Mercurial > repos > fgiacomoni > hmdb_ms_search

comparison wsdl_hmdb.xml @ 1:6d0a0f8f672a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
author fgiacomoni
date Wed, 23 Nov 2016 09:31:50 -0500
parents
children a3744fb3605c
comparison
equal deleted inserted replaced
0:9583f9772198 1:6d0a0f8f672a
1 <tool id="wsdl_hmdb" name="HMDB MS search" version="2016-11-28">
2 <description>
3 search by masses on HMDB online bank
4 </description>
5
6 <requirements>
7 <!-- Waiting for conda improvement in Galaxy
8 <requirement type="package" version="1.19">perl-soap-lite</requirement>
9 <requirement type="package" version="6.15">perl-lwp-simple</requirement>
10 <requirement type="package" version="6.15">perl-libwww-perl</requirement>
11 <requirement type="package" version="2.95">perl-html-template</requirement>
12 <requirement type="package" version="1.71">perl-uri</requirement>
13 <requirement type="package" version="1.33">perl-text-csv</requirement>
14 <requirement type="package" version="3.49">perl-xml-twig</requirement>
15 -->
16 </requirements>
17
18 <stdio>
19 <exit_code range="1" level="fatal" />
20 </stdio>
21
22
23 <command><![CDATA[
24 perl $__tool_directory__/wsdl_hmdb.pl
25 #if str($input_type.choice) == "YES":
26 -masses "${input_type.masses}"
27 -header_choice "${input_type.header.header_choice}"
28 #if str($input_type.header.header_choice) == "yes":
29 -nblineheader "${$input_type.header.nbHeader}"
30 #end if
31 -colfactor "${input_type.colfactor}"
32 -output_tabular "$variableMetadata" -output_html "$HmdbOutWeb" -output_xls "$HmdbOutXlsx"
33 #else:
34 -mass "${input_type.mass}"
35 -output_tabular "$variableMetadata2" -output_html "$HmdbOutWeb2" -output_xls "$HmdbOutXlsx2"
36 #end if
37 -delta "$delta" -mode "$mode" -maxquery "$maxquery"
38
39 ]]></command>
40 <inputs>
41 <conditional name="input_type">
42 <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">
43 <option value="YES">YES</option>
44 <option value="NO">NO</option>
45 </param>
46 <when value="YES">
47 <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" />
48 <conditional name="header">
49 <param name="header_choice" type="select" label="Do you have a header " help="if 'YES' is selected then enter your number of header lines">
50 <option value="no">NO</option>
51 <option value="yes" selected="true">YES</option>
52 </param>
53 <when value="yes">
54 <param name="nbHeader" label="Number of header lines " type="integer" value="1" min="1" size="10" help="number of lines not containing masses"/>
55 </when>
56 <when value="no"/>
57 </conditional>
58 <param name="colfactor" label="Column of masses " type="data_column" data_ref="masses" accept_default="true" />
59 </when>
60 <when value="NO">
61 <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" />
62 </when>
63 </conditional>
64
65 <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)"/>
66 <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"/>
67 <param name="mode" label="Molecular Species " type="select" display="radio" help="">
68 <option value="positive">Positif Mode</option>
69 <option value="negative">Negatif Mode</option>
70 <option value="neutral" selected="True">Neutral Mass</option>
71 </param>
72 </inputs>
73
74 <outputs>
75 <data name="variableMetadata" format="tabular" label="${input_type.masses.name[:-6]}.HMDB.tabular">
76 <filter>input_type['choice'] == "YES"</filter>
77 </data>
78 <data name="HmdbOutWeb" format="html" label="${input_type.masses.name[:-6]}.HMDB_WEB.html">
79 <filter>input_type['choice'] == "YES"</filter>
80 </data>
81 <data name="HmdbOutXlsx" label="${input_type.masses.name[:-6]}.HMDB.xlsx" format="tabular">
82 <filter>input_type['choice'] == "YES"</filter>
83 </data>
84 <data name="variableMetadata2" format="tabular" label="HMDB.tabular">
85 <filter>input_type['choice'] == "NO"</filter>
86 </data>
87 <data name="HmdbOutWeb2" format="html" label="HMDB_WEB.html">
88 <filter>input_type['choice'] == "NO"</filter>
89 </data>
90 <data name="HmdbOutXlsx2" label="HMDB.xlsx" format="tabular">
91 <filter>input_type['choice'] == "NO"</filter>
92 </data>
93 </outputs>
94
95 <tests>
96 <test>
97 <!--test 01 no result - fake-mzrt-input-with-id -->
98 <param name="choice" value="YES"/>
99 <param name="masses" value="input_test01_fake-mzrt-input-with-id.tabular"/>
100 <param name="header_choice" value="yes"/>
101 <param name="nblineheader" value="1"/>
102 <param name="colfactor" value="2"/>
103 <param name="delta" value="0.001"/>
104 <param name="mode" value="neutral"/>
105 <param name="maxquery" value="5"/>
106 <output name="variableMetadata" file="out_test01.tabular"/>
107 <output name="HmdbOutWeb" file="out_test01.html"/>
108 <output name="HmdbOutXlsx" file="out_test01.xlsx"/>
109 </test>
110 <test>
111 <!--test 02 : some results - with-mzrt-input-with-id file-->
112 <param name="choice" value="YES"/>
113 <param name="masses" value="input_test02_mzrt-input-with-id.tabular"/>
114 <param name="header_choice" value="yes"/>
115 <param name="nblineheader" value="1"/>
116 <param name="colfactor" value="2"/>
117 <param name="delta" value="0.001"/>
118 <param name="mode" value="positive"/>
119 <param name="maxquery" value="5"/>
120 <output name="variableMetadata" file="out_test02.tabular"/>
121 <output name="HmdbOutWeb" file="out_test02.html"/>
122 <output name="HmdbOutXlsx" file="out_test02.xlsx"/>
123 </test>
124 <test>
125 <!--test 03 : some results - with-mz list in manual mass mode-->
126 <param name="choice" value="NO"/>
127 <param name="mass" value="175.01 238.19 420.16 780.32 956.25 1100.45"/>
128 <param name="delta" value="0.05"/>
129 <param name="mode" value="positive"/>
130 <param name="maxquery" value="5"/>
131 <output name="variableMetadata2" file="out_test03.tabular"/>
132 <output name="HmdbOutWeb2" file="out_test03.html"/>
133 <output name="HmdbOutXlsx2" file="out_test03.xlsx"/>
134 </test>
135 </tests>
136
137 <help><![CDATA[
138
139 .. class:: infomark
140
141 **Authors** Marion Landi and Franck Giacomoni
142
143 ---------------------------------------------------
144
145 .. class:: infomark
146
147 **Please cite** If you use this tool, please add the following reference
148 | 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.
149
150
151 ---------------------------------------------------
152
153 ==============
154 HMDB MS search
155 ==============
156
157 -----------
158 Description
159 -----------
160
161 | Search informations (like : HMDB id, Name, Adduct, delta mass) on HMDB online bank
162 | with one or more mass(es) in a file or entered manually
163
164
165 -----------------
166 Workflow position
167 -----------------
168
169
170 .. image:: ./static/images/metabolomics/hmdb.png
171 :width: 800
172
173
174 -----------
175 Input files
176 -----------
177
178
179 +-------------------------+-----------+
180 | Parameter : num + label | Format |
181 +=========================+===========+
182 | 1 : File of masses | tabular |
183 +-------------------------+-----------+
184
185 File of masses (Generally variable metadata file) must have at least the following column :
186 * Masses : column with all the masses in the tsv input file
187
188 ----------
189 Parameters
190 ----------
191
192 Would you use a file
193 | Choose whether the masses are in a file or entered manually
194 | YES (default) : parameters **File of masses ; Do you have a header ; Column of masses** are visible
195 | NO : parameter **Mass to submit** is visible
196 |
197
198
199 If 'use file'='YES'
200
201 File of masses
202 | see "Input files" section above
203 | Tabular file format, Generally variable metadata file
204 |
205
206 Do you have a header
207 | YES (default) : parameter **Number of header lines** is visible
208 | NO : all lines are considered to contain masses
209 |
210
211 If 'have a header'='YES'
212
213 Number of header lines
214 | Number of lines not containing masses values, these lines will be ignored
215 |
216
217 In all header cases :
218
219 Column of masses
220 | Specify the column number for the mass in the tsv input file
221 |
222
223
224 If 'use file'='NO'
225
226 Mass to submit
227 | Specify a list of mass to request
228 | one or more mass(es) entered manually
229 | For a masses list, writes : m1 m2 m3
230 | You must separate yours values with space
231 | dot (.) is for float number
232 |
233
234 In all cases :
235
236 Mass-to-charge ratio
237 | Specify a delta (mass-to-charge ratio) to apply on mass - This value is a float, between 0.0000000000000001 and 10.
238 |
239
240 Molecular Species
241 | Type of ionization of the molecule : *positif, negatif, neutral*
242 |
243
244
245 ------------
246 Output files
247 ------------
248
249 Two types of files
250 | HMDB_WEB.HTML: for viewing result via HTML.
251 |
252 | HMDB_TABULAR.tabular: for linking with others modules.
253 |
254 | HMDB_XLSX.xlsx: an excel-like output permitting manual annotation cleaning.
255 |
256
257 ---------------------------------------------------
258
259
260 ---------------
261 Working example
262 ---------------
263
264
265 .. class:: warningmark
266
267 Refer to the corresponding W4M HowTo section: http://workflow4metabolomics.org/howto
268 | Format Data For Postprocessing
269 | Perform LCMS Annotations
270
271 .. class:: warningmark
272
273 And their "W4M courses 2015":
274 | Using Galaxy4Metabolomics - W4M table format for Galaxy
275 | Annotation Banks - Annotation
276
277
278 ]]></help>
279 </tool>