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Init repository for [downloader_bank_hmdb]
author fgiacomoni
date Tue, 14 Jan 2020 05:21:23 -0500
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-1:000000000000 0:7c9269bded0e
1 <tool id="downloader_bank_hmdb" name="HMDB bank downloader" version="2018.12">
2 <description>
3 : get a specific metabolite bank (as Urine...) from HMDB web portal.
4 </description>
5
6 <requirements>
7 <requirement type="package" version="2.161">perl-data-dumper</requirement>
8 <requirement type="package" version="6.15">perl-lwp-simple</requirement>
9 <requirement type="package" version="6.15">perl-libwww-perl</requirement>
10 <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="3.52">perl-xml-twig</requirement>
13 <requirement type="package" version="1.60">perl-archive-zip</requirement>
14 <requirement type="package" version="2.064">perl-io-uncompress-gunzip</requirement>
15 </requirements>
16
17 <stdio>
18 <exit_code range="1" level="fatal" />
19 </stdio>
20
21
22 <command><![CDATA[
23 perl $__tool_directory__/downloader_bank_hmdb.pl
24 -bank "$bank"
25 -verbose "$verbose"
26 -format "$bankformat"
27 -outTab "$outTab"
28
29 ]]></command>
30 <inputs>
31 <param name="bank" type="select" label="What is the specific bank you want to download? " help="All banks are extracted from downloads section on HMDB web portal.">
32 <option value="SERUM" selected="true">Human serum</option>
33 <option value="URINE">Human urine</option>
34 <option value="CSF">Human cerebrospinal fluid</option>
35 <option value="FECES">Human feces</option>
36 <option value="SALIVA">Human saliva</option>
37 <option value="COW">Bovine</option>
38 <option value="RUMEN">Bovine rumen</option>
39 <option value="MILK">Bovine milk</option>
40 </param>
41 <param name="bankformat" type="select" label="Which output format do you need? " help="Proposed formats are lighter than downloaded raw files and adapted to annotation tools.">
42 <option value="tabular" selected="true">tabular (for BiH tool)</option>
43 <!--<option value="json">json (still in construction)</option>-->
44 </param>
45 <param name="verbose" type="select" label="Level of script verbose " help="Information about script running.">
46 <option value="1" selected="true">low</option>
47 <option value="3">high</option>
48 </param>
49 </inputs>
50
51 <outputs>
52 <data name="outTab" format="tabular" label="REF_HMDB_${bank}.tabular"/>
53 <!--<data name="outJson" format="json" label="REF_HMDB_${bank}.json"/>-->
54 </outputs>
55
56 <tests>
57 <test>
58 <!--test 01 CSF download and produce a simple tabular -->
59 <param name="bank" value="CSF"/>
60 <param name="bankformat" value="tabular"/>
61 <param name="verbose" value="1"/>
62 <output name="outTab" file="out01.tabular"/>
63 </test>
64 </tests>
65
66 <help><![CDATA[
67
68 .. class:: infomark
69
70 **Authors** Charlotte Joly, Delphine Centeno and Franck Giacomoni
71
72 ---------------------------------------------------
73
74 .. class:: infomark
75
76 **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.
78
79
80 ---------------------------------------------------
81
82 ====================
83 HMDB bank downloader
84 ====================
85
86 -----------
87 Description
88 -----------
89
90 | Download a bank containing information (like : HMDB id, Name, mz, inchikey)
91 | from HMDB online web portal and convert it into W4M annotation tool input formats.
92 |
93
94
95 -----------------
96 Workflow position
97 -----------------
98
99
100 .. image:: ./static/images/metabolomics/hmdb.png
101 :width: 800
102
103
104
105 ----------
106 Parameters
107 ----------
108
109 What is the specific bank you want to download
110 | Choose whether specific metabolite banks:
111 | Urine
112 | Serum
113 | cerebrospinal fluid
114 | ...
115 |
116
117
118 Which output format do you need
119 | tabular : for W4M BiH annotation tool as example
120 | json : still in construction
121 |
122
123
124
125 ------------
126 Output files
127 ------------
128
129 Two types of files
130 | REF_HMDB_BANKNAME.tabular: for W4M BiH annotation tool as example
131 |
132 | REF_HMDB_BANKNAME.json: for linking with others modules.
133 |
134
135 ---------------------------------------------------
136
137
138 ---------------
139 Working example
140 ---------------
141
142
143 .. class:: warningmark
144
145 Refer to the corresponding W4M HowTo section: http://workflow4metabolomics.org/howto
146 | Format Data For Postprocessing
147 | Perform LCMS Annotations
148
149 .. class:: warningmark
150
151 And their "W4M courses 2018":
152 | Using Galaxy4Metabolomics - W4M table format for Galaxy
153 | Annotation Banks - Annotation
154
155
156 ]]></help>
157 <!-- [RECOMMANDED] All citations associated to this tool (main citation given above and other references). Can be extracted from the history panel -->
158 <citations>
159 <citation type="doi">10.1093/nar/gkx1089</citation>
160 </citations>
161 </tool>