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master branch Updating with tag :CI_COMMIT_TAG - - Fxx
author fgiacomoni
date Wed, 30 Nov 2022 16:14:27 +0000
parents 7c9269bded0e
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1:4373f936111d 2:be504ccbc41c
1 <tool id="downloader_bank_hmdb" name="HMDB bank downloader" version="2018.12"> 1 <tool id="downloader_bank_hmdb" name="Wishart bank downloader" version="1.1.2">
2 <description> 2 <description>
3 : get a specific metabolite bank (as Urine...) from HMDB web portal. 3 : get a specific metabolite bank (as Urine, Serum...) from Wishart web portal.
4 </description> 4 </description>
5 5
6 <requirements> 6 <requirements>
7 <requirement type="package" version="2.161">perl-data-dumper</requirement> 7 <requirement type="package" version="2.161">perl-data-dumper</requirement>
8 <requirement type="package" version="6.15">perl-lwp-simple</requirement> 8 <requirement type="package" version="6.15">perl-lwp-simple</requirement>
9 <requirement type="package" version="6.15">perl-libwww-perl</requirement> 9 <requirement type="package" version="6.15">perl-libwww-perl</requirement>
10 <requirement type="package" version="6.07">perl-lwp-protocol-https</requirement>
10 <requirement type="package" version="1.74">perl-uri</requirement> 11 <requirement type="package" version="1.74">perl-uri</requirement>
11 <requirement type="package" version="1.97">perl-text-csv</requirement> 12 <requirement type="package" version="1.97">perl-text-csv</requirement>
12 <requirement type="package" version="3.52">perl-xml-twig</requirement> 13 <requirement type="package" version="3.52">perl-xml-twig</requirement>
13 <requirement type="package" version="1.60">perl-archive-zip</requirement> 14 <requirement type="package" version="1.60">perl-archive-zip</requirement>
14 <requirement type="package" version="2.064">perl-io-uncompress-gunzip</requirement> 15 <requirement type="package" version="2.064">perl-io-uncompress-gunzip</requirement>
26 -format "$bankformat" 27 -format "$bankformat"
27 -outTab "$outTab" 28 -outTab "$outTab"
28 29
29 ]]></command> 30 ]]></command>
30 <inputs> 31 <inputs>
31 <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."> 32 <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.">
32 <option value="SERUM" selected="true">Human serum</option> 33 <option value="SERUM" selected="true">Human serum</option>
33 <option value="URINE">Human urine</option> 34 <option value="URINE">Human urine</option>
35 <option value="SWEAT">Human sweat</option>
34 <option value="CSF">Human cerebrospinal fluid</option> 36 <option value="CSF">Human cerebrospinal fluid</option>
35 <option value="FECES">Human feces</option> 37 <option value="FECES">Human feces</option>
36 <option value="SALIVA">Human saliva</option> 38 <option value="SALIVA">Human saliva</option>
37 <option value="COW">Bovine</option> 39 <option value="COW">Bovine</option>
38 <option value="RUMEN">Bovine rumen</option>
39 <option value="MILK">Bovine milk</option> 40 <option value="MILK">Bovine milk</option>
41 <option value="TOXIC">Toxin and Toxin Target Database</option>
40 </param> 42 </param>
41 <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."> 43 <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.">
42 <option value="tabular" selected="true">tabular (for BiH tool)</option> 44 <option value="tabular" selected="true">tabular (for BiH tool)</option>
43 <!--<option value="json">json (still in construction)</option>--> 45 <!--<option value="json">json (still in construction)</option>-->
44 </param> 46 </param>
65 67
66 <help><![CDATA[ 68 <help><![CDATA[
67 69
68 .. class:: infomark 70 .. class:: infomark
69 71
70 **Authors** Charlotte Joly, Delphine Centeno and Franck Giacomoni 72 **Authors** Charlotte Joly, Delphine Centeno, Lain Pavot, Yann Guitton and Franck Giacomoni
71 73
72 --------------------------------------------------- 74 ---------------------------------------------------
73 75
74 .. class:: infomark 76 .. class:: infomark
75 77
76 **Please cite** If you use this tool, please add the following reference 78 **Please cite** If you use this tool, please add the following reference
77 | 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. 79 | 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.
78 80
79 81
80 --------------------------------------------------- 82 ---------------------------------------------------
81 83
82 ==================== 84 ====================
126 Output files 128 Output files
127 ------------ 129 ------------
128 130
129 Two types of files 131 Two types of files
130 | REF_HMDB_BANKNAME.tabular: for W4M BiH annotation tool as example 132 | REF_HMDB_BANKNAME.tabular: for W4M BiH annotation tool as example
131 |
132 | REF_HMDB_BANKNAME.json: for linking with others modules.
133 | 133 |
134 134
135 --------------------------------------------------- 135 ---------------------------------------------------
136 136
137 137
146 | Format Data For Postprocessing 146 | Format Data For Postprocessing
147 | Perform LCMS Annotations 147 | Perform LCMS Annotations
148 148
149 .. class:: warningmark 149 .. class:: warningmark
150 150
151 And their "W4M courses 2018": 151 And their "W4M courses 2020":
152 | Using Galaxy4Metabolomics - W4M table format for Galaxy 152 | Using Galaxy4Metabolomics - W4M table format for Galaxy
153 | Annotation Banks - Annotation 153 | Annotation Banks - Annotation
154 154
155 155
156 ]]></help> 156 ]]></help>
157 <!-- [RECOMMANDED] All citations associated to this tool (main citation given above and other references). Can be extracted from the history panel --> 157 <!-- [RECOMMANDED] All citations associated to this tool (main citation given above and other references). Can be extracted from the history panel -->
158 <citations> 158 <citations>
159 <citation type="doi">10.1093/nar/gkx1089</citation> 159 <citation type="doi">10.1093/nar/gkx1089</citation>
160 <citation type="doi">10.1093/nar/gku1004</citation>
161 <citation type="doi">10.1093/nar/gkab1062</citation>
160 </citations> 162 </citations>
161 </tool> 163 </tool>