Mercurial > repos > fgiacomoni > hr2
annotate HR2.xml @ 1:e2cbcf6fa22e draft
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author | fgiacomoni |
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date | Sun, 11 Dec 2022 17:16:43 +0000 |
parents | 86296c048e46 |
children | 23970530a518 |
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1 <tool id="hr2" name="HR2 formula" version="1.1.2"> |
0 | 2 <description> |
3 find a chemical formula from a accurate mass | |
4 </description> | |
5 <requirements> | |
6 <requirement type="package" version="2.161">perl-data-dumper</requirement> | |
7 <requirement type="package" version="1.97">perl-text-csv</requirement> | |
8 <requirement type="package" version="2.97">perl-html-template</requirement> | |
9 <requirement type="package" version="1.04">hr2</requirement> | |
10 </requirements> | |
11 <stdio> | |
12 <exit_code range="1" level="fatal" /> | |
13 </stdio> | |
14 | |
15 | |
16 <command><![CDATA[ | |
17 perl $__tool_directory__/hr2_manager.pl | |
18 #if str($input_type.choice) == "YES": | |
19 -input "${input_type.input}" | |
20 #if str($input_type.header.header_choice) == "yes": | |
21 -nblineheader "${$input_type.header.nbHeader}" | |
22 #end if | |
23 -colId "${input_type.colId}" -colmass "${input_type.colmass}" | |
24 #else: | |
25 -masse "${input_type.masse}" | |
26 #end if | |
27 | |
28 -tolerance "$tol" | |
29 -mode "${mode_condition.mode}" | |
30 #if str($mode_condition.mode) == "neutral": | |
31 -charge "0" | |
32 #else: | |
33 -charge "${mode_condition.qtCharge}" | |
34 #end if | |
35 | |
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36 -regleOr "$regleOr" -atomes_basic "$atomes_basic" -atomes_sup "$atomes_sup" |
0 | 37 -output1 "$variableMetadata" -outputView "$hr2ResView" |
38 -verbose "$verbose" | |
39 ]]></command> | |
40 | |
41 <inputs> | |
42 <conditional name="input_type"> | |
43 <param name="choice" type="select" display="radio" label="Would you use a file " help="if 'NO' is selected then one or more mass(es) must be entered manually"> | |
44 <option value="YES">YES</option> | |
45 <option value="NO">NO</option> | |
46 </param> | |
47 <when value="YES"> | |
48 <param name="input" label="File of masses" format="tabular" type="data" /> | |
49 <conditional name="header"> | |
50 <param name="header_choice" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Do you have a header?" help="if 'YES' is selected then enter your number of header lines" /> | |
51 <when value="yes"> | |
52 <param name="nbHeader" label="Number of header lines" type="integer" value="1" min="1" size="10" help="number of lines not containing masses"/> | |
53 </when> | |
54 <when value="no"/> | |
55 </conditional> | |
56 <param name="colId" label="Column of Id" type="data_column" data_ref="input" accept_default="true" /> | |
57 <param name="colmass" label="Column of masses (MZ)" type="data_column" data_ref="input" accept_default="true" /> | |
58 </when> | |
59 <when value="NO"> | |
60 <param name="masse" size="20" type="text" label="Mass (MZ) to submit" help="For a masses list, writes : m1 m2 m3. Your values must be separated by spaces. You should use dot (.) like decimal separator"/> | |
61 </when> | |
62 </conditional> | |
63 | |
64 <param name="tol" label="Delta of mass (MZ) (in mmu)" type="float" value="1.0" min="0" max="9.0" help="Tolerance should be between 0 and 9.0 mmu. Default value is 1.0 mmu"/> | |
65 <conditional name="mode_condition"> | |
66 <param name="mode" label="Molecular Species Searched" type="select" display="radio" help="Or ionization type of the molecule list. Use neutral only if only if the masses correspond to molecules and not to ions : query doesn't be a [M+H] or [M-H] ion"> | |
67 <option value="positive">positive</option> | |
68 <option value="negative">negative</option> | |
69 <option value="neutral" selected="true">neutral</option> | |
70 </param> | |
71 <when value="neutral"/> | |
72 <when value="positive"> | |
73 <param name="qtCharge" label="Molecule initial charge" type="select" help="Use 'neutral' if the molecule is not charged"> | |
74 <option value="1">1</option> | |
75 <option value="2">2</option> | |
76 <option value="3">3</option> | |
77 </param> | |
78 </when> | |
79 <when value="negative"> | |
80 <param name="qtCharge" label="Molecule initial charge" type="select" help="Use 'neutral' if the molecule is not charged"> | |
81 <option value="1">1</option> | |
82 <option value="2">2</option> | |
83 <option value="3">3</option> | |
84 </param> | |
85 </when> | |
86 </conditional> | |
87 <param name="atomes_basic" label="Please unselect basic atom(s) from following list you want to exclude" type="select" display="checkboxes" multiple="True" help="Unselect one or more basic atoms to exclude them from the generated formula proposition"> | |
88 <option value="C" selected="true">C</option> | |
89 <option value="N" selected="true">N</option> | |
90 <option value="O" selected="true">O</option> | |
91 <option value="H" selected="true">H</option> | |
92 <option value="P" selected="true">P</option> | |
93 </param> | |
94 <param name="regleOr" label="Use all 7 golden rules OR only the first 3 golden rules?" type="select" display="radio" help="Use 'only first 3 rules' if you want more empirical formulas"> | |
95 <option value="YES">only first 3 rules</option> | |
96 <option value="NO" selected="true">all 7 rules</option> | |
97 </param> | |
98 <param name="atomes_sup" label="Add some atom(s) from following list if needed" type="select" display="checkboxes" multiple="True" help="C, H, N, O and P are available in basic atom section"> | |
99 <option value="S">S</option> | |
100 <option value="F">F</option> | |
101 <option value="L">Cl</option> | |
102 <option value="K">K</option> | |
103 <option value="B">Br</option> | |
104 <option value="A">Na</option> | |
105 <option value="1">13C</option> | |
106 </param> | |
107 <param name="verbose" type="select" label="Verbose level" display="radio" help=""> | |
108 <option value="1" selected="true">Low</option> | |
109 <option value="3" >High</option> | |
110 </param> | |
111 </inputs> | |
112 <outputs> | |
113 <data name="variableMetadata" format="tabular" label="${tool.name}_TSV"/> | |
114 <data name="hr2ResView" format="html" label="${tool.name}_VIEW"/> | |
115 </outputs> | |
116 | |
117 <tests> | |
118 <test> | |
119 <param name="choice" value="NO"/> | |
120 <param name="masse" value="175.125"/> | |
121 <param name="tolerance" value="1.0"/> | |
122 <param name="mode" value="negative"/> | |
123 <param name="qtCharge" value="1"/> | |
124 <param name="atomes_basic" value="C,O,N,H"/> | |
125 <param name="regleOr" value="NO"/> | |
126 <param name="verbose" value="3"/> | |
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127 <output name="variableMetadata" file="out1.tabular"/> |
0 | 128 </test> |
129 <test> | |
130 <param name="choice" value="NO"/> | |
131 <param name="masse" value="88.052"/> | |
132 <param name="tolerance" value="1.0"/> | |
133 <param name="mode" value="neutral"/> | |
134 <param name="qtCharge" value="1"/> | |
135 <param name="atomes_basic" value="C,O,H"/> | |
136 <param name="regleOr" value="NO"/> | |
137 <param name="verbose" value="3"/> | |
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138 <output name="variableMetadata" file="out2.tabular"/> |
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139 </test> |
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140 <test> |
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141 <param name="choice" value="NO"/> |
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142 <param name="masse" value="427.019898895"/> |
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143 <param name="tolerance" value="1.0"/> |
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144 <param name="mode" value="neutral"/> |
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145 <param name="qtCharge" value="1"/> |
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146 <param name="atomes_basic" value="C,O,N,H,P"/> |
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147 <param name="atomes_sup" value="S"/> |
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148 <param name="regleOr" value="NO"/> |
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149 <param name="verbose" value="3"/> |
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150 <output name="variableMetadata" file="out3.tabular"/> |
0 | 151 </test> |
152 </tests> | |
153 | |
154 <help><![CDATA[ | |
155 | |
156 .. class:: infomark | |
157 | |
158 **Authors** | |
159 | HR2 original program and its documentation are Copyright (c) 1992-2005 by Joerg Hau under GNU General Public License ("GPL") | |
160 | |
161 .. class:: infomark | |
162 | |
163 **Wrapping** | |
164 | Marion Landi - FLAME ; PFEM ; INRA ; MetaboHUB (for xml interface and Perl wrapper) | |
165 | Franck Giacomoni - PFEM ; INRA ; MetaboHUB (for xml interface, conda dependancies and Perl wrapper) | |
166 | |
167 --------------------------------------------------- | |
168 | |
169 .. class:: infomark | |
170 | |
171 **Please cite** If you use this tool, please cite | |
172 | Tobias Kind and Oliver Fiehn. (2007). "Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry." BMC Bioinformatics p8:105 http://www.ncbi.nlm.nih.gov/pubmed/17389044 | |
173 | HR2 original program and its documentation are under GNU General Public License ("GPL") : GPL is a"contaminating" license. http://fiehnlab.ucdavis.edu/projects/Seven_Golden_Rules/Software | |
174 | |
175 | |
176 --------------------------------------------------- | |
177 | |
178 ============== | |
179 HR2 formula | |
180 ============== | |
181 | |
182 ----------- | |
183 Description | |
184 ----------- | |
185 | |
186 | Find a formula for the masses | |
187 | only molecules with carbon (C) will be search | |
188 | |
189 | |
190 ----------------- | |
191 Workflow position | |
192 ----------------- | |
193 | |
194 | |
195 .. image:: ./static/images/metabolomics/hr2.png | |
196 :width: 800 | |
197 | |
198 | |
199 | |
200 | |
201 ----------- | |
202 Input files | |
203 ----------- | |
204 | |
205 +-------------------------+-----------+ | |
206 | Parameter : num + label | Format | | |
207 +=========================+===========+ | |
208 | 1 : variableMetadata | tabular | | |
209 +-------------------------+-----------+ | |
210 | |
211 File variableMetadata must have at least the 2 following columns : | |
212 * Id : column to identify masses in the csv/tsv input file | |
213 * Masses : column with all the masses in the csv/tsv input file | |
214 | |
215 | |
216 ---------- | |
217 Parameters | |
218 ---------- | |
219 | |
220 Would you use a file | |
221 | Choose whether the masses are in a file or entered manually | |
222 | YES (default) : parameters **File of masses ; Column of Id ; Number of header ; Column of masses** are visible | |
223 | NO : parameter **Mass of the molecule** is visible | |
224 | | |
225 | |
226 | |
227 If 'use file'='YES' | |
228 | |
229 Column of Id | |
230 | Specify the column number for the id in the csv/tsv input file | |
231 | | |
232 | |
233 Number of header lines | |
234 | Number of lines not containing values | |
235 | | |
236 | |
237 Column of masses | |
238 | Specify the column number for the mass in the csv/tsv input file | |
239 | | |
240 | |
241 If 'use file'='NO' | |
242 | |
243 Mass (MZ) to submit | |
244 | Specify a list of mass to request | |
245 | one or more mass(es) entered manually | |
246 | For a masses list, writes : m1 m2 m3 | |
247 | You must separate yours values with space | |
248 | dot (.) is for float number | |
249 | | |
250 | |
251 In all cases : | |
252 | |
253 Delta | |
254 | Tolerance of the gap in the mass | |
255 | It should be between 0 and 9.0 mmu | |
256 | |
257 Ionization | |
258 | Type of ionization of the molecule : *positif, negatif, neutral* | |
259 | Use neutral if query doesn't be a [M+H] or [M-H] ion | |
260 | HR2 knows only the weight of uncharged molecules | |
261 | so we made a correction to the masses of the value of a proton before the search | |
262 | if the masses are those from a spectrometry in positive or negatif mode. | |
263 | **neutral** : will do a search on the mass unchanged. | |
264 | |
265 Initial charge | |
266 | Use 0 if the molecule is not basically charged | |
267 | |
268 Exclude some basic atom(s) | |
269 List of atoms that can be exclude to the molecule : *C, N, O, H, P* | |
270 | |
271 Golden rules | |
272 | There are 7 golden rules | |
273 | Some are too stringent, especially for small molecules | |
274 | Use 'yes' if you want more empirical formulas | |
275 | |
276 Add some optionnal atom(s) | |
277 List of atoms that can be searched in addition to the molecule : *S, F, Cl, K, Br, Na, 13C* | |
278 | |
279 ------------ | |
280 Output files | |
281 ------------ | |
282 | |
283 Two types of files | |
284 | hr2_VIEW.HTML : for viewing result via HTML. | |
285 | hr2_TSV.tabular : for linking with others modules. | |
286 | an excel-like output will be available. | |
287 | |
288 --------------------------------------------------- | |
289 | |
290 | |
291 --------------- | |
292 Working example | |
293 --------------- | |
294 | |
295 | |
296 .. class:: warningmark | |
297 | |
298 Refer to the corresponding "W4M HowTo" in http://workflow4metabolomics.org/howto section | |
299 | Format Data For Postprocessing | |
300 | Perform LCMS Annotations | |
301 | |
302 .. class:: warningmark | |
303 | |
304 And their "W4M courses 2018": | |
305 | Using Galaxy4Metabolomics - W4M table format for Galaxy | |
306 | Les banques d'annotation - Annotation | |
307 | |
308 ]]></help> | |
309 <citations> | |
310 <citation type="doi">10.1186/1471-2105-8-105</citation> | |
311 </citations> | |
312 </tool> | |
313 |