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Repository hmdb_ms_search

Name: hmdb_ms_search

Owner: fgiacomoni

Synopsis: [W4M][Metabolomics][LC-MS] HMDB database MS Search Package - Annotation - Returns annotation results (adducts and metabolites) from The Human Metabolome Database.

Detailed description:

Part of the W4M project: http://workflow4metabolomics.org / HMDB: http://www.hmdb.ca/. The wrapper script use the HMDB 'MS search' resource to annotate a list of m/z. The process returns outputs files (CSV and HTML formats) with links through metabocards.

Content homepage: http://workflow4metabolomics.org

Link to this repository revision: https://toolshed.g2.bx.psu.edu/view/fgiacomoni/hmdb_ms_search/8f7546d0b925

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/fgiacomoni/hmdb_ms_search

Type: unrestricted

Revision: 25:8f7546d0b925

This revision can be installed: True

Times cloned / installed: 893

Repository README files - may contain important installation or license information

Readme files

## ****** HMDB environnemnt : ****** ## # version June 2022 M Landi / F Giacomoni - INRAE - METABOHUB - workflow4metabolomics.org core team ## --- 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 ; use Encode; # libs CPAN PERL : $ perl -e 'use Text::CSV' - OK use LWP::Simple; - OK use LWP::UserAgent; - OK use URI::URL; - OK use SOAP::Lite; - OK use HTML::Template ; - OK use XML::Twig ; - OK $ sudo perl -MCPAN -e shell cpan> install Text::CSV # libs pfem PERL : this lib were included in lib dir. use conf::conf qw( :ALL ) ; use formats::csv qw( :ALL ) ; -- ## --- Conda compliant --- ## This tool and its PERL dependencies are "Conda compliant". The requirements section in the Xml file is still commented, waiting for "Conda" deployment improvement in Galaxy project. ## --- R bin and Packages : --- ## No interaction with R -- ## --- Binary dependencies --- ## No interaction with binary - use only HMDB post method (http://www.hmdb.ca/spectra/ms/search?) -- ## --- Config : --- ## JS and CSS (used in HTML output format) are now hosted on cdn.rawgit.com server - no local config needed PS :If Galaxy can't find the file "hmdb.tmpl", perform this command line : perl -pi -e 's/\r//g' conf_hmdb.cfg -- ## --- XML HELP PART --- ## one image : hmdb.png -- ## --- DATASETS OR TUTORIAL --- ## Please find help on W4M: http://workflow4metabolomics.org/howto -- ## --- ??? COMMENTS ??? --- ## If Galaxy can't find the file "hmdb.tmpl", perform this command line : " perl -pi -e 's/\r//g' " on the conf file "conf_hmdb.cfg". To use fully functionalities of HTML output format file : - check that sanitize_all_html option in universe_wsgi.ini file is uncomment and set to FALSE. --

Name	Description	Version	Minimum Galaxy Version
Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
HMDB MS search View tool metadata	search by masses on HMDB v5 online LCMS bank	1.7.2	16.01