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comparison 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
children
comparison
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5:0f1b15d51801 6:200c5c982dba
1 <tool id="biotransformer" name="BioTransformer" version="@TOOL_VERSION@+galaxy4" profile="21.09"> 1 <tool id="biotransformer" name="BioTransformer" version="@TOOL_VERSION@+galaxy5" profile="23.0">
2 <description>Generate biotransformation products for molecules.</description>
2 <macros> 3 <macros>
3 <import>macros.xml</import> 4 <import>macros.xml</import>
4 </macros> 5 </macros>
5 <expand macro="creator"/> 6 <expand macro="creator"/>
6 <xrefs> 7 <xrefs>
7 <xref type="bio.tools">biotransformer</xref> 8 <xref type="bio.tools">biotransformer</xref>
8 </xrefs> 9 </xrefs>
10
9 <requirements> 11 <requirements>
10 <requirement type="package" version="3.0_20230403">biotransformer</requirement> 12 <requirement type="package" version="3.0_20230403">biotransformer</requirement>
11 <requirement type="package" version="3.1.1">openbabel</requirement> 13 <requirement type="package" version="3.1.1">openbabel</requirement>
12 <requirement type="package" version="1.1.1">pandas</requirement> 14 <requirement type="package" version="2.3.1">pandas</requirement>
13 </requirements> 15 </requirements>
16
17 <required_files>
18 <include path="wrapper_biotransformer.py"/>
19 </required_files>
20
14 <command detect_errors="aggressive"><![CDATA[ 21 <command detect_errors="aggressive"><![CDATA[
15 python3 '${__tool_directory__}/wrapper_biotransformer.py' 22 python3 '${__tool_directory__}/wrapper_biotransformer.py'
16 -k $k 23 -k $k
17 -b $b 24 -b $b
18 -s $steps 25 -s $steps
24 -ocsvDup2 $output_file3 31 -ocsvDup2 $output_file3
25 ]]> 32 ]]>
26 </command> 33 </command>
27 <inputs> 34 <inputs>
28 <param name="k" type="select" value="pred" 35 <param name="k" type="select" value="pred"
29 label="The task to be permed [pred=prediction, cid=compound identification]."> 36 label="The task to be performed [pred=prediction, cid=compound identification]."
37 help="Select the task to be performed.
38 For prediction, the tool will generate biotransformation products for the input molecules.
39 For compound identification, it will identify compounds based on their chemical structure.">
30 <option value="pred" selected="true">pred</option> 40 <option value="pred" selected="true">pred</option>
31 <option value="cid">cid</option> 41 <option value="cid">cid</option>
32 </param> 42 </param>
33 <param name="b" type="select" value="ecbased" label="The type of description."> 43 <param name="b" type="select" value="ecbased" label="The type of description." help="Select the type of biotransformation description to use.
44 Options include EC-based, CYP450, Phase II, Human gut microbial, Super transformer 1 (superbio),
45 Super transformer 2 (allHuman), and Environmental microbial.">
34 <option value="ecbased" selected="true">EC-based</option> 46 <option value="ecbased" selected="true">EC-based</option>
35 <option value="cyp450">CYP450</option> 47 <option value="cyp450">CYP450</option>
36 <option value="phaseII">Phase II</option> 48 <option value="phaseII">Phase II</option>
37 <option value="hgut">Human gut microbial</option> 49 <option value="hgut">Human gut microbial</option>
38 <option value="superbio">Human super transformer 1 (superbio)</option> 50 <option value="superbio">Human super transformer 1 (superbio)</option>
39 <option value="allHuman">Human super transformer 2 (allHuman)</option> 51 <option value="allHuman">Human super transformer 2 (allHuman)</option>
40 <option value="envimicro">Environmental microbial</option> 52 <option value="envimicro">Environmental microbial</option>
41 </param> 53 </param>
42 <param name="steps" type="integer" value="1" label=" The number of steps for the prediction."/> 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."/>
43 <param name="tolerance" type="float" value="0.01" label="Mass tolerance for metabolite identification."/> 55 <param name="tolerance" type="float" value="0.01" label="Mass tolerance for metabolite identification." help="Tolerance is used in Da for identification."/>
44 <param name="input_file" type="data" format="csv" label="Input CSV file."/> 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."/>
45 </inputs> 57 </inputs>
46 58
47 <outputs> 59 <outputs>
48 <data format="tabular" name="output_file" label="BioTransformer on ${on_string}"/> 60 <data format="tabular" name="output_file" label="BioTransformer on ${on_string}"/>
49 <data format="tabular" name="output_file2" label="BioTransformer with filter on ${on_string}"/> 61 <data format="tabular" name="output_file2" label="BioTransformer with filter on ${on_string}"/>
57 <param name="steps" value="1"/> 69 <param name="steps" value="1"/>
58 <param name="tolerance" value="0.01"/> 70 <param name="tolerance" value="0.01"/>
59 <param name="input_file" value="smiles.csv"/> 71 <param name="input_file" value="smiles.csv"/>
60 <output name="output_file"> 72 <output name="output_file">
61 <assert_contents> 73 <assert_contents>
62 <has_size value="9356" delta="300"/> 74 <has_size value="9818" delta="300"/>
63 <has_n_lines n="250" delta="25"/> 75 <has_n_lines n="250" delta="25"/>
64 </assert_contents> 76 </assert_contents>
65 </output> 77 </output>
66 <output name="output_file2"> 78 <output name="output_file2">
67 <assert_contents> 79 <assert_contents>
68 <has_size value="9356" delta="300"/> 80 <has_size value="9818" delta="300"/>
69 <has_n_lines n="250" delta="25"/> 81 <has_n_lines n="250" delta="25"/>
70 </assert_contents> 82 </assert_contents>
71 </output> 83 </output>
72 <output name="output_file3"> 84 <output name="output_file3">
73 <assert_contents> 85 <assert_contents>
74 <has_size value="8135" delta="300"/> 86 <has_size value="8497" delta="300"/>
75 <has_n_lines n="200" delta="25"/> 87 <has_n_lines n="200" delta="25"/>
76 </assert_contents> 88 </assert_contents>
77 </output> 89 </output>
78 </test> 90 </test>
79 </tests> 91 </tests>