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annotate biotransformer.xml @ 6:200c5c982dba draft default tip

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit a57d984a9850c1faa44b6948981eb1303881ba9c
author recetox
date Thu, 14 Aug 2025 12:34:56 +0000
parents 0f1b15d51801
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6
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1 <tool id="biotransformer" name="BioTransformer" version="@TOOL_VERSION@+galaxy5" profile="23.0">
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2 <description>Generate biotransformation products for molecules.</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="creator"/>
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7 <xrefs>
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8 <xref type="bio.tools">biotransformer</xref>
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9 </xrefs>
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10
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11 <requirements>
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12 <requirement type="package" version="3.0_20230403">biotransformer</requirement>
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13 <requirement type="package" version="3.1.1">openbabel</requirement>
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14 <requirement type="package" version="2.3.1">pandas</requirement>
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15 </requirements>
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17 <required_files>
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18 <include path="wrapper_biotransformer.py"/>
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19 </required_files>
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21 <command detect_errors="aggressive"><![CDATA[
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22 python3 '${__tool_directory__}/wrapper_biotransformer.py'
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23 -k $k
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24 -b $b
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25 -s $steps
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26 -t $tolerance
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27 -a
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28 -icsv $input_file
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29 -ocsv $output_file
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30 -ocsvDup $output_file2
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31 -ocsvDup2 $output_file3
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32 ]]>
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33 </command>
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34 <inputs>
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35 <param name="k" type="select" value="pred"
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36 label="The task to be performed [pred=prediction, cid=compound identification]."
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37 help="Select the task to be performed.
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38 For prediction, the tool will generate biotransformation products for the input molecules.
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39 For compound identification, it will identify compounds based on their chemical structure.">
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40 <option value="pred" selected="true">pred</option>
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41 <option value="cid">cid</option>
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42 </param>
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43 <param name="b" type="select" value="ecbased" label="The type of description." help="Select the type of biotransformation description to use.
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44 Options include EC-based, CYP450, Phase II, Human gut microbial, Super transformer 1 (superbio),
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45 Super transformer 2 (allHuman), and Environmental microbial.">
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46 <option value="ecbased" selected="true">EC-based</option>
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47 <option value="cyp450">CYP450</option>
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48 <option value="phaseII">Phase II</option>
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49 <option value="hgut">Human gut microbial</option>
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50 <option value="superbio">Human super transformer 1 (superbio)</option>
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51 <option value="allHuman">Human super transformer 2 (allHuman)</option>
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52 <option value="envimicro">Environmental microbial</option>
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53 </param>
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54 <param name="steps" type="integer" value="1" min="1" max="5" label=" The number of steps for the prediction." help="Number of transformation steps to predict."/>
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55 <param name="tolerance" type="float" value="0.01" label="Mass tolerance for metabolite identification." help="Tolerance is used in Da for identification."/>
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56 <param name="input_file" type="data" format="csv" label="Input CSV file." help="Input table with SMILES strings to predict the biotransformation products for."/>
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57 </inputs>
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59 <outputs>
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60 <data format="tabular" name="output_file" label="BioTransformer on ${on_string}"/>
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61 <data format="tabular" name="output_file2" label="BioTransformer with filter on ${on_string}"/>
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62 <data format="tabular" name="output_file3" label="BioTransformer with super filter on ${on_string}"/>
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63 </outputs>
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64
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65 <tests>
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66 <test>
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67 <param name="k" value="pred"/>
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68 <param name="b" value="allHuman"/>
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69 <param name="steps" value="1"/>
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70 <param name="tolerance" value="0.01"/>
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71 <param name="input_file" value="smiles.csv"/>
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72 <output name="output_file">
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73 <assert_contents>
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74 <has_size value="9818" delta="300"/>
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75 <has_n_lines n="250" delta="25"/>
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76 </assert_contents>
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77 </output>
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78 <output name="output_file2">
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79 <assert_contents>
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80 <has_size value="9818" delta="300"/>
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81 <has_n_lines n="250" delta="25"/>
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82 </assert_contents>
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83 </output>
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84 <output name="output_file3">
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85 <assert_contents>
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86 <has_size value="8497" delta="300"/>
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87 <has_n_lines n="200" delta="25"/>
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88 </assert_contents>
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89 </output>
0
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90 </test>
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91 </tests>
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92 <help>
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93 <![CDATA[
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94 @HELP@
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95 ]]>
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96 </help>
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97 <citations>
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98 <citation type="doi">https://doi.org/10.1186/s13321-018-0324-5</citation>
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99 </citations>
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100 </tool>