Mercurial > repos > fgiacomoni > downloader_bank_hmdb
diff downloader_bank_hmdb.xml @ 2:be504ccbc41c draft default tip
master branch Updating with tag :CI_COMMIT_TAG - - Fxx
author | fgiacomoni |
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date | Wed, 30 Nov 2022 16:14:27 +0000 |
parents | 7c9269bded0e |
children |
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--- a/downloader_bank_hmdb.xml Tue Jan 21 16:09:45 2020 -0500 +++ b/downloader_bank_hmdb.xml Wed Nov 30 16:14:27 2022 +0000 @@ -1,12 +1,13 @@ -<tool id="downloader_bank_hmdb" name="HMDB bank downloader" version="2018.12"> +<tool id="downloader_bank_hmdb" name="Wishart bank downloader" version="1.1.2"> <description> - : get a specific metabolite bank (as Urine...) from HMDB web portal. + : get a specific metabolite bank (as Urine, Serum...) from Wishart web portal. </description> <requirements> <requirement type="package" version="2.161">perl-data-dumper</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="6.07">perl-lwp-protocol-https</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> @@ -28,15 +29,16 @@ ]]></command> <inputs> - <param name="bank" type="select" label="What is the specific bank you want to download? " help="All banks are extracted from downloads section on HMDB web portal."> + <param name="bank" type="select" label="What is the specific bank you want to download? " help="All banks are extracted from downloads section on Whishart web portals."> <option value="SERUM" selected="true">Human serum</option> <option value="URINE">Human urine</option> + <option value="SWEAT">Human sweat</option> <option value="CSF">Human cerebrospinal fluid</option> <option value="FECES">Human feces</option> <option value="SALIVA">Human saliva</option> <option value="COW">Bovine</option> - <option value="RUMEN">Bovine rumen</option> <option value="MILK">Bovine milk</option> + <option value="TOXIC">Toxin and Toxin Target Database</option> </param> <param name="bankformat" type="select" label="Which output format do you need? " help="Proposed formats are lighter than downloaded raw files and adapted to annotation tools."> <option value="tabular" selected="true">tabular (for BiH tool)</option> @@ -67,14 +69,14 @@ .. class:: infomark -**Authors** Charlotte Joly, Delphine Centeno and Franck Giacomoni +**Authors** Charlotte Joly, Delphine Centeno, Lain Pavot, Yann Guitton and Franck Giacomoni --------------------------------------------------- .. class:: infomark **Please cite** If you use this tool, please add the following reference - | Wishart DS, Feunang YD, Marcu A, Guo AC, Liang K, et al., HMDB 4.0 — The Human Metabolome Database for 2018. Nucleic Acids Res. 2018. Jan 4;46(D1):D608-17. + | Wishart DS, Guo AC, Oler E, et al., HMDB 5.0: the Human Metabolome Database for 2022. Nucleic Acids Res. 2022. Jan 7;50(D1):D622–31. --------------------------------------------------- @@ -128,8 +130,6 @@ Two types of files | REF_HMDB_BANKNAME.tabular: for W4M BiH annotation tool as example - | - | REF_HMDB_BANKNAME.json: for linking with others modules. | --------------------------------------------------- @@ -148,7 +148,7 @@ .. class:: warningmark -And their "W4M courses 2018": +And their "W4M courses 2020": | Using Galaxy4Metabolomics - W4M table format for Galaxy | Annotation Banks - Annotation @@ -157,5 +157,7 @@ <!-- [RECOMMANDED] All citations associated to this tool (main citation given above and other references). Can be extracted from the history panel --> <citations> <citation type="doi">10.1093/nar/gkx1089</citation> + <citation type="doi">10.1093/nar/gku1004</citation> + <citation type="doi">10.1093/nar/gkab1062</citation> </citations> </tool> \ No newline at end of file