annotate wsdl_hmdb.xml @ 22:453fbe98925a draft

" master branch Updating with tag :CI_COMMIT_TAG - - Fxx"
author fgiacomoni
date Fri, 20 Nov 2020 17:29:18 +0000
parents 63ba1cb240b7
children 2d8a310e86ce
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
21
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
1 <tool id="wsdl_hmdb" name="HMDB MS search" version="1.6.1">
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
2 <description>
14
625fa968d99a Master branch Updating - - Fxx
fgiacomoni
parents: 13
diff changeset
3 search by masses on HMDB online LCMS bank
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
4 </description>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
5
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
6 <requirements>
12
2203cb539e53 Master branch Updating - - Fxx
fgiacomoni
parents: 11
diff changeset
7 <requirement type="package" version="2.161">perl-data-dumper</requirement>
10
4eb2de7c24d1 Master branch Updating - - Fxx
fgiacomoni
parents: 9
diff changeset
8 <requirement type="package" version="2.97">perl-html-template</requirement>
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
9 <requirement type="package" version="1.19">perl-soap-lite</requirement>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
10 <requirement type="package" version="6.15">perl-lwp-simple</requirement>
21
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
11 <requirement type="package" version="6.15">perl-libwww-perl</requirement>
9
c32280662103 Master branch Updating - - Fxx
fgiacomoni
parents: 7
diff changeset
12 <requirement type="package" version="1.74">perl-uri</requirement>
c32280662103 Master branch Updating - - Fxx
fgiacomoni
parents: 7
diff changeset
13 <requirement type="package" version="1.97">perl-text-csv</requirement>
c32280662103 Master branch Updating - - Fxx
fgiacomoni
parents: 7
diff changeset
14 <requirement type="package" version="3.52">perl-xml-twig</requirement>
21
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
15 <requirement type="package" version="1.91">perl-www-mechanize</requirement>
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
16 </requirements>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
17
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
18 <stdio>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
19 <exit_code range="1" level="fatal" />
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
20 </stdio>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
21
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
22
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
23 <command><![CDATA[
13
3587cb923890 Master branch Updating - - Fxx
fgiacomoni
parents: 12
diff changeset
24 perl $__tool_directory__/wsdl_hmdb.pl
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
25 #if str($input_type.choice) == "YES":
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
26 -masses "${input_type.masses}"
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
27 -header_choice "${input_type.header.header_choice}"
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
28 #if str($input_type.header.header_choice) == "yes":
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
29 -nblineheader "${$input_type.header.nbHeader}"
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
30 #end if
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
31 -colfactor "${input_type.colfactor}"
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
32 -output_tabular "$variableMetadata" -output_html "$HmdbOutWeb" -output_xls "$HmdbOutXlsx"
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
33 #else:
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
34 -mass "${input_type.mass}"
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
35 -output_tabular "$variableMetadata2" -output_html "$HmdbOutWeb2" -output_xls "$HmdbOutXlsx2"
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
36 #end if
21
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
37
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
38 -mode "${mode_type.mode}"
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
39
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
40 #if str($mode_type.mode) == "positive":
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
41 -adduct_type "${mode_type.data_positive_adducts}"
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
42 #elif str($mode_type.mode) == "negative":
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
43 -adduct_type "${mode_type.data_negative_adducts}"
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
44 #elif str($mode_type.mode) == "neutral":
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
45 -adduct_type "${mode_type.data_neutral_adducts}"
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
46 #end if
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
47
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
48 -delta "$delta" -maxquery "$maxquery"
15
beb9619263b0 Master branch Updating - - Fxx
fgiacomoni
parents: 14
diff changeset
49 -advancedFeatures "$advancedFeatures"
beb9619263b0 Master branch Updating - - Fxx
fgiacomoni
parents: 14
diff changeset
50 -verbose "$verbose"
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
51
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
52 ]]></command>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
53 <inputs>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
54 <conditional name="input_type">
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
55 <param name="choice" type="select" label="Would you use a file " help="if 'NO' is selected then one or more mass(es) must be entered manually">
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
56 <option value="YES">YES</option>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
57 <option value="NO">NO</option>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
58 </param>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
59 <when value="YES">
5
520778e357cc planemo upload commit c49b69597de7f1ce2034815e968fbf5d7c0373c4
fgiacomoni
parents: 3
diff changeset
60 <param name="masses" label="File of masses (Variable Metadata) " format="tabular" type="data" help="Generally variable metadata file. Please note : HMDB allows maximum 700 query masses per request" />
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
61 <conditional name="header">
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
62 <param name="header_choice" type="select" label="Do you have a header " help="if 'YES' is selected then enter your number of header lines">
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
63 <option value="no">NO</option>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
64 <option value="yes" selected="true">YES</option>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
65 </param>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
66 <when value="yes">
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
67 <param name="nbHeader" label="Number of header lines " type="integer" value="1" min="1" size="10" help="number of lines not containing masses"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
68 </when>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
69 <when value="no"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
70 </conditional>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
71 <param name="colfactor" label="Column of masses " type="data_column" data_ref="masses" accept_default="true" />
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
72 </when>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
73 <when value="NO">
7
ecf8e43aceda planemo upload commit d1a5cd8f1baf00879ffa44649883f91c64f43392
fgiacomoni
parents: 5
diff changeset
74 <param name="mass" label="Mass to submit " type="text" size="20" help="For a masses list, writes : m1 m2 m3. Your values must be separated by spaces. You should use dot (.) like decimal separator" />
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
75 </when>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
76 </conditional>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
77
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
78 <param name="delta" label="Mass-to-charge ratio " type="float" value="0.05" min="0" max="10" size="10" help="Default value is 0.05 for HMDB (mass-to-charge ratio)"/>
21
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
79 <param name="maxquery" label="Number of maximum entries returned by the query " type="integer" value="10" min="1" max="50" size="10" help="Default value is 10 for each queried mz / max is 50"/>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
80
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
81 <conditional name="mode_type">
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
82 <param name="mode" label="Molecular Species " type="select" display="radio" help="">
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
83 <option value="positive">Positif Mode</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
84 <option value="negative">Negatif Mode</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
85 <option value="neutral" selected="True">Neutral Mass</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
86 </param>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
87 <when value="positive">
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
88 <param name="data_positive_adducts" label="Select multiple adducts" type="select" display="checkboxes" multiple="True" help="">
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
89 <option value="Unknown">Unknown</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
90 <option value="M+H" selected="True">M+H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
91 <option value="M+H-2H2O">M+H-2H2O</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
92 <option value="M+H-H2O">M+H-H2O</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
93 <option value="M+NH4-H2O">M+NH4-H2O</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
94 <option value="M+Li">M+Li</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
95 <option value="M+NH4">M+NH4</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
96 <option value="M+Na">M+Na</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
97 <option value="M+CH3OH+H">M+CH3OH+H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
98 <option value="M+K">M+K</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
99 <option value="M+ACN+H">M+ACN+H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
100 <option value="M+2Na-H">M+2Na-H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
101 <option value="M+IsoProp+H">M+IsoProp+H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
102 <option value="M+ACN+Na">M+ACN+Na</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
103 <option value="M+2K-H">M+2K-H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
104 <option value="M+DMSO+H">M+DMSO+H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
105 <option value="M+2ACN+H">M+2ACN+H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
106 <option value="M+IsoProp+Na+H">M+IsoProp+Na+H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
107 <option value="M+H+HCOONa">M+H+HCOONa</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
108 <option value="2M+H">2M+H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
109 <option value="2M+NH4">2M+NH4</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
110 <option value="2M+Na">2M+Na</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
111 <option value="2M+2H+3H2O">2M+2H+3H2O</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
112 <option value="2M+K">2M+K</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
113 <option value="2M+ACN+H">2M+ACN+H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
114 <option value="2M+ACN+Na">2M+ACN+Na</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
115 <option value="2M+H-H2O">2M+H-H2O</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
116 <option value="M+2H">M+2H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
117 <option value="M+H+NH4">M+H+NH4</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
118 <option value="M+H+Na">M+H+Na</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
119 <option value="M+H+K">M+H+K</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
120 <option value="M+ACN+2H">M+ACN+2H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
121 <option value="M+2Na">M+2Na</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
122 <option value="M+2ACN+2H">M+2ACN+2H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
123 <option value="M+3ACN+2H">M+3ACN+2H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
124 <option value="M+3H">M+3H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
125 <option value="M+2H+Na">M+2H+Na</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
126 <option value="M+H+2Na">M+H+2Na</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
127 <option value="M+3Na">M+3Na</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
128 <option value="M+H+2K">M+H+2K</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
129 </param>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
130 </when>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
131 <when value="negative">
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
132 <param name="data_negative_adducts" label="Select multiple adducts" type="select" display="checkboxes" multiple="True" help="">
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
133 <option value="Unknown">Unknown</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
134 <option value="M-H" selected="True">M-H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
135 <option value="M-H20-H">M-H20-H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
136 <option value="M+F">M+F</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
137 <option value="M+Na-2H">M+Na-2H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
138 <option value="M+Cl">M+Cl</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
139 <option value="M+K-2H">M+K-2H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
140 <option value="M+FA-H">M+FA-H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
141 <option value="M+Hac-H">M+Hac-H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
142 <option value="M+Br">M+Br</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
143 <option value="M+TFA-H">M+TFA-H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
144 <option value="M-H+HCOONa">M-H+HCOONa</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
145 <option value="2M-H">2M-H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
146 <option value="2M+FA-H">2M+FA-H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
147 <option value="2M+Hac-H">2M+Hac-H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
148 <option value="3M-H">3M-H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
149 <option value="M-2H">M-2H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
150 <option value="M-3H">M-3H</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
151 </param>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
152 </when>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
153 <when value="neutral">
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
154 <param name="data_neutral_adducts" label="Select multiple adducts" type="select" display="checkboxes" multiple="True" help="">
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
155 <option value="Unknown">Unknown</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
156 <option value="M" selected="True">M</option>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
157 </param>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
158 </when>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
159 </conditional>
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
160
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
161
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
162
63ba1cb240b7 Prod branch Updating - - Fxx
fgiacomoni
parents: 18
diff changeset
163
15
beb9619263b0 Master branch Updating - - Fxx
fgiacomoni
parents: 14
diff changeset
164 <param name="advancedFeatures" label="Performing advanced annotation " type="select" display="radio" help="Getting more information from HMDB (Inchi, logP, ...) but increase time of tool execution">
beb9619263b0 Master branch Updating - - Fxx
fgiacomoni
parents: 14
diff changeset
165 <option value="1">Advanced mode</option>
beb9619263b0 Master branch Updating - - Fxx
fgiacomoni
parents: 14
diff changeset
166 <option value="0" selected="True">Default mode</option>
beb9619263b0 Master branch Updating - - Fxx
fgiacomoni
parents: 14
diff changeset
167 </param>
beb9619263b0 Master branch Updating - - Fxx
fgiacomoni
parents: 14
diff changeset
168 <param name="verbose" type="select" label="Verbose level" display="radio" help="">
beb9619263b0 Master branch Updating - - Fxx
fgiacomoni
parents: 14
diff changeset
169 <option value="1" selected="true">Low</option>
beb9619263b0 Master branch Updating - - Fxx
fgiacomoni
parents: 14
diff changeset
170 <option value="3" >High</option>
beb9619263b0 Master branch Updating - - Fxx
fgiacomoni
parents: 14
diff changeset
171 </param>
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
172 </inputs>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
173
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
174 <outputs>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
175 <data name="variableMetadata" format="tabular" label="${input_type.masses.name[:-6]}.HMDB.tabular">
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
176 <filter>input_type['choice'] == "YES"</filter>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
177 </data>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
178 <data name="HmdbOutWeb" format="html" label="${input_type.masses.name[:-6]}.HMDB_WEB.html">
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
179 <filter>input_type['choice'] == "YES"</filter>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
180 </data>
2
a3744fb3605c planemo upload commit e3e676478019ab709f0043c09b02ba93e042957f
fgiacomoni
parents: 1
diff changeset
181 <data name="HmdbOutXlsx" label="${input_type.masses.name[:-6]}.HMDB_XLS.txt" format="tabular">
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
182 <filter>input_type['choice'] == "YES"</filter>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
183 </data>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
184 <data name="variableMetadata2" format="tabular" label="HMDB.tabular">
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
185 <filter>input_type['choice'] == "NO"</filter>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
186 </data>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
187 <data name="HmdbOutWeb2" format="html" label="HMDB_WEB.html">
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
188 <filter>input_type['choice'] == "NO"</filter>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
189 </data>
2
a3744fb3605c planemo upload commit e3e676478019ab709f0043c09b02ba93e042957f
fgiacomoni
parents: 1
diff changeset
190 <data name="HmdbOutXlsx2" label="HMDB_XLS.txt" format="tabular">
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
191 <filter>input_type['choice'] == "NO"</filter>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
192 </data>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
193 </outputs>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
194
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
195 <tests>
14
625fa968d99a Master branch Updating - - Fxx
fgiacomoni
parents: 13
diff changeset
196 <!--test 01 no result - fake-mzrt-input-with-id -->
625fa968d99a Master branch Updating - - Fxx
fgiacomoni
parents: 13
diff changeset
197 <!--
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
198 <test>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
199 <param name="choice" value="YES"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
200 <param name="masses" value="input_test01_fake-mzrt-input-with-id.tabular"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
201 <param name="header_choice" value="yes"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
202 <param name="nblineheader" value="1"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
203 <param name="colfactor" value="2"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
204 <param name="delta" value="0.001"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
205 <param name="mode" value="neutral"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
206 <param name="maxquery" value="5"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
207 <output name="variableMetadata" file="out_test01.tabular"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
208 <output name="HmdbOutWeb" file="out_test01.html"/>
2
a3744fb3605c planemo upload commit e3e676478019ab709f0043c09b02ba93e042957f
fgiacomoni
parents: 1
diff changeset
209 <output name="HmdbOutXlsx" file="out_test01.txt"/>
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
210 </test>
14
625fa968d99a Master branch Updating - - Fxx
fgiacomoni
parents: 13
diff changeset
211 -->
625fa968d99a Master branch Updating - - Fxx
fgiacomoni
parents: 13
diff changeset
212 <!--test 02 : some results - with-mzrt-input-with-id file-->
625fa968d99a Master branch Updating - - Fxx
fgiacomoni
parents: 13
diff changeset
213 <!--
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
214 <test>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
215 <param name="choice" value="YES"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
216 <param name="masses" value="input_test02_mzrt-input-with-id.tabular"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
217 <param name="header_choice" value="yes"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
218 <param name="nblineheader" value="1"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
219 <param name="colfactor" value="2"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
220 <param name="delta" value="0.001"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
221 <param name="mode" value="positive"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
222 <param name="maxquery" value="5"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
223 <output name="variableMetadata" file="out_test02.tabular"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
224 <output name="HmdbOutWeb" file="out_test02.html"/>
2
a3744fb3605c planemo upload commit e3e676478019ab709f0043c09b02ba93e042957f
fgiacomoni
parents: 1
diff changeset
225 <output name="HmdbOutXlsx" file="out_test02.txt"/>
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
226 </test>
14
625fa968d99a Master branch Updating - - Fxx
fgiacomoni
parents: 13
diff changeset
227 -->
625fa968d99a Master branch Updating - - Fxx
fgiacomoni
parents: 13
diff changeset
228 <!--test 03 : some results - with-mz list in manual mass mode-->
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
229 <test>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
230 <param name="choice" value="NO"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
231 <param name="mass" value="175.01 238.19 420.16 780.32 956.25 1100.45"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
232 <param name="delta" value="0.05"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
233 <param name="mode" value="positive"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
234 <param name="maxquery" value="5"/>
22
453fbe98925a " master branch Updating with tag :CI_COMMIT_TAG - - Fxx"
fgiacomoni
parents: 21
diff changeset
235 <param name="adduct_type" value="M+H"/>
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
236 <output name="variableMetadata2" file="out_test03.tabular"/>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
237 <output name="HmdbOutWeb2" file="out_test03.html"/>
2
a3744fb3605c planemo upload commit e3e676478019ab709f0043c09b02ba93e042957f
fgiacomoni
parents: 1
diff changeset
238 <output name="HmdbOutXlsx2" file="out_test03.txt"/>
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
239 </test>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
240 </tests>
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
241
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
242 <help><![CDATA[
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
243
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
244 .. class:: infomark
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
245
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
246 **Authors** Marion Landi and Franck Giacomoni
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
247
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
248 ---------------------------------------------------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
249
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
250 .. class:: infomark
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
251
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
252 **Please cite** If you use this tool, please add the following reference
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
253 | Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, et al., HMDB 3.0 — The Human Metabolome Database in 2013. Nucleic Acids Res. 2013.
14
625fa968d99a Master branch Updating - - Fxx
fgiacomoni
parents: 13
diff changeset
254 | 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.
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
255
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
256
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
257 ---------------------------------------------------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
258
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
259 ==============
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
260 HMDB MS search
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
261 ==============
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
262
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
263 -----------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
264 Description
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
265 -----------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
266
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
267 | Search informations (like : HMDB id, Name, Adduct, delta mass) on HMDB online bank
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
268 | with one or more mass(es) in a file or entered manually
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
269
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
270
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
271 -----------------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
272 Workflow position
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
273 -----------------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
274
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
275
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
276 .. image:: ./static/images/metabolomics/hmdb.png
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
277 :width: 800
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
278
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
279
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
280 -----------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
281 Input files
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
282 -----------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
283
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
284
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
285 +-------------------------+-----------+
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
286 | Parameter : num + label | Format |
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
287 +=========================+===========+
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
288 | 1 : File of masses | tabular |
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
289 +-------------------------+-----------+
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
290
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
291 File of masses (Generally variable metadata file) must have at least the following column :
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
292 * Masses : column with all the masses in the tsv input file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
293
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
294 ----------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
295 Parameters
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
296 ----------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
297
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
298 Would you use a file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
299 | Choose whether the masses are in a file or entered manually
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
300 | YES (default) : parameters **File of masses ; Do you have a header ; Column of masses** are visible
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
301 | NO : parameter **Mass to submit** is visible
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
302 |
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
303
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
304
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
305 If 'use file'='YES'
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
306
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
307 File of masses
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
308 | see "Input files" section above
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
309 | Tabular file format, Generally variable metadata file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
310 |
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
311
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
312 Do you have a header
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
313 | YES (default) : parameter **Number of header lines** is visible
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
314 | NO : all lines are considered to contain masses
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
315 |
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
316
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
317 If 'have a header'='YES'
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
318
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
319 Number of header lines
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
320 | Number of lines not containing masses values, these lines will be ignored
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
321 |
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
322
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
323 In all header cases :
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
324
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
325 Column of masses
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
326 | Specify the column number for the mass in the tsv input file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
327 |
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
328
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
329
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
330 If 'use file'='NO'
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
331
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
332 Mass to submit
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
333 | Specify a list of mass to request
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
334 | one or more mass(es) entered manually
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
335 | For a masses list, writes : m1 m2 m3
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
336 | You must separate yours values with space
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
337 | dot (.) is for float number
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
338 |
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
339
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
340 In all cases :
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
341
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
342 Mass-to-charge ratio
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
343 | Specify a delta (mass-to-charge ratio) to apply on mass - This value is a float, between 0.0000000000000001 and 10.
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
344 |
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
345
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
346 Molecular Species
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
347 | Type of ionization of the molecule : *positif, negatif, neutral*
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
348 |
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
349
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
350
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
351 ------------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
352 Output files
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
353 ------------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
354
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
355 Two types of files
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
356 | HMDB_WEB.HTML: for viewing result via HTML.
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
357 |
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
358 | HMDB_TABULAR.tabular: for linking with others modules.
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
359 |
2
a3744fb3605c planemo upload commit e3e676478019ab709f0043c09b02ba93e042957f
fgiacomoni
parents: 1
diff changeset
360 | HMDB_XLS.txt: an excel-like output permitting manual annotation cleaning.
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
361 |
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
362
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
363 ---------------------------------------------------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
364
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
365
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
366 ---------------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
367 Working example
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
368 ---------------
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
369
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
370
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
371 .. class:: warningmark
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
372
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
373 Refer to the corresponding W4M HowTo section: http://workflow4metabolomics.org/howto
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
374 | Format Data For Postprocessing
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
375 | Perform LCMS Annotations
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
376
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
377 .. class:: warningmark
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
378
14
625fa968d99a Master branch Updating - - Fxx
fgiacomoni
parents: 13
diff changeset
379 And their "W4M courses 2018":
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
380 | Using Galaxy4Metabolomics - W4M table format for Galaxy
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
381 | Annotation Banks - Annotation
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
382
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
383
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
384 ]]></help>
3
505956db90c5 planemo upload commit 08ff14d8ba34cbd43461ff041d4a3b8df5bbdba7
fgiacomoni
parents: 2
diff changeset
385 <!-- [RECOMMANDED] All citations associated to this tool (main citation given above and other references). Can be extracted from the history panel -->
505956db90c5 planemo upload commit 08ff14d8ba34cbd43461ff041d4a3b8df5bbdba7
fgiacomoni
parents: 2
diff changeset
386 <citations>
505956db90c5 planemo upload commit 08ff14d8ba34cbd43461ff041d4a3b8df5bbdba7
fgiacomoni
parents: 2
diff changeset
387 <citation type="doi">10.1093/nar/gks1065</citation>
14
625fa968d99a Master branch Updating - - Fxx
fgiacomoni
parents: 13
diff changeset
388 <citation type="doi">10.1093/nar/gkx1089</citation>
3
505956db90c5 planemo upload commit 08ff14d8ba34cbd43461ff041d4a3b8df5bbdba7
fgiacomoni
parents: 2
diff changeset
389 </citations>
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
390 </tool>