Mercurial > repos > recetox > biotransformer
comparison biotransformer.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 | 296bd426527f |
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1 <tool id="biotransformer" name="BioTransformer" version="@TOOL_VERSION@+galaxy0" profile="21.09"> | |
2 <macros> | |
3 <import>macros.xml</import> | |
4 </macros> | |
5 <expand macro="creator"/> | |
6 <requirements> | |
7 <requirement type="package" version="@TOOL_VERSION@">biotransformer</requirement> | |
8 <requirement type="package" version="3.1.1">openbabel</requirement> | |
9 <requirement type="package" version="1.1.1">pandas</requirement> | |
10 </requirements> | |
11 <command detect_errors="aggressive"><![CDATA[ | |
12 python3 '${__tool_directory__}/wrapper_biotransformer.py' | |
13 -k $k | |
14 -b $b | |
15 -s $steps | |
16 -t $tolerance | |
17 -a | |
18 -icsv $input_file | |
19 -ocsv $output_file | |
20 -ocsvDup $output_file2 | |
21 -ocsvDup2 $output_file3 | |
22 ]]> | |
23 </command> | |
24 <inputs> | |
25 <param name="k" type="select" value="pred" | |
26 label="The task to be permed [pred=prediction, cid=compound identification]."> | |
27 <option value="pred" selected="true">pred</option> | |
28 <option value="cid">cid</option> | |
29 </param> | |
30 <param name="b" type="select" value="ecbased" label="The type of description."> | |
31 <option value="ecbased" selected="true">EC-based</option> | |
32 <option value="cyp450">CYP450</option> | |
33 <option value="phaseII">Phase II</option> | |
34 <option value="hgut">Human gut microbial</option> | |
35 <option value="superbio">Human super transformer 1 (superbio)</option> | |
36 <option value="allHuman">Human super transformer 2 (allHuman)</option> | |
37 <option value="envimicro">Environmental microbial</option> | |
38 </param> | |
39 <param name="steps" type="integer" value="1" label=" The number of steps for the prediction."/> | |
40 <param name="tolerance" type="float" value="0.01" label="Mass tolerance for metabolite identification."/> | |
41 <param name="input_file" type="data" format="csv" label="Input CSV file."/> | |
42 </inputs> | |
43 | |
44 <outputs> | |
45 <data format="tsv" name="output_file" label="BioTransformer on ${on_string}"/> | |
46 <data format="tsv" name="output_file2" label="BioTransformer with filter on ${on_string}"/> | |
47 <data format="tsv" name="output_file3" label="BioTransformer with super filter on ${on_string}"/> | |
48 </outputs> | |
49 | |
50 <tests> | |
51 <test> | |
52 <param name="k" value="pred"/> | |
53 <param name="b" value="allHuman"/> | |
54 <param name="steps" value="1"/> | |
55 <param name="tolerance" value="0.01"/> | |
56 <param name="input_file" value="smiles.csv"/> | |
57 <output name="output_file" value="output1.tsv"/> | |
58 <output name="output_file2" value="output2.tsv"/> | |
59 <output name="output_file3" value="output3.tsv"/> | |
60 </test> | |
61 </tests> | |
62 <help> | |
63 <![CDATA[ | |
64 @HELP@ | |
65 ]]> | |
66 </help> | |
67 <citations> | |
68 <citation type="doi">https://doi.org/10.1186/s13321-018-0324-5</citation> | |
69 </citations> | |
70 </tool> |