_error" label="Tolerance in ppm used during annotation step" type="float" value="5" min="0" max="300000" help="Default value is 5 ppm"/> + + <param name="mode" label="Molecular Species " type="select" display="radio" help=""> + <option value="POSITIVE">Positif Mode</option> + <option value="NEGATIVE">Negatif Mode</option> + <option value="NEUTRAL">Neutral Mass</option> + </param> + + </inputs> + <outputs> + <data name="outFull" format="tabular" label="${variableMetadata_in.name[:-6]}.BIH4MACONDA_Full.tabular" /> + <data name="outputTab" format="tabular" label="${variableMetadata_in.name[:-6]}.BIH4MACONDA.tabular" /> + </outputs> + + <help><![CDATA[ + +.. class:: infomark + +**Authors** + | Franck Giacomoni - FLAME ; PFEM ; INRA ; MetaboHUB (for original version and development of this Perl script and for xml interface and Perl wrapper) + +--------------------------------------------------- + + +====================== +bih4MaDonDa +====================== + +----------- +Description +----------- + + | detection of potential contaminants in your peak list based on MaConDa database + + +Keywords +======== + +contaminants + + +----------------- +Workflow position +----------------- + + +.. image:: + :width: 800 + + +----------- +Input files +----------- + + ++--------------------------------+-----------+ +| Parameter : num + label | Format | ++================================+===========+ +| 1 : File with a list of masses | tabular | ++--------------------------------+-----------+ + +File of masses (Generally variable metadata file) must have at least the following column : + | Masses : column with all the masses in the tabular input file + | + + +---------- +Parameters +---------- + +File of masses + | see "Input files" section above + | Tabular file format, Generally variable metadata file + | + +Do you have a header + | YES (default) : parameter **Number of header lines** is visible + | NO : all lines are considered to contain masses + | + +If 'have a header'='YES' + +Number of header lines + | Number of lines not containing masses values, these lines will be ignored + | + +In all header cases : + +Column of Masses + | Specify the column number for the mz in the tabular input file + | + + +In all cases : + +PPM error + | Specify a delta (in ppm) to apply on annotating mass - This value is a float. + | + + +------------ +Output files +------------ + +Two types of files (if you manually enter the masses both files are mingled): + | BIH4MACONDA_(input.name)_FULL.tabular : for linking with others modules. + | BIH4MACONDA_(input.name).tabular : an excel-like output will be available. + | + + +--------------------------------------------------- + +--------------- +Working example +--------------- + + +.. class:: warningmark + +Refer to the corresponding W4M HowTo section: http://workflow4metabolomics.org/howto + | Format Data For Postprocessing + | Perform LCMS Annotations + +.. class:: warningmark + +And their "W4M courses 2018": + | Using Galaxy4Metabolomics - W4M table format for Galaxy + | Annotation Banks - Annotation + + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/bts527</citation> + </citations> +</tool> \ No newline at end of file |
| b |
| diff -r 000000000000 -r de13e2c45971 conf.cfg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/conf.cfg Tue Jan 21 15:49:00 2020 -0500 |
| b |
| @@ -0,0 +1,6 @@ +## Conf file for bih4maconda.pl script +# +## Version the script +VERSION=0.1.0.0 +# +## ARGVT \ No newline at end of file |
| b |
| diff -r 000000000000 -r de13e2c45971 test-data/in_test01_pos.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in_test01_pos.tabular Tue Jan 21 15:49:00 2020 -0500 |
| b |
| @@ -0,0 +1,106 @@ +namecustom mz rt +M163.06T0.91_1 163.0600211 0.912616991 +M203.0526T0.91 203.0525999 0.911566282 +M441.0748T0.92 441.0747851 0.916097247 +M442.0783T0.92 442.0782549 0.916186495 +M55.0175T0.92 55.01752528 0.91666581 +M261.1445T7.64 261.1445305 7.641431623 +M499.0334T0.92 499.0334405 0.917392648 +M261.0113T0.92 261.0112717 0.916542478 +M223.0925T0.93 223.0924754 0.933717413 +M130.0862T1.19 130.0862383 1.188770749 +M351.1263T1 351.1263073 1.004764876 +M295.129T7.97 295.1289569 7.969298229 +M247.1288T6.16 247.1288408 6.164260224 +M501.0308T0.92 501.0308336 0.917928386 +M286.132T14.67 286.1320163 14.67302735 +M520.3397T14.67 520.3397216 14.67197174 +M118.0863T1.19 118.0862558 1.189372545 +M187.0577T1 187.0576896 1.004685352 +M132.1018T2.21 132.1018003 2.205312814 +M558.2954T14.67 558.2953679 14.67181976 +M263.0085T0.92 263.0085388 0.91659379 +M540.3166T14.67_2 540.3165587 14.6715756 +M232.1544T7.19 232.1543851 7.186558325 +M546.7962T14.67_1 546.7961664 14.66986086 +M357.2789T14.73 357.2788908 14.72633365 +M508.3776T17.1 508.3776335 17.09772877 +M302.6499T15.91 302.6499465 15.90538798 +M663.2685T9.4 663.2685122 9.403765695 +M682.242T9.41 682.2420345 9.405045319 +M467.8124T9.41 467.8124249 9.408233843 +M646.7104T9.72 646.7104123 9.723775829 +M657.6995T9.73_1 657.6994811 9.728430954 +M76.0391T1.2 76.03912315 1.202980924 +M690.2267T9.4 690.2267099 9.401721384 +M665.1818T9.73 665.1818291 9.726980925 +M638.7257T9.73_1 638.7257377 9.726128849 +M120.0655T0.9 120.0654827 0.898810452 +M282.6517T15.89 282.651664 15.88516814 +M541.3295T15.55 541.3294815 15.55423805 +M619.7523T9.73_1 619.7522549 9.725702763 +M277.1223T0.99 277.1222795 0.994139884 +M480.3449T15.59 480.3448707 15.5859208 +M118.0862T0.92 118.0862318 0.916688114 +M132.1018T2.52 132.101802 2.515621998 +M482.3605T15.52 482.3604772 15.51560582 +M281.6627T16.66_1 281.6627059 16.65766751 +M205.0573T0.91 205.0573067 0.913112018 +M276.9852T0.92 276.9851713 0.915792625 +M520.3398T14.88 520.3397934 14.8779262 +M323.0026T0.95 323.0025784 0.950513735 +M337.1121T9.27 337.1120525 9.268822682 +M438.8017T9.73_1 438.8017061 9.733084287 +M486.191T9.25 486.1910499 9.254694618 +M558.9894T0.92 558.9893584 0.916720651 +M548.8119T15.55_1 548.8119189 15.55415357 +M506.3607T15.94 506.3606561 15.94271835 +M565.2258T9.1 565.225847 9.097821323 +M72.0805T1.19 72.080525 1.194320605 +M321.6673T16.66_1 321.6673244 16.66299159 +M505.1644T9.26 505.1644212 9.260182382 +M210.0437T8.27 210.0437419 8.266156055 +M390.1359T9.11_2 390.1358901 9.113768325 +M137.5972T1.03 137.5971647 1.033860322 +M225.987T0.72 225.9869922 0.719940404 +M310.1615T16.66_2 310.1615467 16.65966195 +M570.3554T14.98 570.3553711 14.98019772 +M152.0366T0.73 152.0366063 0.725451016 +M542.3328T15.55_2 542.3327789 15.55478817 +M116.0706T0.98 116.0705554 0.9848725 +M105.0039T0.73_1 105.0038616 0.73215505 +M128.0195T0.73_2 128.0194748 0.729305706 +M110.0085T0.73_2 110.0085433 0.728925333 +M522.3554T15.56 522.3554426 15.5630593 +M524.3711T16.66 524.371144 16.65514946 +M556.9921T0.92 556.9920524 0.916955588 +M310.2015T10.61 310.2014857 10.61435039 +M170.0661T0.72_2 170.066114 0.724315422 +M290.6683T16.66_2 290.6682628 16.6615692 +M313.1603T16.66_2 313.1603103 16.66008074 +M62.5241T0.73_1 62.5241145 0.73232796 +M267.0427T8.26 267.0427295 8.26229812 +M389.8019T9.11_1 389.8019187 9.112956985 +M553.8318T16.66_1 553.8317957 16.66084814 +M568.3397T14.65 568.3396938 14.65477094 +M551.8313T16.66_1 551.8313241 16.66042173 +M62.0235T0.73_3 62.02349536 0.731972496 +M268.1544T7.98 268.1544071 7.982259846 +M82.0137T0.73_2 82.01370683 0.731192004 +M66.0185T0.73 66.01854141 0.73167329 +M291.1409T15.55_2 291.140918 15.55435739 +M429.1696T9.35 429.1696046 9.352239803 +M290.1431T15.56_2 290.1431152 15.55509376 +M290.6396T15.55_1 290.6396364 15.55471556 +M228.9558T0.82 228.9558107 0.817588977 +M550.8282T16.66_1 550.8281876 16.66001451 +M311.6638T16.66_1 311.6638456 16.65968704 +M102.5529T0.73_1 102.5529262 0.727739191 +M330.2463T13.4 330.2462958 13.39950997 +M55.0539T1.19 55.05392711 1.192797342 +M224.9902T0.72 224.9902413 0.721571604 +M504.3085T15.12 504.3085371 15.1162676 +M73.5315T0.73_1 73.53153592 0.72986669 +M552.3317T16.66_2 552.3316931 16.66077074 +M311.1625T16.37 311.1625016 16.37256941 +M320.168T16.66 320.1680163 16.66220714 \ No newline at end of file |
| b |
| diff -r 000000000000 -r de13e2c45971 test-data/in_test02_pos.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in_test02_pos.tabular Tue Jan 21 15:49:00 2020 -0500 |
| b |
| b'@@ -0,0 +1,1668 @@\n+VAR\tmz\tmzmin\tmzmax\trt\trtmin\trtmax\tnpeaks\tBio\tBlanc\tX20160802_Ech1xnist_pos_18\tX20160802_Ech2xnist_pos_20\tX20160802_Ech3xnist_pos_19\tX20160802_QC.EI_pos_17\tX20160802_QC.EI_pos_21\tX20160802_QC.EI.dil.1_pos_13\tX20160802_QC.EI.dil.1_pos_14\tX20160802_QC.EI.dil.1_pos_15\tX20160802_QC.EI.dil.2_pos_10\tX20160802_QC.EI.dil.2_pos_11\tX20160802_QC.EI.dil.2_pos_12\tX20160802_QC.EI.dil.4_pos_7\tX20160802_QC.EI.dil.4_pos_8\tX20160802_QC.EI.dil.4_pos_9\tX20160802_QC.EI.dil.8_pos_4\tX20160802_QC.EI.dil.8_pos_5\tX20160802_QC.EI.dil.8_pos_6\tX20160802_Blanc_pos_1\tX20160802_Blanc_pos_2\tX20160802_Blanc_pos_23\tX20160802_Blanc.EI_pos_16\tX20160802_Blanc.EI_pos_22\tX20160802_Blanc.EI_pos_3\n+VAR_1\t85.02824868\t85.02812056\t85.02834255\t60.55622129\t60.10856325\t60.63834513\t19\t17\t0\t1030119.271\t940467.9796\t790004.0272\t934897.5621\t947597.8053\t931172.0304\t878044.6734\t970543.5699\t489843.0727\t514941.5292\t487663.2933\t251849.9638\t248194.9457\t267660.5099\t142883.0165\t127127.5187\t122060.7061\t5013.397107\t3573.418541\t4137.02434\t901.4859458\t964.769447\t1920.914465\n+VAR_3\t86.06000081\t86.05996808\t86.06002745\t81.99327557\t81.79189593\t82.76919047\t9\t9\t0\t384931.8182\t356782.0855\t341385.5795\t381370.5376\t362101.3026\t338433.4251\t326045.8483\t328884.3226\t216403.095\t136483.8536\t227081.9985\t150913.0147\t158834.5488\t168464.9485\t109040.3465\t103152.4302\t111963.9508\t69901.95364\t82200.81962\t62853.39205\t61856.98986\t53115.68993\t71857.62375\n+VAR_5\t86.09638359\t86.09635642\t86.09640705\t80.30741419\t80.02595345\t80.78460356\t17\t17\t0\t15334047.43\t13426986.91\t11304842.3\t13221991.29\t13439443.73\t13490570.26\t13451890.07\t13426417.66\t6976948.246\t6893528.282\t6732783.827\t3419040.811\t3463371.814\t3422912.202\t1688443.278\t1663605.257\t1698440.43\t16289.4166\t12706.17699\t12690.25752\t8498.27405\t5963.797534\t1683.982051\n+VAR_7\t87.09970682\t87.09966188\t87.09975297\t80.40560963\t80.02595345\t83.05253367\t18\t17\t0\t1051009.723\t960616.5878\t727763.2381\t979552.3766\t955353.8236\t929549.6028\t938444.7497\t938574.5566\t480880.2065\t464619.0252\t447176.2101\t219071.4383\t222166.6971\t215816.2984\t103321.2286\t97050.33129\t88162.2024\t0\t0\t0\t0\t440.9795109\t0\n+VAR_13\t90.97651768\t90.97635914\t90.97662343\t45.00889749\t44.88142524\t45.16785076\t17\t17\t0\t5987822.67\t6431121.309\t6192741.114\t6298256.028\t5954451.485\t6203768.854\t6540152.793\t6248776.236\t5844185.95\t6111660.562\t6167698.051\t5423606.783\t5353239.645\t5254270.691\t4461016.444\t4310434.318\t3991122.432\t9917.921317\t9710.242323\t12188.24966\t0\t760.4593787\t6426.410963\n+VAR_14\t91.05411975\t91.05405236\t91.05419001\t254.6362915\t254.0811791\t254.9388284\t15\t15\t0\t896416.2592\t861828.3736\t607057.375\t738229.017\t802076.0195\t775114.1476\t784751.091\t734599.206\t393141.1208\t450755.7106\t427897.8866\t241912.0746\t222541.9915\t294910.0738\t216207.9057\t211991.0636\t138643.7502\t126466.3082\t137780.1758\t95643.63076\t111442.627\t103347.2132\t136469.0711\n+VAR_15\t91.0541234\t91.05408667\t91.05417279\t126.2712486\t125.2480072\t127.5040325\t14\t14\t0\t778150.3696\t700377.216\t585800.2735\t706971.8245\t669245.3205\t686570.0115\t735881.1096\t724398.4054\t364775.1995\t379783.8691\t352486.9225\t206265.3292\t209753.0517\t220623.9969\t175889.7628\t168240.2042\t184553.3921\t110444.2966\t110981.0084\t79141.1006\t99009.72798\t95016.79602\t121745.4352\n+VAR_16\t91.05414565\t91.05411214\t91.05419901\t70.09723308\t69.81107986\t70.4203558\t17\t17\t0\t2070693.9\t1743497.562\t1572237.087\t1842602.737\t1757877.994\t1745851.894\t1767906.963\t1734589.033\t963770.1718\t1086716.551\t1016691.475\t540328.0033\t530433.0416\t568747.0032\t299931.1429\t367456.7633\t313702.92\t127582.6072\t143358.2488\t97553.91503\t139959.6542\t126046.192\t153181.3162\n+VAR_19\t92.05750084\t92.05740534\t92.05757848\t69.88651932\t69.81107986\t70.32514049\t12\t12\t0\t145687.8955\t122421.2797\t97039.75509\t128960.5181\t120956.7346\t133328.235\t127493.5068\t114153.9401\t58022.39216\t64849.42571\t70183.41488\t29849.0395\t33282.89034\t30175.28192\t15292.60601\t23721.30227\t16376.98634\t0\t0\t979.9013818\t839.7008002\t0\t0\n+VAR_22\t93.04464898\t93.04459766\t93.04468872\t64.09930366\t63.3960997\t64.42730107\t18\t17\t1\t158616.0267\t176628.7668\t385332.072\t249001.7896\t245543.0744\t251933.5909\t269586.8638\t2'..b'9.2448452\t371.1009111\t370.7553307\t371.3223388\t13\t13\t0\t311893.7791\t378452.5524\t375392.322\t310084.7915\t365692.719\t347394.9329\t358990.6451\t374556.9571\t157481.2386\t114344.0032\t178994.2348\t78365.14874\t88670.82941\t89630.81839\t41827.68589\t35288.85496\t41935.36732\t1740.353513\t0\t0\t0\t0\t0\n+VAR_2813\t989.4949009\t989.4944011\t989.4954955\t371.0123596\t370.4050569\t371.3223388\t15\t15\t0\t785056.2697\t866787.0006\t807851.5058\t869458.0206\t711974.2675\t800967.1233\t706104.9715\t692510.6581\t394998.0648\t364221.3157\t308014.6614\t159108.3691\t162561.956\t145884.2813\t80680.47652\t57095.58421\t72319.0817\t6113.733376\t3085.991655\t0\t1402.704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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r de13e2c45971 test-data/in_test03_neg.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in_test03_neg.tabular Tue Jan 21 15:49:00 2020 -0500 |
| b |
| b'@@ -0,0 +1,865 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|
| b |
| diff -r 000000000000 -r de13e2c45971 test-data/outFull_test01.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outFull_test01.tabular Tue Jan 21 15:49:00 2020 -0500 |
| b |
| @@ -0,0 +1,106 @@ +namecustom mz rt _MESURED_MONOISOTOPIC_MASS_ _PPM_ERROR_ _COMPUTED_MONOISOTOPIC_MASS_ _ANNOTATION_NAME_ _ANNOTATION_TYPE_ _ANNOTATION_IN_NEG_MODE_ _ANNOTATION_IN_POS_MODE_ _ANNOTATION_FORMULA_ +M163.06T0.91_1 163.0600211 0.912616991 163.0600211 0 0 NA NA NA NA NA +M203.0526T0.91 203.0525999 0.911566282 203.0525999 0 0 NA NA NA NA NA +M441.0748T0.92 441.0747851 0.916097247 441.0747851 0 0 NA NA NA NA NA +M442.0783T0.92 442.0782549 0.916186495 442.0782549 0 0 NA NA NA NA NA +M55.0175T0.92 55.01752528 0.91666581 55.01752528 0 0 NA NA NA NA NA +M261.1445T7.64 261.1445305 7.641431623 261.1445305 0 0 NA NA NA NA NA +M499.0334T0.92 499.0334405 0.917392648 499.0334405 0 0 NA NA NA NA NA +M261.0113T0.92 261.0112717 0.916542478 261.0112717 0 0 NA NA NA NA NA +M223.0925T0.93 223.0924754 0.933717413 223.0924754 0 0 NA NA NA NA NA +M130.0862T1.19 130.0862383 1.188770749 130.0862383 0 0 NA NA NA NA NA +M351.1263T1 351.1263073 1.004764876 351.1263073 0 0 NA NA NA NA NA +M295.129T7.97 295.1289569 7.969298229 295.1289569 0 0 NA NA NA NA NA +M247.1288T6.16 247.1288408 6.164260224 247.1288408 0 0 NA NA NA NA NA +M501.0308T0.92 501.0308336 0.917928386 501.0308336 0 0 NA NA NA NA NA +M286.132T14.67 286.1320163 14.67302735 286.1320163 0 0 NA NA NA NA NA +M520.3397T14.67 520.3397216 14.67197174 520.3397216 0 0 NA NA NA NA NA +M118.0863T1.19 118.0862558 1.189372545 118.0862558 0 0 NA NA NA NA NA +M187.0577T1 187.0576896 1.004685352 187.0576896 0 0 NA NA NA NA NA +M132.1018T2.21 132.1018003 2.205312814 132.1018003 0 0 NA NA NA NA NA +M558.2954T14.67 558.2953679 14.67181976 558.2953679 0 0 NA NA NA NA NA +M263.0085T0.92 263.0085388 0.91659379 263.0085388 0 0 NA NA NA NA NA +M540.3166T14.67_2 540.3165587 14.6715756 540.3165587 0 0 NA NA NA NA NA +M232.1544T7.19 232.1543851 7.186558325 232.1543851 0 0 NA NA NA NA NA +M546.7962T14.67_1 546.7961664 14.66986086 546.7961664 0 0 NA NA NA NA NA +M357.2789T14.73 357.2788908 14.72633365 357.2788908 0 0 NA NA NA NA NA 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+M619.7523T9.73_1 619.7522549 9.725702763 619.7522549 0 0 NA NA NA NA NA +M277.1223T0.99 277.1222795 0.994139884 277.1222795 0 0 NA NA NA NA NA +M480.3449T15.59 480.3448707 15.5859208 480.3448707 0 0 NA NA NA NA NA +M118.0862T0.92 118.0862318 0.916688114 118.0862318 0 0 NA NA NA NA NA +M132.1018T2.52 132.101802 2.515621998 132.101802 0 0 NA NA NA NA NA +M482.3605T15.52 482.3604772 15.51560582 482.3604772 0 0 NA NA NA NA NA +M281.6627T16.66_1 281.6627059 16.65766751 281.6627059 0 0 NA NA NA NA NA +M205.0573T0.91 205.0573067 0.913112018 205.0573067 0 0 NA NA NA NA NA +M276.9852T0.92 276.9851713 0.915792625 276.9851713 0 0 NA NA NA NA NA +M520.3398T14.88 520.3397934 14.8779262 520.3397934 0 0 NA NA NA NA NA +M323.0026T0.95 323.0025784 0.950513735 323.0025784 0 0 NA NA NA NA NA +M337.1121T9.27 337.1120525 9.268822682 337.1120525 0 0 NA NA NA NA NA +M438.8017T9.73_1 438.8017061 9.733084287 438.8017061 0 0 NA NA NA NA NA +M486.191T9.25 486.1910499 9.254694618 486.1910499 0 0 NA NA NA NA NA 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| b |
| diff -r 000000000000 -r de13e2c45971 test-data/outFull_test02.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outFull_test02.tabular Tue Jan 21 15:49:00 2020 -0500 |
| b |
| b'@@ -0,0 +1,1668 @@\n+VAR\tmz\tmzmin\tmzmax\trt\trtmin\trtmax\tnpeaks\tBio\tBlanc\tX20160802_Ech1xnist_pos_18\tX20160802_Ech2xnist_pos_20\tX20160802_Ech3xnist_pos_19\tX20160802_QC.EI_pos_17\tX20160802_QC.EI_pos_21\tX20160802_QC.EI.dil.1_pos_13\tX20160802_QC.EI.dil.1_pos_14\tX20160802_QC.EI.dil.1_pos_15\tX20160802_QC.EI.dil.2_pos_10\tX20160802_QC.EI.dil.2_pos_11\tX20160802_QC.EI.dil.2_pos_12\tX20160802_QC.EI.dil.4_pos_7\tX20160802_QC.EI.dil.4_pos_8\tX20160802_QC.EI.dil.4_pos_9\tX20160802_QC.EI.dil.8_pos_4\tX20160802_QC.EI.dil.8_pos_5\tX20160802_QC.EI.dil.8_pos_6\tX20160802_Blanc_pos_1\tX20160802_Blanc_pos_2\tX20160802_Blanc_pos_23\tX20160802_Blanc.EI_pos_16\tX20160802_Blanc.EI_pos_22\tX20160802_Blanc.EI_pos_3\t_MESURED_MONOISOTOPIC_MASS_\t_PPM_ERROR_\t_COMPUTED_MONOISOTOPIC_MASS_\t_ANNOTATION_NAME_\t_ANNOTATION_TYPE_\t_ANNOTATION_IN_NEG_MODE_\t_ANNOTATION_IN_POS_MODE_\t_ANNOTATION_FORMULA_\n+VAR_1\t85.02824868\t85.02812056\t85.02834255\t60.55622129\t60.10856325\t60.63834513\t19\t17\t0\t1030119.271\t940467.9796\t790004.0272\t934897.5621\t947597.8053\t931172.0304\t878044.6734\t970543.5699\t489843.0727\t514941.5292\t487663.2933\t251849.9638\t248194.9457\t267660.5099\t142883.0165\t127127.5187\t122060.7061\t5013.397107\t3573.418541\t4137.02434\t901.4859458\t964.769447\t1920.914465\t85.02824868\t0\t0\tNA\tNA\tNA\tNA\tNA\n+VAR_3\t86.06000081\t86.05996808\t86.06002745\t81.99327557\t81.79189593\t82.76919047\t9\t9\t0\t384931.8182\t356782.0855\t341385.5795\t381370.5376\t362101.3026\t338433.4251\t326045.8483\t328884.3226\t216403.095\t136483.8536\t227081.9985\t150913.0147\t158834.5488\t168464.9485\t109040.3465\t103152.4302\t111963.9508\t69901.95364\t82200.81962\t62853.39205\t61856.98986\t53115.68993\t71857.62375\t86.06000081\t0\t0\tNA\tNA\tNA\tNA\tNA\n+VAR_5\t86.09638359\t86.09635642\t86.09640705\t80.30741419\t80.02595345\t80.78460356\t17\t17\t0\t15334047.43\t13426986.91\t11304842.3\t13221991.29\t13439443.73\t13490570.26\t13451890.07\t13426417.66\t6976948.246\t6893528.282\t6732783.827\t3419040.811\t3463371.814\t3422912.202\t1688443.278\t1663605.257\t1698440.43\t16289.4166\t12706.17699\t12690.25752\t8498.27405\t5963.797534\t1683.982051\t86.09638359\t0\t0\tNA\tNA\tNA\tNA\tNA\n+VAR_7\t87.09970682\t87.09966188\t87.09975297\t80.40560963\t80.02595345\t83.05253367\t18\t17\t0\t1051009.723\t960616.5878\t727763.2381\t979552.3766\t955353.8236\t929549.6028\t938444.7497\t938574.5566\t480880.2065\t464619.0252\t447176.2101\t219071.4383\t222166.6971\t215816.2984\t103321.2286\t97050.33129\t88162.2024\t0\t0\t0\t0\t440.9795109\t0\t87.09970682\t0\t0\tNA\tNA\tNA\tNA\tNA\n+VAR_13\t90.97651768\t90.97635914\t90.97662343\t45.00889749\t44.88142524\t45.16785076\t17\t17\t0\t5987822.67\t6431121.309\t6192741.114\t6298256.028\t5954451.485\t6203768.854\t6540152.793\t6248776.236\t5844185.95\t6111660.562\t6167698.051\t5423606.783\t5353239.645\t5254270.691\t4461016.444\t4310434.318\t3991122.432\t9917.921317\t9710.242323\t12188.24966\t0\t760.4593787\t6426.410963\t90.97651768\t0\t0\tNA\tNA\tNA\tNA\tNA\n+VAR_14\t91.05411975\t91.05405236\t91.05419001\t254.6362915\t254.0811791\t254.9388284\t15\t15\t0\t896416.2592\t861828.3736\t607057.375\t738229.017\t802076.0195\t775114.1476\t784751.091\t734599.206\t393141.1208\t450755.7106\t427897.8866\t241912.0746\t222541.9915\t294910.0738\t216207.9057\t211991.0636\t138643.7502\t126466.3082\t137780.1758\t95643.63076\t111442.627\t103347.2132\t136469.0711\t91.05411975\t0\t0\tNA\tNA\tNA\tNA\tNA\n+VAR_15\t91.0541234\t91.05408667\t91.05417279\t126.2712486\t125.2480072\t127.5040325\t14\t14\t0\t778150.3696\t700377.216\t585800.2735\t706971.8245\t669245.3205\t686570.0115\t735881.1096\t724398.4054\t364775.1995\t379783.8691\t352486.9225\t206265.3292\t209753.0517\t220623.9969\t175889.7628\t168240.2042\t184553.3921\t110444.2966\t110981.0084\t79141.1006\t99009.72798\t95016.79602\t121745.4352\t91.0541234\t0\t0\tNA\tNA\tNA\tNA\tNA\n+VAR_16\t91.05414565\t91.05411214\t91.05419901\t70.09723308\t69.81107986\t70.4203558\t17\t17\t0\t2070693.9\t1743497.562\t1572237.087\t1842602.737\t1757877.994\t1745851.894\t1767906.963\t1734589.033\t963770.1718\t1086716.551\t1016691.475\t540328.0033\t530433.0416\t568747.0032\t299931.1429\t367456.7633\t313702.92\t127582.6072\t143358.2488\t97553.91503\t139959.6542\t126046.192\t153181.3162\t91.05414565\t0\t0\tNA\tNA\tNA\tNA\tNA\n+VAR_19\t92.05750084\t92.05740534\t92.05757848\t69.88651932\t69.81107986\t70'..b'989.4954955\t371.0123596\t370.4050569\t371.3223388\t15\t15\t0\t785056.2697\t866787.0006\t807851.5058\t869458.0206\t711974.2675\t800967.1233\t706104.9715\t692510.6581\t394998.0648\t364221.3157\t308014.6614\t159108.3691\t162561.956\t145884.2813\t80680.47652\t57095.58421\t72319.0817\t6113.733376\t3085.991655\t0\t1402.704632\t0\t0\t989.4949009\t0\t0\tNA\tNA\tNA\tNA\tNA\n+VAR_2814\t989.7454641\t989.7450768\t989.7461973\t371.2555426\t370.5528292\t371.5653288\t15\t15\t0\t904873.5242\t964332.226\t952588.354\t788882.1914\t827149.7335\t856540.9553\t830209.9552\t899930.3871\t405259.9024\t406629.0868\t383240.7596\t213597.5225\t210659.3845\t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|
| b |
| diff -r 000000000000 -r de13e2c45971 test-data/outFull_test03.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outFull_test03.tabular Tue Jan 21 15:49:00 2020 -0500 |
| [ |
| b'@@ -0,0 +1,865 @@\n+name\tnamecustom\tmz\tmzmin\tmzmax\trt\trtmin\trtmax\tnpeaks\tsample\tblanc\tNbPool\tX.Pool0\tX.PoolNon0\tMean_blanc\tMean_Other\tfold_Other_VS_blanc\tnorm.b1\tnorm.b2\tnorm.b3\tnorm.b4\tCV.samp\tCV.pool\tCV.ind\tsample_mean\tsample_sd\tsample_CV\tpool_mean\tpool_sd\tpool_CV\tpoolCV_over_sampleCV\t_MESURED_MONOISOTOPIC_MASS_\t_PPM_ERROR_\t_COMPUTED_MONOISOTOPIC_MASS_\t_ANNOTATION_NAME_\t_ANNOTATION_TYPE_\t_ANNOTATION_IN_NEG_MODE_\t_ANNOTATION_IN_POS_MODE_\t_ANNOTATION_FORMULA_\n+M45T38\tM44.9981T0.63\t44.9981010714674\t44.9976804761414\t44.9984569216727\t0.634833333333333\t0.308666666666667\t0.668483333333333\t494\t450\t4\t0\t0\t100\t372.125\t106302.726872247\t285.664029216652\t0\t0\t0\t0\t0.387595943667356\t0.0582029852286417\t1\t106302.726872247\t41202.5057364617\t0.387595943667356\t106302.726872247\t6187.1360419097\t0.0582029852286417\t0.150164072095122\t44.9981010714674\t2.27787390043874\t44.9982036\t"Formic acid"\tunknown\t[M-H]-\tNA\tNA\n+M45T427\tM44.9981T7.12\t44.9981024029652\t44.9978232239459\t44.9985756743207\t7.11828333333333\t6.87948333333333\t7.25576666666667\t433\t421\t1\t0\t0\t100\t39.5\t5330.86343612335\t134.958568003123\t1\t1\t1\t1\t0.486770821402075\t0.0755019920383209\t1\t5067.71589705261\t2466.81622984065\t0.486770821402075\t5307.8799418585\t400.755509110564\t0.0755019920383209\t0.15510788387202\t44.9981024029652\t2.24898372588555\t44.9982036\t"Formic acid"\tunknown\t[M-H]-\tNA\tNA\n+M45T909\tM44.9981T15.14\t44.998112256197\t44.9974528882205\t44.9984883944837\t15.1422833333333\t14.6795666666667\t15.45055\t449\t425\t0\t0\t0\t100\t0\t5702.70484581498\tInf\t1\t1\t1\t1\t0.53981872056282\t0.0676576374883456\t1\t5685.11872119033\t3068.9335143207\t0.53981872056282\t5691.48339870913\t385.072320560799\t0.0676576374883456\t0.125333996230818\t44.998112256197\t2.02897400406895\t44.9982036\t"Formic acid"\tunknown\t[M-H]-\tNA\tNA\n+M57T59\tM57.0345T0.98\t57.034452592233\t57.0341895154699\t57.0349020897492\t0.97715\t0.891466666666667\t1.0799\t356\t353\t0\t2\t4\t96\t0\t11698.3942731278\tInf\t1\t0\t0\t0\t0.870673331712721\t0.280007916504815\t1\t12816.0067554922\t11158.5553010572\t0.870673331712721\t11623.434773665\t3254.65375360354\t0.280007916504815\t0.321599279897554\t57.034452592233\t0\t0\tNA\tNA\tNA\tNA\tNA\n+M59T39\tM59.0137T0.65\t59.0137157156687\t59.0135105287772\t59.0139254556355\t0.651733333333333\t0.582795008635214\t0.702561675301881\t405\t404\t0\t0\t0\t100\t0\t104954.370044053\tInf\t1\t1\t1\t1\t0.682371665277953\t0.0561292163222426\t1\t113379.85923403\t77367.2033545047\t0.682371665277953\t104631.322662158\t5872.87414378662\t0.0561292163222426\t0.0822560771180019\t59.0137157156687\t2.33674491307088\t59.0138536\t"Acetic Acid"\tSolvent\t[M-H]-\tNA\tNA\n+M59T47\tM59.0137T0.79\t59.0137129234658\t59.0134415820214\t59.0139307039268\t0.787416666666667\t0.737789375508069\t0.805966666666667\t404\t404\t0\t1\t2\t98\t0\t86687.6563876652\tInf\t1\t1\t0\t0\t0.699295472836914\t0.203036202545209\t1\t94711.9005025219\t66231.6032451938\t0.699295472836914\t86638.2036142797\t17590.691857182\t0.203036202545209\t0.290343939624732\t59.0137129234658\t2.38419162309737\t59.0138536\t"Acetic Acid"\tSolvent\t[M-H]-\tNA\tNA\n+M62T62\tM61.9882T1.03\t61.9882231262141\t61.9879375365369\t61.9886153953783\t1.02705\t0.771633333333333\t1.24938333333333\t572\t391\t0\t0\t0\t100\t0\t5964.59471365639\tInf\t1\t1\t1\t0\t0.772869775235845\t0.114595417144577\t1\t5731.41979586296\t4429.64112941088\t0.772869775235845\t5952.9251522387\t682.17794105124\t0.114595417144577\t0.148272607904233\t61.9882231262141\t0\t0\tNA\tNA\tNA\tNA\tNA\n+M71T38\tM71.0137T0.64\t71.0137007829942\t71.0134767633343\t71.0139365242841\t0.635183333333333\t0.565695008635214\t0.702561675301881\t389\t388\t0\t0\t0\t100\t0\t144096.834801762\tInf\t1\t0\t1\t1\t0.73936154758788\t0.0415654336080057\t1\t135114.575760127\t99898.5218356878\t0.73936154758788\t144256.931636383\t5996.1019144267\t0.0415654336080057\t0.056218008285135\t71.0137007829942\t0\t0\tNA\tNA\tNA\tNA\tNA\n+M71T47\tM71.0137T0.79\t71.0136946160437\t71.0134130011465\t71.0138774244458\t0.787325\t0.737789375508069\t0.8048\t402\t402\t0\t0\t0\t100\t0\t123655.279735683\tInf\t1\t1\t1\t1\t0.614164506961179\t0.104164502024361\t1\t135047.510129742\t82941.3874751677\t0.614164506961179\t123151.266583372\t12827.9903573262\t0.104164502024361\t0.16960358477854\t71.0136946160437\t0\t0\tNA\tNA\tNA\tNA\tNA\n+M73T3'..b'8.21780558257\t0\t0\tNA\tNA\tNA\tNA\tNA\n+M528T1308\tM528.2635T21.79\t528.263516655274\t528.259457858185\t528.26524712255\t21.7942133052719\t21.7120166666667\t22.2077666666667\t438\t432\t0\t1\t2\t98\t0\t10006.8325991189\tInf\t0\t0\t0\t0\t1.07990461335397\t0.194231858409978\t1\t10006.8325991189\t10806.4246888494\t1.07990461335397\t10006.8325991189\t1943.64569252442\t0.194231858409978\t0.17986019876953\t528.263516655274\t0\t0\tNA\tNA\tNA\tNA\tNA\n+M539T841\tM539.2497T14.01\t539.249704833549\t539.246704878734\t539.250965044909\t14.0117083333333\t13.9441450086352\t14.2013333333333\t440\t432\t0\t0\t0\t100\t0\t111174.317180617\tInf\t0\t1\t0\t0\t0.792480262065131\t0.0749274651473984\t1\t115760.916652513\t91738.2415656829\t0.792480262065131\t111069.766048395\t8322.17602452085\t0.0749274651473984\t0.0945480521522951\t539.249704833549\t0\t0\tNA\tNA\tNA\tNA\tNA\n+M541T824\tM541.2653T13.74\t541.265340181727\t541.262598396606\t541.266677688935\t13.7381166666667\t13.6027766029377\t13.7568\t557\t434\t0\t0\t0\t100\t0\t86021\tInf\t0\t0\t0\t0\t0.941002522159995\t0.0684516515502331\t1\t86021\t80945.9779587249\t0.941002522159995\t86021\t5888.2795180026\t0.0684516515502331\t0.0727433242082156\t541.265340181727\t0\t0\tNA\tNA\tNA\tNA\tNA\n+M542T824\tM542.2688T13.74\t542.268754418979\t542.265802195411\t542.270470223424\t13.7383166666667\t13.6182333333333\t13.7565\t436\t372\t0\t0\t0\t100\t0\t24280.640969163\tInf\t0\t0\t0\t0\t1.04757931820445\t0.0737816058993656\t1\t24280.640969163\t25435.8973120427\t1.04757931820445\t24280.640969163\t1791.46468297078\t0.0737816058993656\t0.070430567516193\t542.268754418979\t0\t0\tNA\tNA\tNA\tNA\tNA\n+M545T779\tM545.0607T12.99\t545.060726066373\t545.057988354302\t545.062808882584\t12.9858\t12.9359762774377\t13.0373666666667\t279\t279\t0\t3\t6\t94\t0\t5628.55286343612\tInf\t0\t0\t0\t0\t1.88590495128868\t0.266431663671691\t1\t5628.55286343612\t10614.9157137443\t1.88590495128868\t5628.55286343612\t1499.62470346935\t0.266431663671691\t0.141275234199705\t545.060726066373\t0\t0\tNA\tNA\tNA\tNA\tNA\n+M549T508\tM549.1966T8.47\t549.196578370134\t549.194609696492\t549.198992281771\t8.468475\t8.3336\t8.65851666666667\t430\t423\t0\t0\t0\t100\t0\t3055.55947136564\tInf\t1\t0\t1\t1\t0.51154234405948\t0.0612190278200437\t1\t3046.63935114673\t1558.48503518945\t0.51154234405948\t3053.2550567042\t186.917306258064\t0.0612190278200437\t0.119675386663446\t549.196578370134\t0\t0\tNA\tNA\tNA\tNA\tNA\n+M589T427\tM589.0789T7.12\t589.078922595953\t589.077237536806\t589.081215283794\t7.116475\t6.99778333333333\t7.391\t414\t406\t0\t1\t2\t98\t0\t3541.75991189427\tInf\t1\t1\t1\t1\t0.641058946176718\t0.173421108913947\t1\t3757.7356852892\t2408.93007842215\t0.641058946176718\t3525.09408317299\t611.325724929853\t0.173421108913947\t0.270522874609631\t589.078922595953\t0\t0\tNA\tNA\tNA\tNA\tNA\n+M597T848\tM597.0355T14.13\t597.035458390502\t597.032199718751\t597.037373887769\t14.131675\t13.9101166666667\t14.2874833333333\t306\t292\t0\t1\t2\t98\t0\t1803.56167400881\tInf\t1\t1\t1\t1\t1.0086359197998\t0.183661315560128\t1\t1540.20590950059\t1553.50700421021\t1.0086359197998\t1806.01555904545\t331.695193496347\t0.183661315560128\t0.182088811190248\t597.035458390502\t0\t0\tNA\tNA\tNA\tNA\tNA\n+M620T848\tM620.1114T14.13\t620.11139614437\t620.107847155817\t620.11395716599\t14.1313833333333\t13.9101166666667\t14.2703666666667\t303\t282\t0\t2\t4\t96\t0\t1773.85462555066\tInf\t1\t1\t1\t1\t1.08588450569221\t0.260058900537612\t1\t1564.00011717114\t1698.32349413694\t1.08588450569221\t1779.18600431567\t462.69315613424\t0.260058900537612\t0.239490387029543\t620.11139614437\t0\t0\tNA\tNA\tNA\tNA\tNA\n+M632T48\tM632.2043T0.81\t632.204277707095\t632.201522120288\t632.20679538411\t0.805841666666667\t0.617716666666667\t0.891789375508069\t426\t419\t0\t0\t0\t100\t0\t4752.77092511013\tInf\t0\t0\t0\t0\t0.824210316126959\t0.084483210089128\t1\t4752.77092511013\t3917.28282666404\t0.824210316126959\t4752.77092511013\t401.529344571579\t0.084483210089128\t0.102502005175235\t632.204277707095\t0\t0\tNA\tNA\tNA\tNA\tNA\n+M673T58\tM673.2308T0.96\t673.230782174437\t673.22806226468\t673.234389373999\t0.9599\t0.754975599898232\t1.04541666666667\t539\t431\t0\t0\t0\t100\t0\t3614.26872246696\tInf\t0\t1\t0\t0\t0.634168416277549\t0.0933177917127732\t1\t3506.07207336133\t2223.4401741185\t0.634168416277549\t3615.11878313412\t337.354901621444\t0.0933177917127732\t0.147149856911089\t673.230782174437\t0\t0\tNA\tNA\tNA\tNA\tNA\n' |
| b |
| diff -r 000000000000 -r de13e2c45971 test-data/outTab_test01.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outTab_test01.tabular Tue Jan 21 15:49:00 2020 -0500 |
| b |
| @@ -0,0 +1,106 @@ +_MESURED_MONOISOTOPIC_MASS_ _PPM_ERROR_ _COMPUTED_MONOISOTOPIC_MASS_ _ANNOTATION_NAME_ _ANNOTATION_TYPE_ _ANNOTATION_IN_NEG_MODE_ _ANNOTATION_IN_POS_MODE_ _ANNOTATION_FORMULA_ +163.0600211 0 0 NA NA NA NA NA +203.0525999 0 0 NA NA NA NA NA +441.0747851 0 0 NA NA NA NA NA +442.0782549 0 0 NA NA NA NA NA +55.01752528 0 0 NA NA NA NA NA +261.1445305 0 0 NA NA NA NA NA +499.0334405 0 0 NA NA NA NA NA +261.0112717 0 0 NA NA NA NA NA +223.0924754 0 0 NA NA NA NA NA +130.0862383 0 0 NA NA NA NA NA +351.1263073 0 0 NA NA NA NA NA +295.1289569 0 0 NA NA NA NA NA +247.1288408 0 0 NA NA NA NA NA +501.0308336 0 0 NA NA NA NA NA +286.1320163 0 0 NA NA NA NA NA +520.3397216 0 0 NA NA NA NA NA +118.0862558 0 0 NA NA NA NA NA +187.0576896 0 0 NA NA NA NA NA +132.1018003 0 0 NA NA NA NA NA +558.2953679 0 0 NA NA NA NA NA +263.0085388 0 0 NA NA NA NA NA +540.3165587 0 0 NA NA NA NA NA +232.1543851 0 0 NA NA NA NA NA +546.7961664 0 0 NA NA NA NA NA +357.2788908 0 0 NA NA NA NA NA +508.3776335 0 0 NA NA NA NA NA +302.6499465 0 0 NA NA NA NA NA +663.2685122 0 0 NA NA NA NA NA +682.2420345 0 0 NA NA NA NA NA +467.8124249 0 0 NA NA NA NA NA +646.7104123 0 0 NA NA NA NA NA +657.6994811 0 0 NA NA NA NA NA +76.03912315 0 0 NA NA NA NA NA +690.2267099 0 0 NA NA NA NA NA +665.1818291 0 0 NA NA NA NA NA +638.7257377 0 0 NA NA NA NA NA +120.0654827 0 0 NA NA NA NA NA +282.651664 0 0 NA NA NA NA NA +541.3294815 0 0 NA NA NA NA NA +619.7522549 0 0 NA NA NA NA NA +277.1222795 0 0 NA NA NA NA NA +480.3448707 0 0 NA NA NA NA NA +118.0862318 0 0 NA NA NA NA NA +132.101802 0 0 NA NA NA NA NA +482.3604772 0 0 NA NA NA NA NA +281.6627059 0 0 NA NA NA NA NA +205.0573067 0 0 NA NA NA NA NA +276.9851713 0 0 NA NA NA NA NA +520.3397934 0 0 NA NA NA NA NA +323.0025784 0 0 NA NA NA NA NA +337.1120525 0 0 NA NA NA NA NA +438.8017061 0 0 NA NA NA NA NA +486.1910499 0 0 NA NA NA NA NA +558.9893584 0 0 NA NA NA NA NA +548.8119189 0 0 NA NA NA NA NA +506.3606561 0 0 NA NA NA NA NA +565.225847 0 0 NA NA NA NA NA +72.080525 0 0 NA NA NA NA NA +321.6673244 0 0 NA NA NA NA NA +505.1644212 0 0 NA NA NA NA NA +210.0437419 0 0 NA NA NA NA NA +390.1358901 0 0 NA NA NA NA NA +137.5971647 0 0 NA NA NA NA NA +225.9869922 0 0 NA NA NA NA NA +310.1615467 0 0 NA NA NA NA NA +570.3553711 0 0 NA NA NA NA NA +152.0366063 0 0 NA NA NA NA NA +542.3327789 0 0 NA NA NA NA NA +116.0705554 0 0 NA NA NA NA NA +105.0038616 0 0 NA NA NA NA NA +128.0194748 0 0 NA NA NA NA NA +110.0085433 0 0 NA NA NA NA NA +522.3554426 0 0 NA NA NA NA NA +524.371144 0 0 NA NA NA NA NA +556.9920524 0 0 NA NA NA NA NA +310.2014857 0 0 NA NA NA NA NA +170.066114 0 0 NA NA NA NA NA +290.6682628 0 0 NA NA NA NA NA +313.1603103 0 0 NA NA NA NA NA +62.5241145 0 0 NA NA NA NA NA +267.0427295 0 0 NA NA NA NA NA +389.8019187 0 0 NA NA NA NA NA +553.8317957 0 0 NA NA NA NA NA +568.3396938 0 0 NA NA NA NA NA +551.8313241 0 0 NA NA NA NA NA +62.02349536 0 0 NA NA NA NA NA +268.1544071 0 0 NA NA NA NA NA +82.01370683 0 0 NA NA NA NA NA +66.01854141 0 0 NA NA NA NA NA +291.140918 0 0 NA NA NA NA NA +429.1696046 0 0 NA NA NA NA NA +290.1431152 0 0 NA NA NA NA NA +290.6396364 0 0 NA NA NA NA NA +228.9558107 0 0 NA NA NA NA NA +550.8281876 0 0 NA NA NA NA NA +311.6638456 0 0 NA NA NA NA NA +102.5529262 0 0 NA NA NA NA NA +330.2462958 0 0 NA NA NA NA NA +55.05392711 0 0 NA NA NA NA NA +224.9902413 0 0 NA NA NA NA NA +504.3085371 0 0 NA NA NA NA NA +73.53153592 0 0 NA NA NA NA NA +552.3316931 0 0 NA NA NA NA NA +311.1625016 0 0 NA NA NA NA NA +320.1680163 0 0 NA NA NA NA NA |
| b |
| diff -r 000000000000 -r de13e2c45971 test-data/outTab_test02.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outTab_test02.tabular Tue Jan 21 15:49:00 2020 -0500 |
| [ |
| b'@@ -0,0 +1,1668 @@\n+_MESURED_MONOISOTOPIC_MASS_\t_PPM_ERROR_\t_COMPUTED_MONOISOTOPIC_MASS_\t_ANNOTATION_NAME_\t_ANNOTATION_TYPE_\t_ANNOTATION_IN_NEG_MODE_\t_ANNOTATION_IN_POS_MODE_\t_ANNOTATION_FORMULA_\n+85.02824868\t0\t0\tNA\tNA\tNA\tNA\tNA\n+86.06000081\t0\t0\tNA\tNA\tNA\tNA\tNA\n+86.09638359\t0\t0\tNA\tNA\tNA\tNA\tNA\n+87.09970682\t0\t0\tNA\tNA\tNA\tNA\tNA\n+90.97651768\t0\t0\tNA\tNA\tNA\tNA\tNA\n+91.05411975\t0\t0\tNA\tNA\tNA\tNA\tNA\n+91.0541234\t0\t0\tNA\tNA\tNA\tNA\tNA\n+91.05414565\t0\t0\tNA\tNA\tNA\tNA\tNA\n+92.05750084\t0\t0\tNA\tNA\tNA\tNA\tNA\n+93.04464898\t0\t0\tNA\tNA\tNA\tNA\tNA\n+93.0698056\t0\t0\tNA\tNA\tNA\tNA\tNA\n+95.04905378\t0\t0\tNA\tNA\tNA\tNA\tNA\n+95.04905446\t0\t0\tNA\tNA\tNA\tNA\tNA\n+96.92165507\t0\t0\tNA\tNA\tNA\tNA\tNA\n+98.91909786\t0\t0\tNA\tNA\tNA\tNA\tNA\n+98.98406631\t0\t0\tNA\tNA\tNA\tNA\tNA\n+100.0755839\t1.06419563943209\t100.0756904\t"N-Methyl 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|
| b |
| diff -r 000000000000 -r de13e2c45971 test-data/outTab_test03.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outTab_test03.tabular Tue Jan 21 15:49:00 2020 -0500 |
| [ |
| b'@@ -0,0 +1,865 @@\n+_MESURED_MONOISOTOPIC_MASS_\t_PPM_ERROR_\t_COMPUTED_MONOISOTOPIC_MASS_\t_ANNOTATION_NAME_\t_ANNOTATION_TYPE_\t_ANNOTATION_IN_NEG_MODE_\t_ANNOTATION_IN_POS_MODE_\t_ANNOTATION_FORMULA_\n+44.9981010714674\t2.27787390043874\t44.9982036\t"Formic acid"\tunknown\t[M-H]-\tNA\tNA\n+44.9981024029652\t2.24898372588555\t44.9982036\t"Formic acid"\tunknown\t[M-H]-\tNA\tNA\n+44.998112256197\t2.02897400406895\t44.9982036\t"Formic acid"\tunknown\t[M-H]-\tNA\tNA\n+57.034452592233\t0\t0\tNA\tNA\tNA\tNA\tNA\n+59.0137157156687\t2.33674491307088\t59.0138536\t"Acetic Acid"\tSolvent\t[M-H]-\tNA\tNA\n+59.0137129234658\t2.38419162309737\t59.0138536\t"Acetic Acid"\tSolvent\t[M-H]-\tNA\tNA\n+61.9882231262141\t0\t0\tNA\tNA\tNA\tNA\tNA\n+71.0137007829942\t0\t0\tNA\tNA\tNA\tNA\tNA\n+71.0136946160437\t0\t0\tNA\tNA\tNA\tNA\tNA\n+72.9929608377945\t0\t0\tNA\tNA\tNA\tNA\tNA\n+73.0293713662007\t0\t0\tNA\tNA\tNA\tNA\tNA\n+74.0246025925501\t0\t0\tNA\tNA\tNA\tNA\tNA\n+75.0086106690331\t0\t0\tNA\tNA\tNA\tNA\tNA\n+78.9187053591132\t0\t0\tNA\tNA\tNA\tNA\tNA\n+78.9589162539509\t1.77687342552627\t78.9590566\t"Phosphoric acid"\tunknown\t[M-H3O]-\tNA\tNA\n+79.9572959941509\t0.870464654095999\t79.9573656\t"Sulphuric acid"\tunknown\t[M-H2O]-\tNA\tNA\n+79.9572310694573\t1.68214929658035\t79.9573656\t"Sulphuric acid"\tunknown\t[M-H2O]-\tNA\tNA\n+79.9572880455522\t0.970518159092524\t79.9573656\t"Sulphuric 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|