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annotate biotransformer.xml @ 3:6080aee7c4f6 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 5cdd2628a1a509b3e0ccc599eaab63d664bf031a"
author recetox
date Wed, 13 Jan 2021 11:17:53 +0000
parents 3998017c374b
children 77f693bb14ac
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1 <tool id="biotransformer" name="BioTransformer" version="1.1.5+galaxy1">
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2 <requirements>
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3 <requirement type="package" version="1.1.5">biotransformer</requirement>
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4 <requirement type="package" version="3.1.1">openbabel</requirement>
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5 <requirement type="package" version="1.1.1">pandas</requirement>
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6 <requirement type="package" version="3.7">python</requirement>
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7 </requirements>
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8 <command><![CDATA[ python3 '${__tool_directory__}/wrapper_biotransformer.py'
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9 -k $k
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10 -b $b
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11 -s $steps
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12 -t $tolerance
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13 -a
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14 -icsv $input_file
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15 -ocsv $output_file
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16 -ocsvDup $output_file2
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17 -ocsvDup2 $output_file3
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19 ]]>
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20 </command>
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21 <inputs>
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22 <param name="k" type="select" value="pred" label="The task to be permed [pred=prediction, cid=compound identification].">
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23 <option value="pred" selected="true" >pred</option>
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24 <option value="cid">cid</option>
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25 </param>
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26 <param name="b" type="select" value="ecbased" label="The type of description.">
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27 <option value="ecbased" selected="true" >EC-based</option>
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28 <option value="cyp450">CYP450</option>
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29 <option value="phaseII">Phase II</option>
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30 <option value="hgut">Human gut microbial</option>
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31 <option value="superbio">Human super transformer 1 (superbio)</option>
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32 <option value="allHuman">Human super transformer 2 (allHuman)</option>
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33 <option value="envimicro">Environmental microbial</option>
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34 </param>
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35 <param name="steps" type="integer" value="1" label=" The number of steps for the prediction."/>
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36 <param name="tolerance" type="float" value="0.01" label="Mass tolerance for metabolite identification."/>
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37 <param name="input_file" type="data" format="csv" label="Input CSV file."/>
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38 </inputs>
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40 <outputs>
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41 <data format="csv" name="output_file" label="BioTransformer - output."/>
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42 <data format="csv" name="output_file2" label="BioTransformer - filtered CSV output."/>
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43 <data format="csv" name="output_file3" label="BioTransformer - super-filtered CSV output."/>
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44 </outputs>
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46 <tests>
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47 <test>
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48 <param name="k" value="pred"/>
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49 <param name="b" value="allHuman"/>
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50 <param name="steps" value="1"/>
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51 <param name="tolerance" value="0.01"/>
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52 <param name="input_file" value="smiles.csv"/>
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53 <output name="output_file" value="output1.csv"/>
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54 <output name="output_file2" value="output2.csv"/>
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55 <output name="output_file3" value="output3.csv"/>
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56 </test>
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57 </tests>
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58
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59 <help>
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60 BioTransformer is a software tool that predicts small molecule metabolism in mammals, their gut micr obiota,
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61 as well as the soil/aquatic microbiota. BioTransformer also assists scientists in metabolite identification,
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62 based on the metabolism prediction.
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63
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64 BioTransformer is offered to the public as a freely acessible software package under the GNU License GPL v2.1.
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65
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66 Users are free to copy and redistribute the material in any medium or format. Moreover, they could modify, and
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67 build upon the material under the condition that they must give appropriate credit, provide links to the license,
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68 and indicate if changes were made. Furthermore, the above copyright notice and this permission notice must be
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69 included. Use and re-distribution of the these resources, in whole or in part, for commercial purposes requires
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70 explicit permission of the authors. We ask that all users of the BioTransformer software tool, the BioTransformer
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71 web server, or BioTransformerDB to cite the BioTransformer reference in any resulting publications, and to
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72 acknowledge the authors.
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73
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74 Parameters explanation:
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75
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76 **Input.** Currently, only a CSV file with one SMILES per line is accepted.
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78 **The type of prediction:** EC-based (ecbased), CYP450 (cyp450), Phase II (phaseII), Human gut
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79 microbial (hgut), human super transformer* (superbio, or allHuman), Environmental microbial (envimicro).
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81 **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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82 microbial biotransformers. The default value is 1.
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84 **Mass tolerance for metabolite identification** (default is 0.01).
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85
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86 **Output of BioTransformer** with CSV as an input are 3 CSV files. One without any filtering, second with filtered
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87 duplicates based on 6 columns (InChI, InChIKey, Synonyms, Molecular formula, Major Isotope Mass, AlogP) and third with
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88 filtered duplicates based on 3 columns (Molecular formula, Major Isotope Mass, AlogP).
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89
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90 (* ) While the 'superbio' option runs a set number of transformation steps in a pre-defined order (e.g. deconjugation
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91 first, then Oxidation/reduction, etc.), the 'allHuman' option predicts all possible metabolites from any applicable
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92 reaction(Oxidation, reduction, (de-)conjugation) at each step.
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93 </help>
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94 <citations>
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95 <citation type="doi">https://doi.org/10.1186/s13321-018-0324-5</citation>
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96 </citations>
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97 </tool>