Mercurial > repos > recetox > biotransformer
diff macros.xml @ 0:0b86600b715e draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
author | recetox |
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date | Tue, 06 Jun 2023 11:23:51 +0000 |
parents | |
children | e5fcba090b10 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Jun 06 11:23:51 2023 +0000 @@ -0,0 +1,57 @@ +<macros> + <token name="@TOOL_VERSION@">3.0_20230403</token> + <xml name="creator"> + <creator> + <person + givenName="Martin" + familyName="Čech" + url="https://github.com/martenson" + identifier="0000-0002-9318-1781" /> + <person + givenName="Karolína" + familyName="Trachtová" + url="https://github.com/trachtok" /> + <organization + url="https://www.recetox.muni.cz/" + email="GalaxyToolsDevelopmentandDeployment@space.muni.cz" + name="RECETOX MUNI" /> + </creator> + </xml> + <token name="@HELP@"> + <![CDATA[ + BioTransformer is a software tool that predicts small molecule metabolism in mammals, their gut micr obiota, + as well as the soil/aquatic microbiota. BioTransformer also assists scientists in metabolite identification, + based on the metabolism prediction. + + BioTransformer is offered to the public as a freely acessible software package under the GNU License GPL v3. + + Users are free to copy and redistribute the material in any medium or format. Moreover, they could modify, and + build upon the material under the condition that they must give appropriate credit, provide links to the license, + and indicate if changes were made. Furthermore, the above copyright notice and this permission notice must be + included. Use and re-distribution of the these resources, in whole or in part, for commercial purposes requires + explicit permission of the authors. We ask that all users of the BioTransformer software tool, the BioTransformer + web server, or BioTransformerDB to cite the BioTransformer reference in any resulting publications, and to + acknowledge the authors. + + Parameters explanation: + + **Input.** Currently, only a CSV file with one SMILES per line is accepted. + + **The type of prediction:** EC-based (ecbased), CYP450 (cyp450), Phase II (phaseII), Human gut + microbial (hgut), human super transformer* (superbio, or allHuman), Environmental microbial (envimicro). + + **The number of steps for the prediction:** this option will be used for the EC-based, CYP450, Phase II, and Environmental + microbial biotransformers. The default value is 1. + + **Mass tolerance for metabolite identification** (default is 0.01). + + **Output of BioTransformer** with CSV as an input are 3 TSV files. One without any filtering, second with filtered + duplicates based on 6 columns (InChI, InChIKey, Synonyms, Molecular formula, Major Isotope Mass, AlogP) and third with + filtered duplicates based on 3 columns (Molecular formula, Major Isotope Mass, AlogP). + + (* ) While the 'superbio' option runs a set number of transformation steps in a pre-defined order (e.g. deconjugation + first, then Oxidation/reduction, etc.), the 'allHuman' option predicts all possible metabolites from any applicable + reaction(Oxidation, reduction, (de-)conjugation) at each step. + ]]> + </token> +</macros>