Mercurial > repos > fgiacomoni > hmdb_ms_search
comparison hmdb/wsdl_hmdb.xml @ 0:9583f9772198 draft
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author | fgiacomoni |
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date | Thu, 28 Jan 2016 10:52:26 -0500 |
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-1:000000000000 | 0:9583f9772198 |
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1 <tool id="wsdl_hmdb" name="HMDB MS search" version="2016-01-28"> | |
2 <description> | |
3 search by masses on HMDB online bank | |
4 </description> | |
5 <command interpreter="perl"> | |
6 wsdl_hmdb.pl | |
7 #if str($input_type.choice) == "YES": | |
8 -masses "${input_type.masses}" | |
9 -header_choice "${input_type.header.header_choice}" | |
10 #if str($input_type.header.header_choice) == "yes": | |
11 -nblineheader "${$input_type.header.nbHeader}" | |
12 #end if | |
13 -colfactor "${input_type.colfactor}" | |
14 #else: | |
15 -mass "${input_type.mass}" | |
16 #end if | |
17 -delta "$delta" -mode "$mode" | |
18 -output "$variableMetadata" -view "$HmdbResView" -outputxls "$HmdbResXls" | |
19 </command> | |
20 <inputs> | |
21 <conditional name="input_type"> | |
22 <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"> | |
23 <option value="YES">YES</option> | |
24 <option value="NO">NO</option> | |
25 </param> | |
26 <when value="YES"> | |
27 <param name="masses" label="File of masses (Variable Metadata) " format="tabular" type="data" help="Generally variable metadata file. Please note : HMDB allows maximum 150 query masses per request" /> | |
28 <conditional name="header"> | |
29 <param name="header_choice" type="select" label="Do you have a header " help="if 'YES' is selected then enter your number of header lines"> | |
30 <option value="no">NO</option> | |
31 <option value="yes" selected="true">YES</option> | |
32 </param> | |
33 <when value="yes"> | |
34 <param name="nbHeader" label="Number of header lines " type="integer" value="1" min="1" size="10" help="number of lines not containing masses"/> | |
35 </when> | |
36 </conditional> | |
37 <param name="colfactor" label="Column of masses " type="data_column" data_ref="masses" accept_default="true" /> | |
38 </when> | |
39 <when value="NO"> | |
40 <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" /> | |
41 </when> | |
42 </conditional> | |
43 | |
44 <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)"/> | |
45 <param name="mode" label="Molecular Species " type="select" display="radio" help=""> | |
46 <option value="positive">Positif Mode</option> | |
47 <option value="negative">Negatif Mode</option> | |
48 <option value="neutral" selected="True">Neutral Mass</option> | |
49 </param> | |
50 </inputs> | |
51 | |
52 <outputs> | |
53 <data name="variableMetadata" format="tabular" label="${tool.name}_TSV"/> | |
54 <data name="HmdbResView" format="html" label="${tool.name}_VIEW"/> | |
55 <data name="HmdbResXls" label="${tool.name}_XLS" format="tabular" /> | |
56 </outputs> | |
57 | |
58 <tests> | |
59 <test> | |
60 <!--test 01 no result - fake-mzrt-input-with-id --> | |
61 <param name="choice" value="YES"/> | |
62 <param name="masses" value="input_test01_fake-mzrt-input-with-id.tsv"/> | |
63 <param name="header_choice" value="yes"/> | |
64 <param name="nblineheader" value="1"/> | |
65 <param name="colfactor" value="2"/> | |
66 <param name="delta" value="0.001"/> | |
67 <param name="mode" value="neutral"/> | |
68 <output name="variableMetadata" file="out_test01.tsv"/> | |
69 <output name="HmdbResView" file="out_test01.html"/> | |
70 <output name="HmdbResXls" file="out_test01.csv"/> | |
71 </test> | |
72 <test> | |
73 <!--test 02 : some results - with-mzrt-input-with-id file--> | |
74 <param name="choice" value="YES"/> | |
75 <param name="masses" value="input_test02_mzrt-input-with-id.tsv"/> | |
76 <param name="header_choice" value="yes"/> | |
77 <param name="nblineheader" value="1"/> | |
78 <param name="colfactor" value="2"/> | |
79 <param name="delta" value="0.001"/> | |
80 <param name="mode" value="positive"/> | |
81 <output name="variableMetadata" file="out_test02.tsv"/> | |
82 <output name="HmdbResView" file="out_test02.html"/> | |
83 <output name="HmdbResXls" file="out_test02.csv"/> | |
84 </test> | |
85 <test> | |
86 <!--test 03 : some results - with-mz list in manual mass mode--> | |
87 <param name="choice" value="NO"/> | |
88 <param name="mass" value="175.01 238.19 420.16 780.32 956.25 1100.45"/> | |
89 <param name="delta" value="0.05"/> | |
90 <param name="mode" value="positive"/> | |
91 <output name="variableMetadata" file="out_test03.tsv"/> | |
92 <output name="HmdbResView" file="out_test03.html"/> | |
93 <output name="HmdbResXls" file="out_test03.csv"/> | |
94 </test> | |
95 </tests> | |
96 | |
97 <help> | |
98 | |
99 .. class:: infomark | |
100 | |
101 **Authors** Marion Landi and Franck Giacomoni | |
102 | |
103 --------------------------------------------------- | |
104 | |
105 .. class:: infomark | |
106 | |
107 **Please cite** If you use this tool, please cite | |
108 | `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. <http://www.ncbi.nlm.nih.gov/pubmed/23161693>`_ | |
109 | |
110 | |
111 --------------------------------------------------- | |
112 | |
113 ============== | |
114 HMDB MS search | |
115 ============== | |
116 | |
117 ----------- | |
118 Description | |
119 ----------- | |
120 | |
121 | Search informations (like : HMDB id, Name, Adduct, delta mass) on HMDB online bank | |
122 | with one or more mass(es) in a file or entered manually | |
123 | |
124 | |
125 ----------------- | |
126 Workflow position | |
127 ----------------- | |
128 | |
129 | |
130 .. image:: ./static/images/metabolomics/hmdb.png | |
131 :width: 800 | |
132 | |
133 | |
134 ----------- | |
135 Input files | |
136 ----------- | |
137 | |
138 | |
139 +-------------------------+-----------+ | |
140 | Parameter : num + label | Format | | |
141 +=========================+===========+ | |
142 | 1 : File of masses | tabular | | |
143 +-------------------------+-----------+ | |
144 | |
145 File of masses (Generally variable metadata file) must have at least the following column : | |
146 * Masses : column with all the masses in the tsv input file | |
147 | |
148 ---------- | |
149 Parameters | |
150 ---------- | |
151 | |
152 Would you use a file | |
153 | Choose whether the masses are in a file or entered manually | |
154 | YES (default) : parameters **File of masses ; Do you have a header ; Column of masses** are visible | |
155 | NO : parameter **Mass to submit** is visible | |
156 | | |
157 | |
158 | |
159 If 'use file'='YES' | |
160 | |
161 File of masses | |
162 | see "Input files" section above | |
163 | Tabular file format, Generally variable metadata file | |
164 | | |
165 | |
166 Do you have a header | |
167 | YES (default) : parameter **Number of header lines** is visible | |
168 | NO : all lines are considered to contain masses | |
169 | | |
170 | |
171 If 'have a header'='YES' | |
172 | |
173 Number of header lines | |
174 | Number of lines not containing masses values, these lines will be ignored | |
175 | | |
176 | |
177 In all header cases : | |
178 | |
179 Column of masses | |
180 | Specify the column number for the mass in the tsv input file | |
181 | | |
182 | |
183 | |
184 If 'use file'='NO' | |
185 | |
186 Mass to submit | |
187 | Specify a list of mass to request | |
188 | one or more mass(es) entered manually | |
189 | For a masses list, writes : m1 m2 m3 | |
190 | You must separate yours values with space | |
191 | dot (.) is for float number | |
192 | | |
193 | |
194 In all cases : | |
195 | |
196 Mass-to-charge ratio | |
197 | Specify a delta (mass-to-charge ratio) to apply on mass - This value is a float, between 0.0000000000000001 and 10. | |
198 | | |
199 | |
200 Molecular Species | |
201 | Type of ionization of the molecule : *positif, negatif, neutral* | |
202 | | |
203 | |
204 | |
205 ------------ | |
206 Output files | |
207 ------------ | |
208 | |
209 Two types of files | |
210 | wsdl_hmdb_VIEW.HTML : for viewing result via HTML. | |
211 | | |
212 | wsdl_hmdb_TSV.tabular : for linking with others modules. | |
213 | | |
214 | an excel-like output will be available. | |
215 | | |
216 | |
217 --------------------------------------------------- | |
218 | |
219 | |
220 --------------- | |
221 Working example | |
222 --------------- | |
223 | |
224 | |
225 .. class:: warningmark | |
226 | |
227 Refer to the corresponding `"W4M HowTo" <http://workflow4metabolomics.org/howto>`_ page: | |
228 | Format Data For Postprocessing | |
229 | Perform LCMS Annotations | |
230 | |
231 .. class:: warningmark | |
232 | |
233 And their "W4M courses 2015": | |
234 | Using Galaxy4Metabolomics - W4M table format for Galaxy | |
235 | Annotation Banks - Annotation | |
236 | |
237 | |
238 </help> | |
239 </tool> |