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"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
author computational-metabolomics
date Wed, 05 Feb 2020 12:30:06 -0500
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children 9ee2e2ceb2c9
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1 <tool id="metfrag" name="MetFrag" version="2.4.5+galaxy1">
2 <description>
3 in silico fragmentor for compound annotation of mass spectrometry fragmentation spectra
4 </description>
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8 <requirements>
9 <requirement type="package" version="2.4.5">metfrag</requirement>
10 </requirements>
11 <stdio>
12 <regex match="Cannot allocate memory"
13 source="stderr"
14 level="fatal_oom"
15 description="Out of memory error occurred" />
16 </stdio>
17 <command detect_errors="exit_code">
18 <![CDATA[
19 python '$__tool_directory__/metfrag.py'
20 --input_pth '$input'
21 --result_pth '$results'
22 --temp_dir './temp/'
23
24 --cores_top_level \${GALAXY_SLOTS:-4}
25
26 --MetFragDatabaseType '$db_select.MetFragDatabaseType'
27
28 #if $db_select.MetFragDatabaseType == 'LocalCSV':
29 --LocalDatabasePath '$db_select.LocalDatabasePath'
30 #elif $db_select.MetFragDatabaseType == 'MetChem':
31 --LocalMetChemDatabaseServerIp '$db_select.LocalMetChemDatabaseServerIp'
32 #end if
33
34 --DatabaseSearchRelativeMassDeviation $DatabaseSearchRelativeMassDeviation
35 --FragmentPeakMatchRelativeMassDeviation $FragmentPeakMatchRelativeMassDeviation
36 --FragmentPeakMatchAbsoluteMassDeviation $FragmentPeakMatchAbsoluteMassDeviation
37 --polarity '$polarity'
38
39 --MetFragScoreTypes '$suspectlist.MetFragScoreTypes'
40 --MetFragScoreWeights '$suspectlist.MetFragScoreWeights'
41
42 #if $suspectlist.suspectselector == 'includesuspects':
43 #if $suspectlist.includesuspects_default_cond:
44 --ScoreSuspectLists '$__tool_directory__/UNPD_DB.inchikeys.txt'
45 #else
46 --ScoreSuspectLists '$suspectlist.includesuspects_custom_cond.ScoreSuspectLists'
47 #end if
48 #end if
49
50 --meta_select_col $meta_select_col
51 --minMSMSpeaks $minMSMSpeaks
52 --schema $schema
53
54 $PreProcessFilter.UnconnectedCompoundFilter
55 $PreProcessFilter.IsotopeFilter
56
57 --FilterMinimumElements '$PreProcessFilter.FilterMinimumElements'
58 --FilterMaximumElements '$PreProcessFilter.FilterMaximumElements'
59 --FilterSmartsInclusionList '$PreProcessFilter.FilterSmartsInclusionList'
60 --FilterSmartsExclusionList '$PreProcessFilter.FilterSmartsExclusionList'
61 --FilterIncludedElements '$PreProcessFilter.FilterIncludedElements'
62 --FilterExcludedElements '$PreProcessFilter.FilterExcludedElements'
63 --FilterIncludedExclusiveElements '$PreProcessFilter.FilterIncludedExclusiveElements'
64
65 $skip_invalid_adducts
66 --score_thrshld $PostProcessFilter.score_thrshld
67 --pctexplpeak_thrshld $PostProcessFilter.pctexplpeak_thrshld
68
69 ]]></command>
70 <inputs>
71 <param name="input" type="data" format="msp" label="MSP file (Output from Create MSP tool)"/>
72 <conditional name="db_select">
73 <param argument="--MetFragDatabaseType" type="select" label="Choose Compound Database">
74 <option value="PubChem" selected="true">PubChem</option>
75 <option value="KEGG">KEGG</option>
76 <option value="LocalCSV">Local database (csv)</option>
77 <option value="MetChem">MetChem</option>
78 </param>
79 <when value="MetChem">
80 <param argument="--LocalMetChemDatabaseServerIp" type="text" label="MetChem URL"/>
81 </when>
82 <when value="LocalCSV">
83 <param argument="--LocalDatabasePath" type="data" format="csv"
84 label="Local database of compounds (CSV format)" />
85 </when>
86 <when value="KEGG"/>
87 <when value="PubChem"/>
88 </conditional>
89 <param argument="--DatabaseSearchRelativeMassDeviation" type="float" min="0" value="10"
90 label="Relative Mass Deviation for database search (ppm)"
91 help="A value in ppm that defines the deviation of theoretical masses in the database
92 vs. the measured masses"/>
93 <param argument="--FragmentPeakMatchRelativeMassDeviation" type="float" min="0" value="5"
94 label="Fragment Peak Match Relative Mass Deviation (ppm)"
95 help="Relative mass deviation in ppm of theoretical fragment peaks vs. measured fragment peaks" />
96 <param argument="--FragmentPeakMatchAbsoluteMassDeviation" type="float" min="0" value="0.001"
97 label="Fragment Peak Match Absolute Mass Deviation (Da)"
98 help="Absolute mass deviation in Dalton of theoretical fragment peaks vs. measured fragment peaks" />
99 <param argument="--polarity" type="select" label="Polarity"
100 help="The polarity used for the mode of acquisition">
101 <option value="pos" selected="true">Positive</option>
102 <option value="neg">Negative</option>
103 </param>
104 <param argument="--schema" type="select" label="Schema"
105 help="The schema used for the MSP file (auto will try automatically determine the schema)">
106 <option value="auto" selected="True">Auto</option>
107 <option value="msp">Generic MSP</option>
108 <option value="massbank">MassBank</option>
109 </param>
110 <param argument="--meta_select_col" type="select"
111 label="Choose how additional metadata columns are extracted"
112 help="The MetFrag output can have additional meta data columns added, these can be either extracted
113 from all MSP parameters or from the 'Name' and 'RECORD_TITLE' MSP parameter. Additionally, columns
114 can be added from the 'Name' or 'RECORD_TITLE' parameter by splitting on | and :
115 e.g. 'MZ:100.2 | RT:20 | xcms_grp_id:1' would create MZ,RT and xcms_grp_id columns">
116 <option value="name" selected="true">Extra metadata columns from the Name or RECORD_TITLE</option>
117 <option value="name_split">Extra metadata columns from the Name or RECORD_TITLE (each column is split on "|" and ":" ) </option>
118 <option value="all">Extra metadata columns from all MSP parameters</option>
119 </param>
120 <conditional name="suspectlist">
121 <param name="suspectselector" type="select" label="Suspect list"
122 help="Choose whether to include a suspect list">
123 <option value="includesuspects" >Include suspect list</option>
124 <option value="excludesuspects" selected="True">Do not include suspect list</option>
125 </param>
126 <when value="includesuspects">
127 <conditional name="includesuspects_default_cond">
128 <param name="includesuspects_default_bool" type="boolean"
129 label="Use default list of suspect compounds?"
130 help="Either provide a file containing a list of suspect compounds or a default file
131 of an aggregated list of in silico predicted MS/MS spectra of natural products
132 from the Universal Natural Products Database (http://pkuxxj.pku.edu.cn/UNPD/index.php).
133 The list is an aggregated version of the github repository https://github.com/oolonek/ISDB/tree/master/Data/dbs."/>
134 <when value="true"/>
135 <when value="false">
136 <param argument="--ScoreSuspectLists" type="data" format="txt" optional="True"
137 label="Suspect list file" help="File containing a list of suspects inchikeys" />
138 </when>
139 </conditional>
140 <expand macro="metfrag_scoring"/>
141 </when>
142 <when value="excludesuspects">
143 <expand macro="metfrag_scoring" suspectlistscore="False" weights="1.0,1.0"/>
144 </when>
145 </conditional>
146 <param argument="--minMSMSpeaks" type="integer" label="Minimum number of MS/MS peaks" value="0"/>
147 <param argument="--skip_invalid_adducts" type="boolean" label="Skip invalid or undefined adduct types?"
148 truevalue="--skip_invalid_adducts" falsevalue="" checked="true"
149 help="If no adduct type is provided within the MSP file or if the adduct type is not usable
150 with MetFrag, set to 'yes' if these spectra should be skipped or 'no' if the default
151 of [M+H]+ for pos data or [M-H]- for neg data should be used"/>
152 <section name="PreProcessFilter" title="PreProcessing filters" expanded="False">
153 <param argument="--UnconnectedCompoundFilter" type="boolean" checked="false"
154 truevalue="--UnconnectedCompoundFilter" falsevalue=""
155 label="filter non-connected compounds (e.g. salts)" help=""/>
156 <param argument="--IsotopeFilter" type="boolean" checked="false" truevalue="--IsotopeFilter"
157 falsevalue="" label="filter compounds containing non-standard isotopes" help=""/>
158 <param argument="--FilterMinimumElements" type="text"
159 optional="true" label="Minimum Elements Filter"
160 help="Filter by minimum of contained elements. Ex: N2O3 include compounds with at least
161 2 nitrogens and 3 oxygens">
162 <expand macro="text-alphanumeric-regex-validator"/>
163 </param>
164 <param argument="--FilterMaximumElements" type="text"
165 optional="true" label="Maximum Elements Filter"
166 help="Filter by maximum of contained elements. Ex: N5O7 filter out compounds with at
167 maximum 5 nitrogens and 7 oxygens">
168 <expand macro="text-alphanumeric-regex-validator"/>
169 </param>
170 <param argument="--FilterSmartsInclusionList" type="text"
171 optional="true" label="Include substructures"
172 help="Filter by presence of defined sub-structures. Ex: c1ccccc1 include compounds
173 containing benzene"/>
174 <param argument="--FilterSmartsExclusionList" type="text"
175 optional="true" label="Exclude substructures"
176 help="Filter by absence of defined sub-structures. Ex: [OX2H] filter out compounds
177 containing hydroxyl groups"/>
178 <param argument="--FilterIncludedElements" type="text"
179 optional="true" label="Include elements"
180 help="Filter by presence of defined elements (other elements are allowed).
181 Ex: 'N,O' include compounds containing nitrogen and oxygen" >
182 <expand macro="text-alphanumeric-comma-regex-validator"/>
183 </param>
184 <param argument="--FilterIncludedExclusiveElements" type="text"
185 optional="true" label="Include elements (exclusive)"
186 help="Filter by presence of defined elements (no other elements are allowed).
187 Ex: 'N,O' include compounds only composed of nitrogen and oxygen" >
188 <expand macro="text-alphanumeric-comma-regex-validator"/>
189 </param>
190 <param argument="--FilterExcludedElements" type="text"
191 optional="true" label="Exclude elements"
192 help="Filter by absence of defined sub-structures. Ex: 'Cl,Br' filter out
193 compounds including bromine or chlorine">
194 <expand macro="text-alphanumeric-comma-regex-validator"/>
195 </param>
196 </section>
197 <section name="PostProcessFilter" title="PostProcessing filters" expanded="False">
198 <param argument="--score_thrshld" type="float" label="Threshold for score after MetFrag search"
199 max="1" min="0" value="0"/>
200 <param argument="--pctexplpeak_thrshld" type="float" label="Minimum percentage of explain peaks"
201 max="100" min="0" value="0"/>
202 </section>
203 </inputs>
204 <outputs>
205 <data name="results" format="tabular"/>
206 </outputs>
207 <tests>
208 <test>
209 <!-- Test "massbank" style data format -->
210 <param name="input" value="massbank_format.txt"/>
211 <param name="schema" value="massbank"/>
212 <param name="skip_invalid_adducts" value="false"/>
213 <param name="MetFragDatabaseType" value="PubChem"/>
214 <param name="MetFragDatabaseType" value="LocalCSV"/>
215 <param name="LocalDatabasePath" value="demo_db.csv"/>
216 <output name="results" file="metfrag_massbank.tabular"/>
217 </test>
218 <test>
219 <!-- Test "generic" style data format -->
220 <param name="input" value="generic_format.msp"/>
221 <param name="schema" value="msp"/>
222 <param name="MetFragDatabaseType" value="PubChem"/>
223 <param name="skip_invalid_adducts" value="false"/>
224 <param name="MetFragDatabaseType" value="LocalCSV"/>
225 <param name="LocalDatabasePath" value="demo_db.csv"/>
226 <output name="results" file="metfrag_msp.tabular"/>
227 </test>
228 <test>
229 <!-- Test PubChem API with "winter" dataset -->
230 <param name="input" value="winter_pos.msp"/>
231 <section name="PostProcessFilter">
232 <param name="score_thrshld" value="0.9"/>
233 </section>
234 <param name="MetFragDatabaseType" value="PubChem"/>
235 <output name="results" file="winter_pos.tabular"/>
236 </test>
237 <test>
238 <!-- Test actual MassBank data for Glucose -->
239 <param name="input" value="RP022611.txt"/>
240 <param name="MetFragDatabaseType" value="LocalCSV"/>
241 <param name="LocalDatabasePath" value="demo_db.csv"/>
242 <output name="results" file="RP022611.tabular"/>
243 </test>
244 <test>
245 <!-- Test actual MassBank data for Glucose (all metadata columns in output-->
246 <param name="input" value="RP022611.txt"/>
247 <param name="schema" value="massbank"/>
248 <param name="MetFragDatabaseType" value="LocalCSV"/>
249 <param name="LocalDatabasePath" value="demo_db.csv"/>
250 <param name="meta_select_col" value="all"/>
251 <output name="results" file="RP022611_all_col.tabular"/>
252 </test>
253 <test>
254 <!-- Test actual MassBank data for Glucose (include suspect list - default)-->
255 <param name="input" value="RP022611.txt"/>
256 <param name="schema" value="massbank"/>
257 <conditional name="suspectlist">
258 <param name="suspectselector" value="includesuspects"/>
259 <conditional name="includesuspects_default_cond">
260 <param name="includesuspects_default_bool" value="true"/>
261 </conditional>
262 </conditional>
263 <output name="results" file="RP022611_suspect_default.txt"/>
264 </test>
265 <test>
266 <!-- Test invalid adduct -->
267 <param name="input" value="invalid_adduct.msp"/>
268 <param name="skip_invalid_adducts" value="true"/>
269 <output name="results" file="invalid_adduct_result.txt" ftype="tabular"/>
270 </test>
271 </tests>
272 <help>
273 -------
274 MetFrag
275 -------
276
277 Description
278 -----------
279
280 MetFrag is a freely available software for the annotation of high precision tandem mass spectra of metabolites which is
281 a first and critical step for the identification of a molecule's structure. Candidate molecules of different databases
282 are fragmented "in silico" and matched against mass to charge values. A score calculated using the fragment peak
283 matches gives hints to the quality of the candidate spectrum assignment.
284
285 Website: http://ipb-halle.github.io/MetFrag/
286
287 Parameters
288 ----------
289
290 **\1. MSP file**
291
292 MSP file created using *Create MSP* tool
293
294 **\2a. MetFragDatabaseType (public databases)**
295
296 * PubChem
297
298 * KEGG
299
300
301 **\2b. MetFragDatabaseType (local CSV file database)**
302
303
304 Custom database file in CSV format with the following structure:
305
306 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
307 | Identifier | MonoisotopicMass | SMILES | InChI | Name |...|
308 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
309 | HMDB0000123 | 75.03202841 | NCC(O)=O | InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) | Glycine |...|
310 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
311 | HMDB0002151 | 78.0139355 | CS(C)=O | InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 | Dimethyl sulfoxide |...|
312 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
313 | ... | ... | ... | ... | ... |...|
314 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
315
316
317 Table continued:
318
319 +---+------------------+-----------------------------+------------------+------------+-------------+
320 |...| MolecularFormula | InChIKey | InChIKey1 | InChIKey2 | InChIKey3 |
321 +---+------------------+-----------------------------+------------------+------------+-------------+
322 |...| C2H5NO2 | DHMQDGOQFOQNFH-UHFFFAOYSA-N | DHMQDGOQFOQNFH | UHFFFAOYSA | N |
323 +---+------------------+-----------------------------+------------------+------------+-------------+
324 |...| C2H6OS | IAZDPXIOMUYVGZ-UHFFFAOYSA-N | IAZDPXIOMUYVGZ | UHFFFAOYSA | N |
325 +---+------------------+-----------------------------+------------------+------------+-------------+
326 |...| ... | ... | ... | ... | ... |
327 +---+------------------+-----------------------------+------------------+------------+-------------+
328
329
330
331 **\2b. MetFragDatabaseType MetChem**
332
333 MetChem is a modified PubChem database and can be used in replace of PubChem
334 for performing API calls to the public PubChem instance.
335
336 **\3. Database Search Relative Mass Deviation - ppm**
337
338 A value in ppm that defines the deviation of theoretical masses in the database vs. the measured masses.
339
340 **\4. Fragment Peak Match Relative Mass Deviation - ppm**
341
342 Relative mass deviation in ppm of theoretical fragment peaks vs. measured fragment peaks.
343
344 **\5. Fragment Peak Match Absolute Mass Deviation (Da)**
345
346 Absolute mass deviation in Dalton of theoretical fragment peaks vs. measured fragment peaks.
347
348 **\6. Polarity**
349
350 The polarity used for the mode of acquisition.
351
352 **\7. Schema**
353
354 The Schema used by the MSP file (e.g. generic MSP format or MassBank format)
355
356 **\8. Suspect list**
357
358 Choose whether to include a file containing a list of suspects.
359
360 **\9. MetFrag Score Types**
361
362 The type of scores MetFrac is using for the calculations. Please do not change the values unless you know what you are doing!
363
364 **\10. MetFrag Score Weights**
365
366 The weights of the different score types, separated with a comma and without whitespaces. 1.0 means 100%.
367
368 **\11. MetFrag Database Type**
369
370 Database to choose from.
371
372 **\12. minMSMSpeaks**
373
374 Minimum MS/MS peaks within a MS/MS spectra to be used for the MetFrag calculation
375
376 **\13. PreProcessFilter**
377
378 Various filters can be performed on the potential compounds prior to predicting the in silico spectra
379
380 **\14. PostProcessFilter**
381
382 To make the output more manageble results below certain criteria can be removed from the various filters can be
383 performed on the potential compounds prior to predicting the in silico spectra
384
385 Output
386 -------
387
388 These columns are derived from any metadata in the MSP input file (additional columns can included if they are recorded in the MSP file)
389
390 +-------------+--------------------------------------------+---+
391 | adduct | name |...|
392 +-------------+--------------------------------------------+---+
393 | [M-H]- | D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; |...|
394 +-------------+--------------------------------------------+---+
395 | [M-H]- | D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; |...|
396 +-------------+--------------------------------------------+---+
397 | ... | ... |...|
398 +-------------+--------------------------------------------+---+
399
400 Table continued (these columns are derived from the MetFrag result):
401
402 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
403 |...| sample_name | ExplPeaks | FormulasOfExplPeaks | ... |
404 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
405 |...| 1_metfrag_result | 59.0138_715.8;71.014_679.7;89.0251_999.0;101.0234_103.0 | 59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H- | ... |
406 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
407 |...| 1_metfrag_result | 59.0138_715.8;71.014_679.7;89.0251_999.0;101.0234_103.0 | 59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H- | ... |
408 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
409 |...| ... | ... | ... | ... |
410 +---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+
411
412
413 Table continued (columns are derived from the MetFrag result):
414
415 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
416 |...| FragmenterScore | FragmenterScore_Values | FormulasOfExplPeaks | Identifier | InChI |...|
417 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
418 |...| 105.844569063138 | 696.0;1156.0;696.0;1156.0 | 6-(hydroxymethyl)oxane-2,3,4,5-tetrol | 206 | InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H |...|
419 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
420 |...| 105.844569063138 | 696.0;1156.0;696.0;1156.0 | (3R,4S,5S,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol | 5793 | InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6?/m1/s1 |...|
421 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
422 |...| ... | ... | ... | ... | ... |...|
423 +---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+
424
425 Table continued (columns are derived from the MetFrag result):
426
427
428 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
429 |...| NoExplPeaks | NumberPeaksUsed | OfflineMetFusionScore | SMILES | Score | SuspectListScore | XlogP3 |
430 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
431 |...| 4 | 5 | 2.84566828424078 | C(C1C(C(C(C(O1)O)O)O)O)O | 1.82678219603441 | 1 | -2.6 |
432 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
433 |...| 4 | 5 | 2.84566828424078 | C([C@@H]1[C@H]([C@@H]([C@H](C(O1)O)O)O)O)O | 1.82678219603441 | 1 | -2.6 |
434 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
435 |...| ... | ... | ... | ... | ... | ... | ... |
436 +---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+
437
438
439 Additional notes
440 --------------------
441
442 The following adducts (and format) are currently supported in the MSP file. The neutral mass is automatically
443 calculated for the precursor m/z by subtracting the adduct mass
444
445 - '[M+H]+': 1.007276,
446 - '[M+NH4]+': 18.034374,
447 - '[M+Na]+': 22.989218,
448 - '[M+K]+': 38.963158,
449 - '[M+CH3OH+H]+': 33.033489,
450 - '[M+ACN+H]+': 42.033823,
451 - '[M+ACN+Na]+': 64.015765,
452 - '[M+2ACN+H]+': 83.06037,
453 - '[M-H]-': -1.007276,
454 - '[M+Cl]-': 34.969402,
455 - '[M+HCOO]-': 44.99819,
456 - '[M-H+HCOOH]-': 44.99819,
457 - '[M+CH3COO]-': 59.01385,
458 - '[M-H+CH3COOH]-': 59.01385
459
460 Developers and contributors
461 ---------------------------
462 - **Jordi Capellades (j.capellades.to@gmail.com) - Universitat Rovira i Virgili (SP)**
463 - **Julien Saint-Vanne (julien.saint-vanne@sb-roscoff.fr) - ABiMS (France)**
464 - **Tom Lawson (t.n.lawson@bham.ac.uk) - University of Birmingham (UK)**
465 - **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)**
466 - **Kristian Peters (kpeters@ipb-halle.de) - IPB Halle (Germany)**
467 - **Payam Emami (payam.emami@medsci.uu.se) - Uppsala Universitet (Sweden)**
468 - **Christoph Ruttkies (christoph.ruttkies@ipb-halle.de) - IPB Halle (Germany)**
469 </help>
470 <citations>
471 <citation type="doi">10.1186/s13321-016-0115-9</citation>
472 </citations>
473 </tool>