Mercurial > repos > chemteam > biobb_pytorch
comparison biobb_train_mdae.xml @ 0:0d9f162a7d2c draft default tip
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biobb_pytorch commit 891dd7da50f0a362969b9fb1cf8db9171b04f78a
author | chemteam |
---|---|
date | Thu, 05 Dec 2024 17:20:02 +0000 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:0d9f162a7d2c |
---|---|
1 <tool id="biobb_pytorch_train_mdae" name="TrainMdae" version="@TOOL_VERSION@" profile="22.05"> | |
2 <description>Train a Molecular Dynamics AutoEncoder (MDAE) PyTorch model</description> | |
3 <macros> | |
4 <token name="@TOOL_VERSION@">4.2.1</token> | |
5 </macros> | |
6 | |
7 <requirements> | |
8 <requirement type="package" version="@TOOL_VERSION@">biobb_pytorch</requirement> | |
9 </requirements> | |
10 | |
11 <command detect_errors="exit_code"><![CDATA[ | |
12 | |
13 ln -s '$input_train_npy_path' ./input_train_npy_path.$input_train_npy_path.ext && | |
14 | |
15 #if $input_model_pth_path: | |
16 ln -s '$input_model_pth_path' ./input_model_pth_path.$input_model_pth_path.ext && | |
17 #end if | |
18 #if $config_json: | |
19 ln -s '$config_json' ./config_json.$config_json.ext && | |
20 #end if | |
21 | |
22 train_mdae | |
23 | |
24 #if $config_json: | |
25 --config ./config_json.$config_json.ext | |
26 #end if | |
27 | |
28 --input_train_npy_path ./input_train_npy_path.$input_train_npy_path.ext | |
29 #if $input_model_pth_path: | |
30 --input_model_pth_path ./input_model_pth_path.$input_model_pth_path.ext | |
31 #end if | |
32 --output_model_pth_path ./output_model_pth_path.pth | |
33 #if $output_train_data_npz_path: | |
34 --output_train_data_npz_path ./output_train_data_npz_path.npz | |
35 #end if | |
36 #if $output_performance_npz_path: | |
37 --output_performance_npz_path ./output_performance_npz_path.npz | |
38 #end if | |
39 ; | |
40 ]]> | |
41 </command> | |
42 | |
43 <inputs> | |
44 <param name="input_train_npy_path" type="data" format="npy" optional="False" label="Input NPY file" help="Input train NPY data file"/> | |
45 <param name="input_model_pth_path" type="data" format="pth" optional="True" label="Input PTH file" help="Input model PTH file"/> | |
46 <param name="config_json" type="data" format="json" optional="True" label="Configuration file" help="File containing tool settings"/> | |
47 </inputs> | |
48 | |
49 <outputs> | |
50 <data format="pth" name="output_model_pth_path" from_work_dir="output_model_pth_path.pth" label="output_model_pth_path" /> | |
51 <data format="npz" name="output_train_data_npz_path" from_work_dir="output_train_data_npz_path.npz" label="output_train_data_npz_path" /> | |
52 <data format="npz" name="output_performance_npz_path" from_work_dir="output_performance_npz_path.npz" label="output_performance_npz_path" /> | |
53 </outputs> | |
54 | |
55 <tests> | |
56 <test> | |
57 <param name="config_json" value="config_train_mdae.json" ftype="json" /> | |
58 <param name="input_train_npy_path" value="train_mdae_traj.npy" ftype="npy" /> | |
59 <output name="output_model_pth_path" file="ref_output_model.pth" compare="sim_size" /> | |
60 <output name="output_train_data_npz_path"> | |
61 <assert_contents> | |
62 <has_size value="1k" delta="500"/> | |
63 </assert_contents> | |
64 </output> | |
65 <output name="output_performance_npz_path"> | |
66 <assert_contents> | |
67 <has_size value="124k" delta="50k"/> | |
68 </assert_contents> | |
69 </output> | |
70 </test> | |
71 </tests> | |
72 | |
73 <help> | |
74 .. class:: infomark | |
75 | |
76 Check the syntax for the tool parameters at the original library documentation: https://biobb-pytorch.readthedocs.io/en/latest | |
77 </help> | |
78 | |
79 <citations> | |
80 <citation type="bibtex"> | |
81 @misc{githubbiobb, | |
82 author = {Andrio P, Bayarri, G., Hospital A, Gelpi JL}, | |
83 year = {2019-21}, | |
84 title = {biobb: BioExcel building blocks }, | |
85 publisher = {GitHub}, | |
86 journal = {GitHub repository}, | |
87 url = {https://github.com/bioexcel/biobb_pytorch}, | |
88 } | |
89 </citation> | |
90 <citation type="doi">10.1038/s41597-019-0177-4</citation> | |
91 </citations> | |
92 </tool> |