Mercurial > repos > recetox > biotransformer
changeset 0:b5b62d04625a draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b9cf078bf1136d497d624b62eae7f56f58d1f03"
author | recetox |
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date | Thu, 27 Aug 2020 12:55:38 +0000 |
parents | |
children | 362a66a3889c |
files | biotransformer.xml |
diffstat | 1 files changed, 129 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biotransformer.xml Thu Aug 27 12:55:38 2020 +0000 @@ -0,0 +1,129 @@ +<tool id="biotransformer" name="BioTransformer" version="1.1.0"> + <requirements> + <container type="docker">registry.gitlab.ics.muni.cz:443/recetox/mass-spectrometry/biotransformer:1.1.0</container> + </requirements> + <command><![CDATA[ cd /biotransformer && python3 wrapper_biotransformer.py + -k $k + -b $b + -s $steps + -t $tolerance + -a + #if $input.type_selector == "sdf" + -isdf $input.input_format + #else if $input.type_selector == "csv" + -icsv $input.input_format + #else + -ismi "$input.input_format" + #end if + + #if $output.type_selector == "csv" + #if $input.type_selector == "csv" + -ocsv $output_file + -ocsvDup $output_file2 + -ocsvDup2 $output_file3 + #else if $input.type_selector == "smile" + -ocsv $output_file + #end if + #else + -osdf $output_file + #end if + + ]]> + </command> + <inputs> + <param name="k" type="select" value="pred" label="The task to be permed [pred=prediction, cid=compound identification]."> + <option value="pred" selected="true" >pred</option> + <option value="cid">cid</option> + </param> + <param name="b" type="select" value="ecbased" label="The type of description."> + <option value="ecbased" selected="true" >EC-based</option> + <option value="cyp450">CYP450</option> + <option value="phaseII">Phase II</option> + <option value="hgut">Human gut microbial</option> + <option value="superbio">Human super transformer 1 (superbio)</option> + <option value="allHuman">Human super transformer 2 (allHuman)</option> + <option value="envimicro">Environmental microbial</option> + </param> + <param name="steps" type="integer" value="1" label=" The number of steps for the prediction."/> + <param name="tolerance" type="float" value="0.01" label="Mass tolerance for metabolite identification."/> + + <conditional name="input"> + <param name="type_selector" type="select" label="Input format [SMILES, SDF, CSV]."> + <option value="smile" selected="true">SMILES</option> + <option value="sdf">SDF</option> + <option value="csv">CSV</option> + </param> + <when value="sdf"> + <param name="input_format" argument="-isdf" type="data" format="sdf" label="SDF"/> + </when> + <when value="smile"> + <param name="input_format" argument="-ismi" type="text" label="SMILES (example string format: CC(C)C1=CC=C(C)C=C1O )."/> + </when> + <when value="csv"> + <param name="input_format" argument="-csv" type="data" format="csv" label="CSV with one molecule (SMILES format) per line."/> + </when> + </conditional> + + <conditional name="output"> + <param name="type_selector" type="select" label="Output format [CSV, SDF]."> + <option value="osdf" selected="true">SDF</option> + <option value="csv">CSV</option> + </param> + </conditional> + </inputs> + + <outputs> + <data format="csv" name="output_file" label="BioTransformer - output."> + <change_format> + <when input="output.type_selector" value="osdf" format="sdf" /> + </change_format> + </data> + <data format="csv" name="output_file2" label="BioTransformer - filtered CSV output."> + <filter>input['type_selector'] == 'csv'</filter> + </data> + <data format="csv" name="output_file3" label="BioTransformer - super-filtered CSV output."> + <filter>input['type_selector'] == 'csv'</filter> + </data> + </outputs> + <help> +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 v2.1. + +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. User can chose from SDF, SMILES and CSV. CSV expects file with one moleluce in SMILES format per line. If CSV +is selected, OUTPUT MUST BE CSV AS WELL! + +The type of description: Type of biotransformer - 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 CSV 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). + +Output of BioTransformer with SMILES as an input is 1 CSV file. + +(* ) 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. + </help> + <citations> + <citation type="doi">https://doi.org/10.1186/s13321-018-0324-5</citation> + </citations> +</tool>