Mercurial > repos > tomnl > metfrag
diff metfrag.xml @ 9:5763234618d4 draft default tip
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6bc059c100f1f968d99c1d5ad5e7259e83d386b6"
| author | tomnl |
|---|---|
| date | Fri, 04 Oct 2019 07:15:52 -0400 |
| parents | 9a3019c609d9 |
| children |
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--- a/metfrag.xml Fri Sep 13 08:27:59 2019 -0400 +++ b/metfrag.xml Fri Oct 04 07:15:52 2019 -0400 @@ -1,5 +1,10 @@ -<tool id="metfrag" name="MetFrag" version="2.4.5+galaxy0.1.13"> - <description> </description> +<tool id="metfrag" name="MetFrag" version="2.4.5+galaxy1"> + <description> + in silico fragmentor for compound annotation of mass spectrometry fragmentation spectra + </description> + <macros> + <import>macros.xml</import> + </macros> <requirements> <requirement type="package" version="2.4.5">metfrag</requirement> </requirements> @@ -11,9 +16,8 @@ </stdio> <command detect_errors="exit_code"> <![CDATA[ - - python $__tool_directory__/metfrag.py - --input_pth "$input" + python '$__tool_directory__/metfrag.py' + --input_pth '$input' --result_pth '$results' --temp_dir './temp/' @@ -21,9 +25,9 @@ --MetFragDatabaseType '$db_select.MetFragDatabaseType' - #if $db_select.MetFragDatabaseType == "LocalCSV": + #if $db_select.MetFragDatabaseType == 'LocalCSV': --LocalDatabasePath '$db_select.LocalDatabasePath' - #elif $db_select.MetFragDatabaseType == "MetChem": + #elif $db_select.MetFragDatabaseType == 'MetChem': --LocalMetChemDatabaseServerIp '$db_select.LocalMetChemDatabaseServerIp' #end if @@ -37,7 +41,7 @@ #if $suspectlist.suspectselector == 'includesuspects': #if $suspectlist.includesuspects_default_cond: - --ScoreSuspectLists '$__tool_directory__/test-data/UNPD_DB.inchikeys.txt' + --ScoreSuspectLists '$__tool_directory__/UNPD_DB.inchikeys.txt' #else --ScoreSuspectLists '$suspectlist.includesuspects_custom_cond.ScoreSuspectLists' #end if @@ -50,7 +54,6 @@ $PreProcessFilter.UnconnectedCompoundFilter $PreProcessFilter.IsotopeFilter - --FilterMinimumElements '$PreProcessFilter.FilterMinimumElements' --FilterMaximumElements '$PreProcessFilter.FilterMaximumElements' --FilterSmartsInclusionList '$PreProcessFilter.FilterSmartsInclusionList' @@ -63,133 +66,151 @@ --score_thrshld $PostProcessFilter.score_thrshld --pctexplpeak_thrshld $PostProcessFilter.pctexplpeak_thrshld - - - - ]]></command> <inputs> - - <param name="input" type="data" format="msp,txt" label="MSP file (Output from Create MSP tool)"/> + <param name="input" type="data" format="msp" label="MSP file (Output from Create MSP tool)"/> <conditional name="db_select"> - <param name="MetFragDatabaseType" type="select" label="Choose Compound Database" - argument="--MetFragDatabaseType"> + <param argument="--MetFragDatabaseType" type="select" label="Choose Compound Database"> <option value="PubChem" selected="true">PubChem</option> <option value="KEGG">KEGG</option> <option value="LocalCSV">Local database (csv)</option> <option value="MetChem">MetChem</option> </param> <when value="MetChem"> - <param name="LocalMetChemDatabaseServerIp" type="text" label="MetChem URL" - argument="--LocalMetChemDatabaseServerIp" /> + <param argument="--LocalMetChemDatabaseServerIp" type="text" label="MetChem URL"/> </when> <when value="LocalCSV"> - <param name="LocalDatabasePath" type="data" format="csv" label="Local database of compounds (CSV format)" argument="--LocalDatabasePath"/> + <param argument="--LocalDatabasePath" type="data" format="csv" + label="Local database of compounds (CSV format)" /> </when> - <when value="KEGG"> - </when> - <when value="PubChem"> - </when> + <when value="KEGG"/> + <when value="PubChem"/> </conditional> - <param name="DatabaseSearchRelativeMassDeviation" type="float" value="10" - label="Relative Mass Deviation for database search (ppm)" argument="--DatabaseSearchRelativeMassDeviation" - help="A value in ppm that defines the deviation of theoretical masses in the database vs. the measured masses"/> - <param name="FragmentPeakMatchRelativeMassDeviation" type="float" value="5" - label="Fragment Peak Match Relative Mass Deviation (ppm)" argument="--FragmentPeakMatchRelativeMassDeviation" + <param argument="--DatabaseSearchRelativeMassDeviation" type="float" min="0" value="10" + label="Relative Mass Deviation for database search (ppm)" + help="A value in ppm that defines the deviation of theoretical masses in the database + vs. the measured masses"/> + <param argument="--FragmentPeakMatchRelativeMassDeviation" type="float" min="0" value="5" + label="Fragment Peak Match Relative Mass Deviation (ppm)" help="Relative mass deviation in ppm of theoretical fragment peaks vs. measured fragment peaks" /> - <param name="FragmentPeakMatchAbsoluteMassDeviation" type="float" value="0.001" - label="Fragment Peak Match Absolute Mass Deviation (Da)" argument="FragmentPeakMatchAbsoluteMassDeviation" + <param argument="--FragmentPeakMatchAbsoluteMassDeviation" type="float" min="0" value="0.001" + label="Fragment Peak Match Absolute Mass Deviation (Da)" help="Absolute mass deviation in Dalton of theoretical fragment peaks vs. measured fragment peaks" /> - <param name="polarity" type="select" label="Polarity" help="The polarity used for the mode of acquisition"> + <param argument="--polarity" type="select" label="Polarity" + help="The polarity used for the mode of acquisition"> <option value="pos" selected="true">Positive</option> <option value="neg">Negative</option> </param> - <param name="schema" type="select" label="Schema" + <param argument="--schema" type="select" label="Schema" help="The schema used for the MSP file (auto will try automatically determine the schema)"> <option value="auto" selected="True">Auto</option> - <option value="msp" >Generic MSP</option> + <option value="msp">Generic MSP</option> <option value="massbank">MassBank</option> </param> - <param name="meta_select_col" type="select" label="Choose how additional metadata columns are extracted" + <param argument="--meta_select_col" type="select" + label="Choose how additional metadata columns are extracted" help="The MetFrag output can have additional meta data columns added, these can be either extracted from all MSP parameters or from the 'Name' and 'RECORD_TITLE' MSP parameter. Additionally, columns can be added from the 'Name' or 'RECORD_TITLE' parameter by splitting on | and : e.g. 'MZ:100.2 | RT:20 | xcms_grp_id:1' would create MZ,RT and xcms_grp_id columns"> <option value="name" selected="true">Extra metadata columns from the Name or RECORD_TITLE</option> - <option value="name_split" >Extra metadata columns from the Name or RECORD_TITLE (each column is split on "|" and ":" ) </option> + <option value="name_split">Extra metadata columns from the Name or RECORD_TITLE (each column is split on "|" and ":" ) </option> <option value="all">Extra metadata columns from all MSP parameters</option> </param> - <conditional name="suspectlist"> - <param name="suspectselector" type="select" optional="False" label="Suspect list" help="Choose whether to include a suspect list"> + <param name="suspectselector" type="select" label="Suspect list" + help="Choose whether to include a suspect list"> <option value="includesuspects" >Include suspect list</option> <option value="excludesuspects" selected="True">Do not include suspect list</option> </param> <when value="includesuspects"> <conditional name="includesuspects_default_cond"> - <param name="includesuspects_default_bool" type="boolean" label="Use default list of suspect compounds?" + <param name="includesuspects_default_bool" type="boolean" + label="Use default list of suspect compounds?" help="Either provide a file containing a list of suspect compounds or a default file - of of an aggregated list of in silico predicted MS/MS spectra of natural products + of an aggregated list of in silico predicted MS/MS spectra of natural products from the Universal Natural Products Database (http://pkuxxj.pku.edu.cn/UNPD/index.php). The list is an aggregated version of the github repository https://github.com/oolonek/ISDB/tree/master/Data/dbs."/> - <when value="true"> - </when> + <when value="true"/> <when value="false"> - <param name="ScoreSuspectLists" type="data" format="txt" optional="False" label="Suspect list file" - help="File containing a list of suspects inchikeys" /> + <param argument="--ScoreSuspectLists" type="data" format="txt" optional="True" + label="Suspect list file" help="File containing a list of suspects inchikeys" /> </when> </conditional> - - <param name="MetFragScoreTypes" type="text" value="FragmenterScore,OfflineMetFusionScore,SuspectListScore" optional="False" label="MetFrag Score Types" help="The type of scores MetFrag is calculating. Please do not change the value unless you know what you are doing." /> - <param name="MetFragScoreWeights" type="text" value="0.4,0.6,1.0" optional="False" label="MetFrag Score Weights" help="The weights of the different score types, separated with a comma and without whitespaces. 1.0 means 100 percent." /> + <expand macro="metfrag_scoring"/> </when> <when value="excludesuspects"> - <param name="MetFragScoreTypes" type="text" value="FragmenterScore,OfflineMetFusionScore" optional="False" label="MetFrag Score Types" help="The type of scores MetFrag is calculating. Please do not change the value unless you know what you are doing." /> - <param name="MetFragScoreWeights" type="text" value="1.0,1.0" optional="False" label="MetFrag Score Weights" help="The weights of the different score types, separated with a comma and without whitespaces. 1.0 means 100 percent." /> + <expand macro="metfrag_scoring" suspectlistscore="False" weights="1.0,1.0"/> </when> </conditional> - - <param name="minMSMSpeaks" type="integer" label="Minimum number of MS/MS peaks" value="0"/> - <param name="skip_invalid_adducts" type="boolean" label="Skip invalid or undefined adduct types?" + <param argument="--minMSMSpeaks" type="integer" label="Minimum number of MS/MS peaks" value="0"/> + <param argument="--skip_invalid_adducts" type="boolean" label="Skip invalid or undefined adduct types?" truevalue="--skip_invalid_adducts" falsevalue="" checked="true" help="If no adduct type is provided within the MSP file or if the adduct type is not usable with MetFrag, set to 'yes' if these spectra should be skipped or 'no' if the default of [M+H]+ for pos data or [M-H]- for neg data should be used"/> <section name="PreProcessFilter" title="PreProcessing filters" expanded="False"> - <param name="UnconnectedCompoundFilter" type="boolean" checked="false" truevalue="--UnconnectedCompoundFilter" - falsevalue="" label="filter non-connected compounds (e.g. salts)" help=""/> - <param name="IsotopeFilter" type="boolean" checked="false" truevalue="--IsotopeFilter" falsevalue="" - label="filter compounds containing non-standard isotopes" help=""/> - <param name="FilterMinimumElements" type="text" label="Minimum Elements Filter" - help="Filter by minimum of contained elements. Ex: N2O3 include compounds with at least 2 nitrogens and 3 oxygens"/> - <param name="FilterMaximumElements" type="text" label="Maximum Elements Filter" - help="Filter by maximum of contained elements. Ex: N5O7 filter out compounds with at maximum 5 nitrogens and 7 oxygens"/> - <param name="FilterSmartsInclusionList" type="text" label="Include substructures" - help="Filter by presence of defined sub-structures. Ex: c1ccccc1 include compounds containing benzene"/> - <param name="FilterSmartsExclusionList" type="text" label="Exclude substructures" - help="Filter by absence of defined sub-structures. Ex: [OX2H] filter out compounds containing hydroxyl groups"/> - <param name="FilterIncludedElements" type="text" label="Include elements" - help="Filter by presence of defined elements (other elements are allowed). Ex: 'N,O' include compounds containing nitrogen and oxygen" /> - <param name="FilterIncludedExclusiveElements" type="text" label="Include elements (exclusive)" - help="Filter by presence of defined elements (no other elements are allowed). Ex: 'N,O' include compounds only composed of nitrogen and oxygen" /> - <param name="FilterExcludedElements" type="text" label="Exclude elements" - help="Filter by absence of defined sub-structures. Ex: 'Cl,Br' filter out compounds including bromine or chlorine"/> + <param argument="--UnconnectedCompoundFilter" type="boolean" checked="false" + truevalue="--UnconnectedCompoundFilter" falsevalue="" + label="filter non-connected compounds (e.g. salts)" help=""/> + <param argument="--IsotopeFilter" type="boolean" checked="false" truevalue="--IsotopeFilter" + falsevalue="" label="filter compounds containing non-standard isotopes" help=""/> + <param argument="--FilterMinimumElements" type="text" + optional="true" label="Minimum Elements Filter" + help="Filter by minimum of contained elements. Ex: N2O3 include compounds with at least + 2 nitrogens and 3 oxygens"> + <expand macro="text-alphanumeric-regex-validator"/> + </param> + <param argument="--FilterMaximumElements" type="text" + optional="true" label="Maximum Elements Filter" + help="Filter by maximum of contained elements. Ex: N5O7 filter out compounds with at + maximum 5 nitrogens and 7 oxygens"> + <expand macro="text-alphanumeric-regex-validator"/> + </param> + <param argument="--FilterSmartsInclusionList" type="text" + optional="true" label="Include substructures" + help="Filter by presence of defined sub-structures. Ex: c1ccccc1 include compounds + containing benzene"/> + <param argument="--FilterSmartsExclusionList" type="text" + optional="true" label="Exclude substructures" + help="Filter by absence of defined sub-structures. Ex: [OX2H] filter out compounds + containing hydroxyl groups"/> + <param argument="--FilterIncludedElements" type="text" + optional="true" label="Include elements" + help="Filter by presence of defined elements (other elements are allowed). + Ex: 'N,O' include compounds containing nitrogen and oxygen" > + <expand macro="text-alphanumeric-comma-regex-validator"/> + </param> + <param argument="--FilterIncludedExclusiveElements" type="text" + optional="true" label="Include elements (exclusive)" + help="Filter by presence of defined elements (no other elements are allowed). + Ex: 'N,O' include compounds only composed of nitrogen and oxygen" > + <expand macro="text-alphanumeric-comma-regex-validator"/> + </param> + <param argument="--FilterExcludedElements" type="text" + optional="true" label="Exclude elements" + help="Filter by absence of defined sub-structures. Ex: 'Cl,Br' filter out + compounds including bromine or chlorine"> + <expand macro="text-alphanumeric-comma-regex-validator"/> + </param> </section> - <section name="PostProcessFilter" title="PostProcessing filters" expanded="False"> - <param name="score_thrshld" type="float" label="Threshold for score after MetFrag search" max="1" min="0" value="0"/> - <param name="pctexplpeak_thrshld" type="float" label="Minimum percentage of explain peaks" max="100" min="0" value="0"/> + <param argument="--score_thrshld" type="float" label="Threshold for score after MetFrag search" + max="1" min="0" value="0"/> + <param argument="--pctexplpeak_thrshld" type="float" label="Minimum percentage of explain peaks" + max="100" min="0" value="0"/> </section> - </inputs> <outputs> - <data name="results" format="tabular" label="${tool.name} results of ${input.name}" /> + <data name="results" format="tabular"/> </outputs> <tests> <test> <!-- Test "massbank" style data format --> <param name="input" value="massbank_format.txt"/> <param name="schema" value="massbank"/> + <param name="skip_invalid_adducts" value="false"/> + <param name="MetFragDatabaseType" value="PubChem"/> <param name="MetFragDatabaseType" value="LocalCSV"/> <param name="LocalDatabasePath" value="demo_db.csv"/> <output name="results" file="metfrag_massbank.tabular"/> @@ -198,6 +219,8 @@ <!-- Test "generic" style data format --> <param name="input" value="generic_format.msp"/> <param name="schema" value="msp"/> + <param name="MetFragDatabaseType" value="PubChem"/> + <param name="skip_invalid_adducts" value="false"/> <param name="MetFragDatabaseType" value="LocalCSV"/> <param name="LocalDatabasePath" value="demo_db.csv"/> <output name="results" file="metfrag_msp.tabular"/> @@ -205,7 +228,9 @@ <test> <!-- Test PubChem API with "winter" dataset --> <param name="input" value="winter_pos.msp"/> - <param name="PostProcessFilter|score_thrshld" value="0.9"/> + <section name="PostProcessFilter"> + <param name="score_thrshld" value="0.9"/> + </section> <param name="MetFragDatabaseType" value="PubChem"/> <output name="results" file="winter_pos.tabular"/> </test> @@ -229,28 +254,19 @@ <!-- Test actual MassBank data for Glucose (include suspect list - default)--> <param name="input" value="RP022611.txt"/> <param name="schema" value="massbank"/> - <param name="suspectlist|suspectselector" value="includesuspects"/> - <param name="suspectlist|includesuspects_default_cond|includesuspects_default_bool" value="true"/> - <param name="suspectlist|MetFragScoreTypes" value="FragmenterScore,OfflineMetFusionScore,SuspectListScore"/> - <param name="suspectlist|MetFragScoreWeights" value="0.4,0.6,1.0"/> + <conditional name="suspectlist"> + <param name="suspectselector" value="includesuspects"/> + <conditional name="includesuspects_default_cond"> + <param name="includesuspects_default_bool" value="true"/> + </conditional> + </conditional> <output name="results" file="RP022611_suspect_default.txt"/> </test> <test> - <!-- Test actual MassBank data for Glucose (include suspect list - custom)--> - <param name="input" value="RP022611.txt"/> - <param name="schema" value="massbank"/> - <param name="suspectlist|suspectselector" value="includesuspects"/> - <param name="suspectlist|includesuspects_default_cond|includesuspects_default_bool" value="false"/> - <param name="suspectlist|includesuspects_default_cond|ScoreSuspectLists" value="UNPD_DB.inchikeys.txt"/> - <param name="suspectlist|MetFragScoreTypes" value="FragmenterScore,OfflineMetFusionScore,SuspectListScore"/> - <param name="suspectlist|MetFragScoreWeights" value="0.4,0.6,1.0"/> - <output name="results" file="RP022611_suspect_default.txt"/> - </test> - <test> - <!-- Test actual MassBank data for Glucose (include suspect list - custom)--> + <!-- Test invalid adduct --> <param name="input" value="invalid_adduct.msp"/> <param name="skip_invalid_adducts" value="true"/> - <output name="results" file="invalid_adduct_result.txt"/> + <output name="results" file="invalid_adduct_result.txt" ftype="tabular"/> </test> </tests> <help> @@ -261,9 +277,12 @@ Description ----------- -MetFrag is a freely available software for the annotation of high precision tandem mass spectra of metabolites which is a first and critical step for the identification of a molecule's structure. Candidate molecules of different databases are fragmented "in silico" and matched against mass to charge values. A score calculated using the fragment peak matches gives hints to the quality of the candidate spectrum assignment. +MetFrag is a freely available software for the annotation of high precision tandem mass spectra of metabolites which is +a first and critical step for the identification of a molecule's structure. Candidate molecules of different databases +are fragmented "in silico" and matched against mass to charge values. A score calculated using the fragment peak +matches gives hints to the quality of the candidate spectrum assignment. -Website: http://c-ruttkies.github.io/MetFrag +Website: http://ipb-halle.github.io/MetFrag/ Parameters ---------- @@ -281,6 +300,7 @@ **\2b. MetFragDatabaseType (local CSV file database)** + Custom database file in CSV format with the following structure: +-------------+------------------+----------+---------------------------------------------+----------------------+---+ @@ -307,11 +327,11 @@ +---+------------------+-----------------------------+------------------+------------+-------------+ -**\2b. MetFragDatabaseType MetChem local database** + +**\2b. MetFragDatabaseType MetChem** MetChem is a modified PubChem database and can be used in replace of PubChem -for performing API calls to the public PubChem instance. Details regarding how to serve the database can be located -here: +for performing API calls to the public PubChem instance. **\3. Database Search Relative Mass Deviation - ppm** @@ -362,6 +382,60 @@ To make the output more manageble results below certain criteria can be removed from the various filters can be performed on the potential compounds prior to predicting the in silico spectra +Output +------- + +These columns are derived from any metadata in the MSP input file (additional columns can included if they are recorded in the MSP file) + ++-------------+--------------------------------------------+---+ +| adduct | name |...| ++-------------+--------------------------------------------+---+ +| [M-H]- | D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; |...| ++-------------+--------------------------------------------+---+ +| [M-H]- | D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; |...| ++-------------+--------------------------------------------+---+ +| ... | ... |...| ++-------------+--------------------------------------------+---+ + +Table continued (these columns are derived from the MetFrag result): + ++---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+ +|...| sample_name | ExplPeaks | FormulasOfExplPeaks | ... | ++---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+ +|...| 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- | ... | ++---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+ +|...| 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- | ... | ++---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+ +|...| ... | ... | ... | ... | ++---+------------------+----------------------------------------------------------+-------------------------------------------------------------------------------------+-----+ + + +Table continued (columns are derived from the MetFrag result): + ++---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+ +|...| FragmenterScore | FragmenterScore_Values | FormulasOfExplPeaks | Identifier | InChI |...| ++---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+ +|...| 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 |...| ++---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+ +|...| 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 |...| ++---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+ +|...| ... | ... | ... | ... | ... |...| ++---+------------------+----------------------------+------------------------------------------------------+------------+---------------------------------------------------------------------------------+---+ + +Table continued (columns are derived from the MetFrag result): + + ++---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+ +|...| NoExplPeaks | NumberPeaksUsed | OfflineMetFusionScore | SMILES | Score | SuspectListScore | XlogP3 | ++---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+ +|...| 4 | 5 | 2.84566828424078 | C(C1C(C(C(C(O1)O)O)O)O)O | 1.82678219603441 | 1 | -2.6 | ++---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+ +|...| 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 | ++---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+ +|...| ... | ... | ... | ... | ... | ... | ... | ++---+-------------+-----------------+-----------------------+----------------------------------------------+------------------+------------------+--------+ + + Additional notes -------------------- @@ -392,8 +466,6 @@ - **Kristian Peters (kpeters@ipb-halle.de) - IPB Halle (Germany)** - **Payam Emami (payam.emami@medsci.uu.se) - Uppsala Universitet (Sweden)** - **Christoph Ruttkies (christoph.ruttkies@ipb-halle.de) - IPB Halle (Germany)** - - </help> <citations> <citation type="doi">10.1186/s13321-016-0115-9</citation>