Mercurial > repos > fgiacomoni > hmdb_ms_search
annotate wsdl_hmdb.xml @ 27:144e4a8ad000 draft
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author | fgiacomoni |
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date | Mon, 06 Nov 2023 17:32:31 +0000 |
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1 <tool id="wsdl_hmdb" name="HMDB MS search" version="1.7.4"> |
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2 <description> |
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3 search by masses on HMDB v5 online LCMS bank |
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4 </description> |
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5 |
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6 <requirements> |
12 | 7 <requirement type="package" version="2.161">perl-data-dumper</requirement> |
10 | 8 <requirement type="package" version="2.97">perl-html-template</requirement> |
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9 <requirement type="package" version="1.19">perl-soap-lite</requirement> |
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10 <requirement type="package" version="6.15">perl-lwp-simple</requirement> |
21 | 11 <requirement type="package" version="6.15">perl-libwww-perl</requirement> |
9 | 12 <requirement type="package" version="1.74">perl-uri</requirement> |
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13 <requirement type="package" version="1.1.1">perl-uri-encode</requirement> |
9 | 14 <requirement type="package" version="1.97">perl-text-csv</requirement> |
15 <requirement type="package" version="3.52">perl-xml-twig</requirement> | |
21 | 16 <requirement type="package" version="1.91">perl-www-mechanize</requirement> |
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17 </requirements> |
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18 |
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19 <stdio> |
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20 <exit_code range="1" level="fatal" /> |
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21 </stdio> |
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22 |
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23 |
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24 <command><![CDATA[ |
13 | 25 perl $__tool_directory__/wsdl_hmdb.pl |
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26 #if str($input_type.choice) == "YES": |
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27 -masses "${input_type.masses}" |
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28 -header_choice "${input_type.header.header_choice}" |
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29 #if str($input_type.header.header_choice) == "yes": |
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30 -nblineheader "${$input_type.header.nbHeader}" |
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31 #end if |
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32 -colfactor "${input_type.colfactor}" |
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33 -output_tabular "$variableMetadata" -output_html "$HmdbOutWeb" -output_xlsx "$HmdbOutXlsx" |
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34 #else: |
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35 -mass "${input_type.mass}" |
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36 -output_tabular "$variableMetadata2" -output_html "$HmdbOutWeb2" -output_xlsx "$HmdbOutXlsx2" |
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37 #end if |
21 | 38 |
39 -mode "${mode_type.mode}" | |
40 | |
41 #if str($mode_type.mode) == "positive": | |
42 -adduct_type "${mode_type.data_positive_adducts}" | |
43 #elif str($mode_type.mode) == "negative": | |
44 -adduct_type "${mode_type.data_negative_adducts}" | |
45 #elif str($mode_type.mode) == "neutral": | |
46 -adduct_type "${mode_type.data_neutral_adducts}" | |
47 #end if | |
48 | |
49 -delta "$delta" -maxquery "$maxquery" | |
15 | 50 -advancedFeatures "$advancedFeatures" |
51 -verbose "$verbose" | |
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52 |
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53 ]]></command> |
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54 <inputs> |
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55 <conditional name="input_type"> |
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56 <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"> |
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57 <option value="YES">YES</option> |
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58 <option value="NO">NO</option> |
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59 </param> |
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60 <when value="YES"> |
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61 <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" /> |
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62 <conditional name="header"> |
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63 <param name="header_choice" type="select" label="Do you have a header " help="if 'YES' is selected then enter your number of header lines"> |
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64 <option value="no">NO</option> |
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65 <option value="yes" selected="true">YES</option> |
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66 </param> |
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67 <when value="yes"> |
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68 <param name="nbHeader" label="Number of header lines " type="integer" value="1" min="1" size="10" help="number of lines not containing masses"/> |
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69 </when> |
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70 <when value="no"/> |
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71 </conditional> |
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72 <param name="colfactor" label="Column of masses " type="data_column" data_ref="masses" accept_default="true" /> |
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73 </when> |
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74 <when value="NO"> |
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75 <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" /> |
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76 </when> |
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77 </conditional> |
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78 |
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79 <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 | 80 <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"/> |
81 | |
82 <conditional name="mode_type"> | |
83 <param name="mode" label="Molecular Species " type="select" display="radio" help=""> | |
84 <option value="positive">Positif Mode</option> | |
85 <option value="negative">Negatif Mode</option> | |
86 <option value="neutral" selected="True">Neutral Mass</option> | |
87 </param> | |
88 <when value="positive"> | |
89 <param name="data_positive_adducts" label="Select multiple adducts" type="select" display="checkboxes" multiple="True" help=""> | |
90 <option value="Unknown">Unknown</option> | |
91 <option value="M+H" selected="True">M+H</option> | |
92 <option value="M+H-2H2O">M+H-2H2O</option> | |
93 <option value="M+H-H2O">M+H-H2O</option> | |
94 <option value="M+NH4-H2O">M+NH4-H2O</option> | |
95 <option value="M+Li">M+Li</option> | |
96 <option value="M+NH4">M+NH4</option> | |
97 <option value="M+Na">M+Na</option> | |
98 <option value="M+CH3OH+H">M+CH3OH+H</option> | |
99 <option value="M+K">M+K</option> | |
100 <option value="M+ACN+H">M+ACN+H</option> | |
101 <option value="M+2Na-H">M+2Na-H</option> | |
102 <option value="M+IsoProp+H">M+IsoProp+H</option> | |
103 <option value="M+ACN+Na">M+ACN+Na</option> | |
104 <option value="M+2K-H">M+2K-H</option> | |
105 <option value="M+DMSO+H">M+DMSO+H</option> | |
106 <option value="M+2ACN+H">M+2ACN+H</option> | |
107 <option value="M+IsoProp+Na+H">M+IsoProp+Na+H</option> | |
108 <option value="M+H+HCOONa">M+H+HCOONa</option> | |
109 <option value="2M+H">2M+H</option> | |
110 <option value="2M+NH4">2M+NH4</option> | |
111 <option value="2M+Na">2M+Na</option> | |
112 <option value="2M+2H+3H2O">2M+2H+3H2O</option> | |
113 <option value="2M+K">2M+K</option> | |
114 <option value="2M+ACN+H">2M+ACN+H</option> | |
115 <option value="2M+ACN+Na">2M+ACN+Na</option> | |
116 <option value="2M+H-H2O">2M+H-H2O</option> | |
117 <option value="M+2H">M+2H</option> | |
118 <option value="M+H+NH4">M+H+NH4</option> | |
119 <option value="M+H+Na">M+H+Na</option> | |
120 <option value="M+H+K">M+H+K</option> | |
121 <option value="M+ACN+2H">M+ACN+2H</option> | |
122 <option value="M+2Na">M+2Na</option> | |
123 <option value="M+2ACN+2H">M+2ACN+2H</option> | |
124 <option value="M+3ACN+2H">M+3ACN+2H</option> | |
125 <option value="M+3H">M+3H</option> | |
126 <option value="M+2H+Na">M+2H+Na</option> | |
127 <option value="M+H+2Na">M+H+2Na</option> | |
128 <option value="M+3Na">M+3Na</option> | |
129 <option value="M+H+2K">M+H+2K</option> | |
130 </param> | |
131 </when> | |
132 <when value="negative"> | |
133 <param name="data_negative_adducts" label="Select multiple adducts" type="select" display="checkboxes" multiple="True" help=""> | |
134 <option value="Unknown">Unknown</option> | |
135 <option value="M-H" selected="True">M-H</option> | |
136 <option value="M-H20-H">M-H20-H</option> | |
137 <option value="M+F">M+F</option> | |
138 <option value="M+Na-2H">M+Na-2H</option> | |
139 <option value="M+Cl">M+Cl</option> | |
140 <option value="M+K-2H">M+K-2H</option> | |
141 <option value="M+FA-H">M+FA-H</option> | |
142 <option value="M+Hac-H">M+Hac-H</option> | |
143 <option value="M+Br">M+Br</option> | |
144 <option value="M+TFA-H">M+TFA-H</option> | |
145 <option value="M-H+HCOONa">M-H+HCOONa</option> | |
146 <option value="2M-H">2M-H</option> | |
147 <option value="2M+FA-H">2M+FA-H</option> | |
148 <option value="2M+Hac-H">2M+Hac-H</option> | |
149 <option value="3M-H">3M-H</option> | |
150 <option value="M-2H">M-2H</option> | |
151 <option value="M-3H">M-3H</option> | |
152 </param> | |
153 </when> | |
154 <when value="neutral"> | |
155 <param name="data_neutral_adducts" label="Select multiple adducts" type="select" display="checkboxes" multiple="True" help=""> | |
156 <option value="Unknown">Unknown</option> | |
157 <option value="M" selected="True">M</option> | |
158 </param> | |
159 </when> | |
160 </conditional> | |
161 | |
162 | |
163 | |
164 | |
15 | 165 <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"> |
166 <option value="1">Advanced mode</option> | |
167 <option value="0" selected="True">Default mode</option> | |
168 </param> | |
169 <param name="verbose" type="select" label="Verbose level" display="radio" help=""> | |
170 <option value="1" selected="true">Low</option> | |
171 <option value="3" >High</option> | |
172 </param> | |
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173 </inputs> |
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174 |
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175 <outputs> |
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176 <data name="variableMetadata" format="tabular" label="${input_type.masses.name[:-6]}.HMDB.tabular"> |
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177 <filter>input_type['choice'] == "YES"</filter> |
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178 </data> |
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179 <data name="HmdbOutWeb" format="html" label="${input_type.masses.name[:-6]}.HMDB_WEB.html"> |
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180 <filter>input_type['choice'] == "YES"</filter> |
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181 </data> |
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182 <data name="HmdbOutXlsx" label="${input_type.masses.name[:-6]}.HMDB_XLS.txt" format="tabular"> |
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183 <filter>input_type['choice'] == "YES"</filter> |
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184 </data> |
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185 <data name="variableMetadata2" format="tabular" label="HMDB.tabular"> |
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186 <filter>input_type['choice'] == "NO"</filter> |
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187 </data> |
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188 <data name="HmdbOutWeb2" format="html" label="HMDB_WEB.html"> |
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189 <filter>input_type['choice'] == "NO"</filter> |
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190 </data> |
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191 <data name="HmdbOutXlsx2" label="HMDB_XLS.txt" format="tabular"> |
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192 <filter>input_type['choice'] == "NO"</filter> |
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193 </data> |
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194 </outputs> |
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195 |
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196 <tests> |
14 | 197 <!--test 01 no result - fake-mzrt-input-with-id --> |
198 <!-- | |
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199 <test> |
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200 <param name="choice" value="YES"/> |
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201 <param name="masses" value="input_test01_fake-mzrt-input-with-id.tabular"/> |
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202 <param name="header_choice" value="yes"/> |
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203 <param name="nblineheader" value="1"/> |
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204 <param name="colfactor" value="2"/> |
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205 <param name="delta" value="0.001"/> |
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206 <param name="mode" value="neutral"/> |
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207 <param name="maxquery" value="5"/> |
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208 <output name="variableMetadata" file="out_test01.tabular"/> |
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209 <output name="HmdbOutWeb" file="out_test01.html"/> |
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210 <output name="HmdbOutXlsx" file="out_test01.txt"/> |
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211 </test> |
14 | 212 --> |
213 <!--test 02 : some results - with-mzrt-input-with-id file--> | |
214 <!-- | |
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215 <test> |
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216 <param name="choice" value="YES"/> |
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217 <param name="masses" value="input_test02_mzrt-input-with-id.tabular"/> |
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218 <param name="header_choice" value="yes"/> |
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219 <param name="nblineheader" value="1"/> |
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220 <param name="colfactor" value="2"/> |
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221 <param name="delta" value="0.001"/> |
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222 <param name="mode" value="positive"/> |
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223 <param name="maxquery" value="5"/> |
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224 <output name="variableMetadata" file="out_test02.tabular"/> |
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225 <output name="HmdbOutWeb" file="out_test02.html"/> |
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226 <output name="HmdbOutXlsx" file="out_test02.txt"/> |
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227 </test> |
14 | 228 --> |
229 <!--test 03 : some results - with-mz list in manual mass mode--> | |
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230 <test> |
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231 <param name="choice" value="NO"/> |
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232 <param name="mass" value="175.01 238.19 420.16 780.32 956.25 1100.45"/> |
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233 <param name="delta" value="0.05"/> |
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234 <param name="mode" value="positive"/> |
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235 <param name="maxquery" value="5"/> |
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236 <param name="data_positive_adducts" value="M+H"/> |
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237 <output name="variableMetadata2" file="out_test03.tabular"/> |
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238 <output name="HmdbOutWeb2" file="out_test03.html"/> |
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239 <output name="HmdbOutXlsx2" file="out_test03.txt"/> |
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240 </test> |
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241 </tests> |
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242 |
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243 <help><![CDATA[ |
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244 |
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245 .. class:: infomark |
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246 |
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247 **Authors** Marion Landi, Yann Guitton and Franck Giacomoni |
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248 |
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249 --------------------------------------------------- |
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250 |
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251 .. class:: infomark |
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252 |
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253 **Please cite** If you use this tool, please add the following reference |
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254 | 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 | 255 | 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. |
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256 | Wishart DS et al, HMDB 5.0 - the Human Metabolome Database for 2022, Nucleic Acids Res. 2022. |
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257 |
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258 |
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259 --------------------------------------------------- |
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260 |
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261 ============== |
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262 HMDB MS search |
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263 ============== |
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264 |
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265 ----------- |
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266 Description |
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267 ----------- |
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268 |
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269 | Search informations (like : HMDB id, Name, Adduct, delta mass) on HMDB online bank |
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270 | with one or more mass(es) in a file or entered manually |
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271 |
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272 |
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273 ----------------- |
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274 Workflow position |
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275 ----------------- |
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276 |
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277 |
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278 .. image:: ./static/images/metabolomics/hmdb.png |
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279 :width: 800 |
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280 |
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281 |
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282 ----------- |
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283 Input files |
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284 ----------- |
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285 |
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286 |
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287 +-------------------------+-----------+ |
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288 | Parameter : num + label | Format | |
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289 +=========================+===========+ |
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290 | 1 : File of masses | tabular | |
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291 +-------------------------+-----------+ |
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292 |
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293 File of masses (Generally variable metadata file) must have at least the following column : |
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294 * Masses : column with all the masses in the tsv input file |
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295 |
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296 ---------- |
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297 Parameters |
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298 ---------- |
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299 |
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300 Would you use a file |
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301 | Choose whether the masses are in a file or entered manually |
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302 | YES (default) : parameters **File of masses ; Do you have a header ; Column of masses** are visible |
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303 | NO : parameter **Mass to submit** is visible |
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304 | |
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305 |
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306 |
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307 If 'use file'='YES' |
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308 |
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309 File of masses |
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310 | see "Input files" section above |
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311 | Tabular file format, Generally variable metadata file |
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312 | |
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313 |
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314 Do you have a header |
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315 | YES (default) : parameter **Number of header lines** is visible |
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316 | NO : all lines are considered to contain masses |
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317 | |
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318 |
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319 If 'have a header'='YES' |
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320 |
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321 Number of header lines |
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322 | Number of lines not containing masses values, these lines will be ignored |
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323 | |
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324 |
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325 In all header cases : |
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326 |
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327 Column of masses |
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328 | Specify the column number for the mass in the tsv input file |
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329 | |
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330 |
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331 |
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332 If 'use file'='NO' |
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333 |
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334 Mass to submit |
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335 | Specify a list of mass to request |
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336 | one or more mass(es) entered manually |
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337 | For a masses list, writes : m1 m2 m3 |
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338 | You must separate yours values with space |
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339 | dot (.) is for float number |
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340 | |
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341 |
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342 In all cases : |
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343 |
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344 Mass-to-charge ratio |
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345 | Specify a delta (mass-to-charge ratio) to apply on mass - This value is a float, between 0.0000000000000001 and 10. |
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346 | |
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347 |
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348 Molecular Species |
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349 | Type of ionization of the molecule : *positif, negatif, neutral* |
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350 | |
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351 |
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352 |
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353 ------------ |
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354 Output files |
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355 ------------ |
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356 |
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357 Two types of files |
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358 | HMDB_WEB.HTML: for viewing result via HTML. |
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359 | |
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360 | HMDB_TABULAR.tabular: for linking with others modules. |
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361 | |
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362 | HMDB_XLS.txt: an excel-like output permitting manual annotation cleaning. |
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363 | |
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364 |
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365 --------------------------------------------------- |
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366 |
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367 |
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368 --------------- |
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369 Working example |
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370 --------------- |
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371 |
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372 |
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373 .. class:: warningmark |
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374 |
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375 Refer to the corresponding W4M HowTo section: http://workflow4metabolomics.org/howto |
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376 | Format Data For Postprocessing |
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377 | Perform LCMS Annotations |
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378 |
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379 .. class:: warningmark |
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380 |
24
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381 And their "W4M courses 2022": |
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382 | Using Galaxy4Metabolomics - W4M table format for Galaxy |
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383 | Annotation Banks - Annotation |
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384 |
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385 |
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386 ]]></help> |
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387 <!-- [RECOMMANDED] All citations associated to this tool (main citation given above and other references). Can be extracted from the history panel --> |
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388 <citations> |
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389 <citation type="doi">10.1093/nar/gks1065</citation> |
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391 <citation type="doi">10.1093/nar/gkab1062</citation> |
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392 </citations> |
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393 </tool> |