Mercurial > repos > fgiacomoni > hr2
annotate HR2.xml @ 1:e2cbcf6fa22e draft
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| author | fgiacomoni |
|---|---|
| date | Sun, 11 Dec 2022 17:16:43 +0000 |
| parents | 86296c048e46 |
| children | 23970530a518 |
| rev | line source |
|---|---|
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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 |