Mercurial > repos > fgiacomoni > hmdb_ms_search

comparison wsdl_hmdb.xml @ 21:63ba1cb240b7 draft

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Prod branch Updating - - Fxx
author fgiacomoni
date Thu, 14 Feb 2019 08:36:52 -0500
parents ec7c05889e67
children 453fbe98925a
comparison
equal deleted inserted replaced
20:b5a1d5e43685 21:63ba1cb240b7
1 <tool id="wsdl_hmdb" name="HMDB MS search" version="1.6.0"> 1 <tool id="wsdl_hmdb" name="HMDB MS search" version="1.6.1">
2 <description> 2 <description>
3 search by masses on HMDB online LCMS bank 3 search by masses on HMDB online LCMS bank
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="2.97">perl-html-template</requirement> 8 <requirement type="package" version="2.97">perl-html-template</requirement>
9 <requirement type="package" version="1.19">perl-soap-lite</requirement> 9 <requirement type="package" version="1.19">perl-soap-lite</requirement>
10 <requirement type="package" version="6.15">perl-lwp-simple</requirement> 10 <requirement type="package" version="6.15">perl-lwp-simple</requirement>
11 <requirement type="package" version="6.15">perl-libwww-perl</requirement> 11 <requirement type="package" version="6.15">perl-libwww-perl</requirement>
12 <requirement type="package" version="1.74">perl-uri</requirement> 12 <requirement type="package" version="1.74">perl-uri</requirement>
13 <requirement type="package" version="1.97">perl-text-csv</requirement> 13 <requirement type="package" version="1.97">perl-text-csv</requirement>
14 <requirement type="package" version="3.52">perl-xml-twig</requirement> 14 <requirement type="package" version="3.52">perl-xml-twig</requirement>
15 <requirement type="package" version="1.91">perl-www-mechanize</requirement>
15 </requirements> 16 </requirements>
16 17
17 <stdio> 18 <stdio>
18 <exit_code range="1" level="fatal" /> 19 <exit_code range="1" level="fatal" />
19 </stdio> 20 </stdio>
31 -output_tabular "$variableMetadata" -output_html "$HmdbOutWeb" -output_xls "$HmdbOutXlsx" 32 -output_tabular "$variableMetadata" -output_html "$HmdbOutWeb" -output_xls "$HmdbOutXlsx"
32 #else: 33 #else:
33 -mass "${input_type.mass}" 34 -mass "${input_type.mass}"
34 -output_tabular "$variableMetadata2" -output_html "$HmdbOutWeb2" -output_xls "$HmdbOutXlsx2" 35 -output_tabular "$variableMetadata2" -output_html "$HmdbOutWeb2" -output_xls "$HmdbOutXlsx2"
35 #end if 36 #end if
36 -delta "$delta" -mode "$mode" -maxquery "$maxquery" 37
38 -mode "${mode_type.mode}"
39
40 #if str($mode_type.mode) == "positive":
41 -adduct_type "${mode_type.data_positive_adducts}"
42 #elif str($mode_type.mode) == "negative":
43 -adduct_type "${mode_type.data_negative_adducts}"
44 #elif str($mode_type.mode) == "neutral":
45 -adduct_type "${mode_type.data_neutral_adducts}"
46 #end if
47
48 -delta "$delta" -maxquery "$maxquery"
37 -advancedFeatures "$advancedFeatures" 49 -advancedFeatures "$advancedFeatures"
38 -verbose "$verbose" 50 -verbose "$verbose"
39 51
40 ]]></command> 52 ]]></command>
41 <inputs> 53 <inputs>
62 <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" /> 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" />
63 </when> 75 </when>
64 </conditional> 76 </conditional>
65 77
66 <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)"/> 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)"/>
67 <param name="maxquery" label="Number of maximum entries returned by the query " type="integer" value="20" min="1" max="50" size="10" help="Default value is 20 for each queried mz / max is 50"/> 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"/>
68 <param name="mode" label="Molecular Species " type="select" display="radio" help=""> 80
69 <option value="positive">Positif Mode</option> 81 <conditional name="mode_type">
70 <option value="negative">Negatif Mode</option> 82 <param name="mode" label="Molecular Species " type="select" display="radio" help="">
71 <option value="neutral" selected="True">Neutral Mass</option> 83 <option value="positive">Positif Mode</option>
72 </param> 84 <option value="negative">Negatif Mode</option>
85 <option value="neutral" selected="True">Neutral Mass</option>
86 </param>
87 <when value="positive">
88 <param name="data_positive_adducts" label="Select multiple adducts" type="select" display="checkboxes" multiple="True" help="">
89 <option value="Unknown">Unknown</option>
90 <option value="M+H" selected="True">M+H</option>
91 <option value="M+H-2H2O">M+H-2H2O</option>
92 <option value="M+H-H2O">M+H-H2O</option>
93 <option value="M+NH4-H2O">M+NH4-H2O</option>
94 <option value="M+Li">M+Li</option>
95 <option value="M+NH4">M+NH4</option>
96 <option value="M+Na">M+Na</option>
97 <option value="M+CH3OH+H">M+CH3OH+H</option>
98 <option value="M+K">M+K</option>
99 <option value="M+ACN+H">M+ACN+H</option>
100 <option value="M+2Na-H">M+2Na-H</option>
101 <option value="M+IsoProp+H">M+IsoProp+H</option>
102 <option value="M+ACN+Na">M+ACN+Na</option>
103 <option value="M+2K-H">M+2K-H</option>
104 <option value="M+DMSO+H">M+DMSO+H</option>
105 <option value="M+2ACN+H">M+2ACN+H</option>
106 <option value="M+IsoProp+Na+H">M+IsoProp+Na+H</option>
107 <option value="M+H+HCOONa">M+H+HCOONa</option>
108 <option value="2M+H">2M+H</option>
109 <option value="2M+NH4">2M+NH4</option>
110 <option value="2M+Na">2M+Na</option>
111 <option value="2M+2H+3H2O">2M+2H+3H2O</option>
112 <option value="2M+K">2M+K</option>
113 <option value="2M+ACN+H">2M+ACN+H</option>
114 <option value="2M+ACN+Na">2M+ACN+Na</option>
115 <option value="2M+H-H2O">2M+H-H2O</option>
116 <option value="M+2H">M+2H</option>
117 <option value="M+H+NH4">M+H+NH4</option>
118 <option value="M+H+Na">M+H+Na</option>
119 <option value="M+H+K">M+H+K</option>
120 <option value="M+ACN+2H">M+ACN+2H</option>
121 <option value="M+2Na">M+2Na</option>
122 <option value="M+2ACN+2H">M+2ACN+2H</option>
123 <option value="M+3ACN+2H">M+3ACN+2H</option>
124 <option value="M+3H">M+3H</option>
125 <option value="M+2H+Na">M+2H+Na</option>
126 <option value="M+H+2Na">M+H+2Na</option>
127 <option value="M+3Na">M+3Na</option>
128 <option value="M+H+2K">M+H+2K</option>
129 </param>
130 </when>
131 <when value="negative">
132 <param name="data_negative_adducts" label="Select multiple adducts" type="select" display="checkboxes" multiple="True" help="">
133 <option value="Unknown">Unknown</option>
134 <option value="M-H" selected="True">M-H</option>
135 <option value="M-H20-H">M-H20-H</option>
136 <option value="M+F">M+F</option>
137 <option value="M+Na-2H">M+Na-2H</option>
138 <option value="M+Cl">M+Cl</option>
139 <option value="M+K-2H">M+K-2H</option>
140 <option value="M+FA-H">M+FA-H</option>
141 <option value="M+Hac-H">M+Hac-H</option>
142 <option value="M+Br">M+Br</option>
143 <option value="M+TFA-H">M+TFA-H</option>
144 <option value="M-H+HCOONa">M-H+HCOONa</option>
145 <option value="2M-H">2M-H</option>
146 <option value="2M+FA-H">2M+FA-H</option>
147 <option value="2M+Hac-H">2M+Hac-H</option>
148 <option value="3M-H">3M-H</option>
149 <option value="M-2H">M-2H</option>
150 <option value="M-3H">M-3H</option>
151 </param>
152 </when>
153 <when value="neutral">
154 <param name="data_neutral_adducts" label="Select multiple adducts" type="select" display="checkboxes" multiple="True" help="">
155 <option value="Unknown">Unknown</option>
156 <option value="M" selected="True">M</option>
157 </param>
158 </when>
159 </conditional>
160
161
162
163
73 <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"> 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">
74 <option value="1">Advanced mode</option> 165 <option value="1">Advanced mode</option>
75 <option value="0" selected="True">Default mode</option> 166 <option value="0" selected="True">Default mode</option>
76 </param> 167 </param>
77 <param name="verbose" type="select" label="Verbose level" display="radio" help=""> 168 <param name="verbose" type="select" label="Verbose level" display="radio" help="">