Mercurial > repos > fgiacomoni > hr2
annotate HR2.xml @ 3:78afd7f439f3 draft default tip
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| author | fgiacomoni |
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| date | Wed, 15 Feb 2023 15:57:49 +0000 |
| parents | 23970530a518 |
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| rev | line source |
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1 <tool id="hr2" name="HR2 formula" version="1.2.0"> |
| 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": | |
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21 -nbHeader "${$input_type.header.nbHeader}" |
| 0 | 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" |
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37 |
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38 #if str($max_custom_atom_condition.max_custom_atom_choice) == "YES": |
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39 -C12_max_value "${max_custom_atom_condition.C12_max_value}" |
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40 -C13_max_value "${max_custom_atom_condition.C13_max_value}" |
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41 -H_max_value "${max_custom_atom_condition.H_max_value}" |
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42 -N_max_value "${max_custom_atom_condition.N_max_value}" |
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43 -O_max_value "${max_custom_atom_condition.O_max_value}" |
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44 -P_max_value "${max_custom_atom_condition.P_max_value}" |
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45 -S_max_value "${max_custom_atom_condition.S_max_value}" |
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46 -F_max_value "${max_custom_atom_condition.F_max_value}" |
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47 -Cl_max_value "${max_custom_atom_condition.Cl_max_value}" |
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48 -K_max_value "${max_custom_atom_condition.K_max_value}" |
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49 -Br_max_value "${max_custom_atom_condition.Br_max_value}" |
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50 -Na_max_value "${max_custom_atom_condition.Na_max_value}" |
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51 |
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52 #end if |
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53 |
| 0 | 54 -output1 "$variableMetadata" -outputView "$hr2ResView" |
| 55 -verbose "$verbose" | |
| 56 ]]></command> | |
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57 <!-- -customAtomValues "-C 0-${max_custom_atom_condition.C12_max_value} -1 0-${max_custom_atom_condition.C13_max_value} -H 0-${max_custom_atom_condition.H_max_value} -N 0-${max_custom_atom_condition.N_max_value} -O 0-${max_custom_atom_condition.O_max_value} -P 0-${max_custom_atom_condition.P_max_value} -S 0-${max_custom_atom_condition.S_max_value} -F 0-${max_custom_atom_condition.F_max_value} -L 0-${max_custom_atom_condition.Cl_max_value} -K 0-${max_custom_atom_condition.K_max_value} -B 0-${max_custom_atom_condition.Br_max_value} -A 0-${max_custom_atom_condition.Na_max_value}" --> |
| 0 | 58 |
| 59 <inputs> | |
| 60 <conditional name="input_type"> | |
| 61 <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"> | |
| 62 <option value="YES">YES</option> | |
| 63 <option value="NO">NO</option> | |
| 64 </param> | |
| 65 <when value="YES"> | |
| 66 <param name="input" label="File of masses" format="tabular" type="data" /> | |
| 67 <conditional name="header"> | |
| 68 <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" /> | |
| 69 <when value="yes"> | |
| 70 <param name="nbHeader" label="Number of header lines" type="integer" value="1" min="1" size="10" help="number of lines not containing masses"/> | |
| 71 </when> | |
| 72 <when value="no"/> | |
| 73 </conditional> | |
| 74 <param name="colId" label="Column of Id" type="data_column" data_ref="input" accept_default="true" /> | |
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75 <param name="colmass" label="Column of masses (mz)" type="data_column" data_ref="input" accept_default="true" /> |
| 0 | 76 </when> |
| 77 <when value="NO"> | |
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78 <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"/> |
| 0 | 79 </when> |
| 80 </conditional> | |
| 81 | |
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82 <param name="tol" label="Delta of mass " type="float" value="1.0" min="0" max="9.0" help="Tolerance should be between 0 and 9.0 Da. Default value is 1.0 mmu"/> |
| 0 | 83 <conditional name="mode_condition"> |
| 84 <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"> | |
| 85 <option value="positive">positive</option> | |
| 86 <option value="negative">negative</option> | |
| 87 <option value="neutral" selected="true">neutral</option> | |
| 88 </param> | |
| 89 <when value="neutral"/> | |
| 90 <when value="positive"> | |
| 91 <param name="qtCharge" label="Molecule initial charge" type="select" help="Use 'neutral' if the molecule is not charged"> | |
| 92 <option value="1">1</option> | |
| 93 <option value="2">2</option> | |
| 94 <option value="3">3</option> | |
| 95 </param> | |
| 96 </when> | |
| 97 <when value="negative"> | |
| 98 <param name="qtCharge" label="Molecule initial charge" type="select" help="Use 'neutral' if the molecule is not charged"> | |
| 99 <option value="1">1</option> | |
| 100 <option value="2">2</option> | |
| 101 <option value="3">3</option> | |
| 102 </param> | |
| 103 </when> | |
| 104 </conditional> | |
| 105 <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"> | |
| 106 <option value="C" selected="true">C</option> | |
| 107 <option value="N" selected="true">N</option> | |
| 108 <option value="O" selected="true">O</option> | |
| 109 <option value="H" selected="true">H</option> | |
| 110 <option value="P" selected="true">P</option> | |
| 111 </param> | |
| 112 <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"> | |
| 113 <option value="YES">only first 3 rules</option> | |
| 114 <option value="NO" selected="true">all 7 rules</option> | |
| 115 </param> | |
| 116 <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"> | |
| 117 <option value="S">S</option> | |
| 118 <option value="F">F</option> | |
| 119 <option value="L">Cl</option> | |
| 120 <option value="K">K</option> | |
| 121 <option value="B">Br</option> | |
| 122 <option value="A">Na</option> | |
| 123 <option value="1">13C</option> | |
| 124 </param> | |
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125 <conditional name="max_custom_atom_condition"> |
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126 <param name="max_custom_atom_choice" label="Do you want to manage custom maximum number atoms?" type="select" display="radio" help="To work only with [13]C isotopes for example, use YES - ()Don't forget to select wanted atoms below)"> |
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127 <option value="NO" selected="true">NO</option> |
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128 <option value="YES">YES</option> |
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129 </param> |
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130 <when value="YES"> |
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131 <param name="C12_max_value" label="[12]C atom max number " type="integer" value="0" min="0" max="100" help="The maximum of [12]C you need to (should be between 0 and 100 atoms per structure). Default value is 0"/> |
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132 <param name="C13_max_value" label="[13]C atom max number " type="integer" value="40" min="0" max="100" help="The maximum of [13]C you need to (should be between 0 and 100 atoms per structure). Default value is 40"/> |
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133 <param name="H_max_value" label="[1]H atom max number " type="integer" value="200" min="0" max="200" help="The maximum of H you need to (should be between 0 and 200 atoms per structure). Default value is 200"/> |
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134 <param name="N_max_value" label="[15]N atom max number " type="integer" value="40" min="0" max="100" help="The maximum of N you need to (should be between 0 and 100 atoms per structure). Default value is 40"/> |
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135 <param name="O_max_value" label="[16]O atom max number " type="integer" value="70" min="0" max="100" help="The maximum of O you need to (should be between 0 and 100 atoms per structure). Default value is 70"/> |
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136 <param name="P_max_value" label="[31]P atom max number " type="integer" value="10" min="0" max="100" help="The maximum of P you need to (should be between 0 and 100 atoms per structure). Default value is 10"/> |
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137 <param name="S_max_value" label="[32]S atom max number " type="integer" value="10" min="0" max="100" help="The maximum of S you need to (should be between 0 and 100 atoms per structure). Default value is 10"/> |
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138 <param name="F_max_value" label="[19]F atom max number " type="integer" value="10" min="0" max="100" help="The maximum of F you need to (should be between 0 and 100 atoms per structure). Default value is 10"/> |
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139 <param name="Cl_max_value" label="[35]Cl atom max number " type="integer" value="10" min="0" max="100" help="The maximum of Cl you need to (should be between 0 and 100 atoms per structure). Default value is 10"/> |
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140 <param name="K_max_value" label="[13]K atom max number " type="integer" value="10" min="0" max="100" help="The maximum of K you need to (should be between 0 and 100 atoms per structure). Default value is 10"/> |
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141 <param name="Br_max_value" label="[80]Br atom max number " type="integer" value="10" min="0" max="100" help="The maximum of Br you need to (should be between 0 and 100 atoms per structure). Default value is 10"/> |
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142 <param name="Na_max_value" label="[23]Na atom max number " type="integer" value="10" min="0" max="100" help="The maximum of Na you need to (should be between 0 and 40 atoms per structure). Default value is 10"/> |
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143 </when> |
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144 <when value="NO"> |
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145 </when> |
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146 </conditional> |
| 0 | 147 <param name="verbose" type="select" label="Verbose level" display="radio" help=""> |
| 148 <option value="1" selected="true">Low</option> | |
| 149 <option value="3" >High</option> | |
| 150 </param> | |
| 151 </inputs> | |
| 152 <outputs> | |
| 153 <data name="variableMetadata" format="tabular" label="${tool.name}_TSV"/> | |
| 154 <data name="hr2ResView" format="html" label="${tool.name}_VIEW"/> | |
| 155 </outputs> | |
| 156 | |
| 157 <tests> | |
| 158 <test> | |
| 159 <param name="choice" value="NO"/> | |
| 160 <param name="masse" value="175.125"/> | |
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161 <param name="tol" value="1.0"/> |
| 0 | 162 <param name="mode" value="negative"/> |
| 163 <param name="qtCharge" value="1"/> | |
| 164 <param name="atomes_basic" value="C,O,N,H"/> | |
| 165 <param name="regleOr" value="NO"/> | |
| 166 <param name="verbose" value="3"/> | |
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167 <output name="variableMetadata" file="out1.tabular"/> |
| 0 | 168 </test> |
| 169 <test> | |
| 170 <param name="choice" value="NO"/> | |
| 171 <param name="masse" value="88.052"/> | |
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172 <param name="tol" value="1.0"/> |
| 0 | 173 <param name="mode" value="neutral"/> |
| 174 <param name="qtCharge" value="1"/> | |
| 175 <param name="atomes_basic" value="C,O,H"/> | |
| 176 <param name="regleOr" value="NO"/> | |
| 177 <param name="verbose" value="3"/> | |
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178 <output name="variableMetadata" file="out2.tabular"/> |
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179 </test> |
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180 <test> |
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181 <param name="choice" value="NO"/> |
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182 <param name="masse" value="427.019898895"/> |
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183 <param name="tol" value="1.0"/> |
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184 <param name="mode" value="neutral"/> |
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185 <param name="qtCharge" value="1"/> |
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186 <param name="atomes_basic" value="C,O,N,H,P"/> |
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187 <param name="atomes_sup" value="S"/> |
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188 <param name="S_max_value" value="40"/> |
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189 <param name="regleOr" value="NO"/> |
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190 <param name="verbose" value="3"/> |
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191 <output name="variableMetadata" file="out3.tabular"/> |
| 0 | 192 </test> |
| 193 </tests> | |
| 194 | |
| 195 <help><![CDATA[ | |
| 196 | |
| 197 .. class:: infomark | |
| 198 | |
| 199 **Authors** | |
| 200 | HR2 original program and its documentation are Copyright (c) 1992-2005 by Joerg Hau under GNU General Public License ("GPL") | |
| 201 | |
| 202 .. class:: infomark | |
| 203 | |
| 204 **Wrapping** | |
| 205 | Marion Landi - FLAME ; PFEM ; INRA ; MetaboHUB (for xml interface and Perl wrapper) | |
| 206 | Franck Giacomoni - PFEM ; INRA ; MetaboHUB (for xml interface, conda dependancies and Perl wrapper) | |
| 207 | |
| 208 --------------------------------------------------- | |
| 209 | |
| 210 .. class:: infomark | |
| 211 | |
| 212 **Please cite** If you use this tool, please cite | |
| 213 | 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 | |
| 214 | 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 | |
| 215 | |
| 216 | |
| 217 --------------------------------------------------- | |
| 218 | |
| 219 ============== | |
| 220 HR2 formula | |
| 221 ============== | |
| 222 | |
| 223 ----------- | |
| 224 Description | |
| 225 ----------- | |
| 226 | |
| 227 | Find a formula for the masses | |
| 228 | only molecules with carbon (C) will be search | |
| 229 | |
| 230 | |
| 231 ----------------- | |
| 232 Workflow position | |
| 233 ----------------- | |
| 234 | |
| 235 | |
|
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236 .. image:: hr2.png |
| 0 | 237 :width: 800 |
| 238 | |
| 239 | |
| 240 | |
| 241 | |
| 242 ----------- | |
| 243 Input files | |
| 244 ----------- | |
| 245 | |
| 246 +-------------------------+-----------+ | |
| 247 | Parameter : num + label | Format | | |
| 248 +=========================+===========+ | |
| 249 | 1 : variableMetadata | tabular | | |
| 250 +-------------------------+-----------+ | |
| 251 | |
| 252 File variableMetadata must have at least the 2 following columns : | |
| 253 * Id : column to identify masses in the csv/tsv input file | |
| 254 * Masses : column with all the masses in the csv/tsv input file | |
| 255 | |
| 256 | |
| 257 ---------- | |
| 258 Parameters | |
| 259 ---------- | |
| 260 | |
| 261 Would you use a file | |
| 262 | Choose whether the masses are in a file or entered manually | |
| 263 | YES (default) : parameters **File of masses ; Column of Id ; Number of header ; Column of masses** are visible | |
| 264 | NO : parameter **Mass of the molecule** is visible | |
| 265 | | |
| 266 | |
| 267 | |
| 268 If 'use file'='YES' | |
| 269 | |
| 270 Column of Id | |
| 271 | Specify the column number for the id in the csv/tsv input file | |
| 272 | | |
| 273 | |
| 274 Number of header lines | |
| 275 | Number of lines not containing values | |
| 276 | | |
| 277 | |
| 278 Column of masses | |
| 279 | Specify the column number for the mass in the csv/tsv input file | |
| 280 | | |
| 281 | |
| 282 If 'use file'='NO' | |
| 283 | |
| 284 Mass (MZ) to submit | |
| 285 | Specify a list of mass to request | |
| 286 | one or more mass(es) entered manually | |
| 287 | For a masses list, writes : m1 m2 m3 | |
| 288 | You must separate yours values with space | |
| 289 | dot (.) is for float number | |
| 290 | | |
| 291 | |
| 292 In all cases : | |
| 293 | |
| 294 Delta | |
| 295 | Tolerance of the gap in the mass | |
| 296 | It should be between 0 and 9.0 mmu | |
| 297 | |
| 298 Ionization | |
| 299 | Type of ionization of the molecule : *positif, negatif, neutral* | |
| 300 | Use neutral if query doesn't be a [M+H] or [M-H] ion | |
| 301 | HR2 knows only the weight of uncharged molecules | |
| 302 | so we made a correction to the masses of the value of a proton before the search | |
| 303 | if the masses are those from a spectrometry in positive or negatif mode. | |
| 304 | **neutral** : will do a search on the mass unchanged. | |
| 305 | |
| 306 Initial charge | |
| 307 | Use 0 if the molecule is not basically charged | |
| 308 | |
| 309 Exclude some basic atom(s) | |
| 310 List of atoms that can be exclude to the molecule : *C, N, O, H, P* | |
| 311 | |
| 312 Golden rules | |
| 313 | There are 7 golden rules | |
| 314 | Some are too stringent, especially for small molecules | |
| 315 | Use 'yes' if you want more empirical formulas | |
| 316 | |
| 317 Add some optionnal atom(s) | |
| 318 List of atoms that can be searched in addition to the molecule : *S, F, Cl, K, Br, Na, 13C* | |
| 319 | |
| 320 ------------ | |
| 321 Output files | |
| 322 ------------ | |
| 323 | |
| 324 Two types of files | |
| 325 | hr2_VIEW.HTML : for viewing result via HTML. | |
| 326 | hr2_TSV.tabular : for linking with others modules. | |
| 327 | an excel-like output will be available. | |
| 328 | |
| 329 --------------------------------------------------- | |
| 330 | |
| 331 | |
| 332 --------------- | |
| 333 Working example | |
| 334 --------------- | |
| 335 | |
| 336 | |
| 337 .. class:: warningmark | |
| 338 | |
| 339 Refer to the corresponding "W4M HowTo" in http://workflow4metabolomics.org/howto section | |
| 340 | Format Data For Postprocessing | |
| 341 | Perform LCMS Annotations | |
| 342 | |
| 343 .. class:: warningmark | |
| 344 | |
| 345 And their "W4M courses 2018": | |
| 346 | Using Galaxy4Metabolomics - W4M table format for Galaxy | |
| 347 | Les banques d'annotation - Annotation | |
| 348 | |
| 349 ]]></help> | |
| 350 <citations> | |
| 351 <citation type="doi">10.1186/1471-2105-8-105</citation> | |
| 352 </citations> | |
| 353 </tool> | |
| 354 |