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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 038d752ab3a1eb53f9599f219da97faaa67bf08d
author recetox
date Fri, 23 Jun 2023 10:06:47 +0000
parents c0fe7ad30ade
children
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77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
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1 <macros>
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c0fe7ad30ade planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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2 <token name="@TOOL_VERSION@">3.0_20230403</token>
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3 <xml name="creator">
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
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4 <creator>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
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5 <person
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
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6 givenName="Martin"
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7 familyName="Čech"
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8 url="https://github.com/martenson"
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9 identifier="0000-0002-9318-1781" />
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10 <person
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
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11 givenName="Karolína"
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12 familyName="Trachtová"
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13 url="https://github.com/trachtok" />
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14 <organization
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
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15 url="https://www.recetox.muni.cz/"
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
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16 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
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17 name="RECETOX MUNI" />
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18 </creator>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
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19 </xml>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
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20 <token name="@HELP@">
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
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21 <![CDATA[
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
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22 BioTransformer is a software tool that predicts small molecule metabolism in mammals, their gut micr obiota,
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
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23 as well as the soil/aquatic microbiota. BioTransformer also assists scientists in metabolite identification,
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24 based on the metabolism prediction.
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77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
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26 BioTransformer is offered to the public as a freely acessible software package under the GNU License GPL v3.
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
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77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
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28 Users are free to copy and redistribute the material in any medium or format. Moreover, they could modify, and
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
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29 build upon the material under the condition that they must give appropriate credit, provide links to the license,
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
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30 and indicate if changes were made. Furthermore, the above copyright notice and this permission notice must be
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
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31 included. Use and re-distribution of the these resources, in whole or in part, for commercial purposes requires
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
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32 explicit permission of the authors. We ask that all users of the BioTransformer software tool, the BioTransformer
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
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33 web server, or BioTransformerDB to cite the BioTransformer reference in any resulting publications, and to
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34 acknowledge the authors.
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36 Parameters explanation:
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38 **Input.** Currently, only a CSV file with one SMILES per line is accepted.
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40 **The type of prediction:** EC-based (ecbased), CYP450 (cyp450), Phase II (phaseII), Human gut
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41 microbial (hgut), human super transformer* (superbio, or allHuman), Environmental microbial (envimicro).
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43 **The number of steps for the prediction:** this option will be used for the EC-based, CYP450, Phase II, and Environmental
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44 microbial biotransformers. The default value is 1.
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46 **Mass tolerance for metabolite identification** (default is 0.01).
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48 **Output of BioTransformer** with CSV as an input are 3 TSV files. One without any filtering, second with filtered
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49 duplicates based on 6 columns (InChI, InChIKey, Synonyms, Molecular formula, Major Isotope Mass, AlogP) and third with
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50 filtered duplicates based on 3 columns (Molecular formula, Major Isotope Mass, AlogP).
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52 (* ) While the 'superbio' option runs a set number of transformation steps in a pre-defined order (e.g. deconjugation
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53 first, then Oxidation/reduction, etc.), the 'allHuman' option predicts all possible metabolites from any applicable
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54 reaction(Oxidation, reduction, (de-)conjugation) at each step.
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55 ]]>
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56 </token>
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57 </macros>