diff --git a/tool_test_output.html b/tool_test_output.html
new file mode 100644
index 00000000..6c774a2c
--- /dev/null
+++ b/tool_test_output.html
@@ -0,0 +1,291 @@
+
+
+
+
+
+
+ Test Results (powered by Planemo)
+
+
+
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+
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+
\ No newline at end of file
diff --git a/tool_test_output.json b/tool_test_output.json
new file mode 100644
index 00000000..c0501a12
--- /dev/null
+++ b/tool_test_output.json
@@ -0,0 +1,101 @@
+{
+ "summary": {
+ "num_errors": 0,
+ "num_failures": 0,
+ "num_skips": 0,
+ "num_tests": 1
+ },
+ "tests": [
+ {
+ "data": {
+ "inputs": {
+ "config_json": {
+ "id": "8638ae59da399d18",
+ "src": "hda"
+ },
+ "input_train_npy_path": {
+ "id": "52e55242f7275d02",
+ "src": "hda"
+ },
+ "outname_output_model_pth_path": "output_model.pth",
+ "outname_output_performance_npz_path": "output_performance.npz",
+ "outname_output_train_data_npz_path": "output_train_data.npz"
+ },
+ "job": {
+ "command_line": "ln -s /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/files/2/4/5/dataset_245bf14d-1659-4578-a68b-afb1ce9308f1.dat ./input_train_npy_path.npy; ln -s /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/files/2/4/9/dataset_249a96e0-a3d5-42bd-8d9f-8aeb075051f2.dat ./config_json.json; train_mdae --config ./config_json.json --input_train_npy_path ./input_train_npy_path.npy --output_model_pth_path output_model.pth --output_train_data_npz_path output_train_data.npz --output_performance_npz_path output_performance.npz ; mv output_model.pth /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/outputs/dataset_d4a02c99-cb7c-4e22-a5bb-da3d294518d4.dat; if test -f output_train_data.npz; then mv output_train_data.npz /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/outputs/dataset_c853af5a-bc40-41fe-8d2f-8380b5c52aa8.dat; fi; if test -f output_performance.npz; then mv output_performance.npz /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/outputs/dataset_340d714b-ea61-4f02-9a06-3a509f31fc47.dat; fi;",
+ "command_version": "",
+ "copied_from_job_id": null,
+ "create_time": "2024-06-28T09:00:51.154276",
+ "dependencies": [],
+ "exit_code": 0,
+ "external_id": "66123",
+ "galaxy_version": "24.0",
+ "handler": null,
+ "history_id": "52e55242f7275d02",
+ "id": "63581132e3d3fcd7",
+ "inputs": {
+ "config_json": {
+ "id": "8638ae59da399d18",
+ "src": "hda",
+ "uuid": "249a96e0-a3d5-42bd-8d9f-8aeb075051f2"
+ },
+ "input_train_npy_path": {
+ "id": "52e55242f7275d02",
+ "src": "hda",
+ "uuid": "245bf14d-1659-4578-a68b-afb1ce9308f1"
+ }
+ },
+ "job_messages": [],
+ "job_metrics": [],
+ "job_runner_name": null,
+ "job_stderr": "",
+ "job_stdout": "",
+ "model_class": "Job",
+ "output_collections": {},
+ "outputs": {
+ "output_model_pth_path": {
+ "id": "63581132e3d3fcd7",
+ "src": "hda",
+ "uuid": "d4a02c99-cb7c-4e22-a5bb-da3d294518d4"
+ },
+ "output_performance_npz_path": {
+ "id": "97f585e74de64884",
+ "src": "hda",
+ "uuid": "340d714b-ea61-4f02-9a06-3a509f31fc47"
+ },
+ "output_train_data_npz_path": {
+ "id": "3567654777edac40",
+ "src": "hda",
+ "uuid": "c853af5a-bc40-41fe-8d2f-8380b5c52aa8"
+ }
+ },
+ "params": {
+ "__input_ext": "\"npy\"",
+ "chromInfo": "\"/Users/pau/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
+ "dbkey": "\"?\"",
+ "input_model_pth_path": null,
+ "outname_output_model_pth_path": "\"output_model.pth\"",
+ "outname_output_performance_npz_path": "\"output_performance.npz\"",
+ "outname_output_train_data_npz_path": "\"output_train_data.npz\""
+ },
+ "state": "ok",
+ "stderr": "",
+ "stdout": "2024-06-28 11:00:56,519 [MainThread ] [INFO ] Executing biobb_pytorch.mdae.train_mdae Version: 4.2.1\n2024-06-28 11:00:56,520 [MainThread ] [INFO ] Copy: ./input_train_npy_path.npy to /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a\n2024-06-28 11:00:56,520 [MainThread ] [INFO ] Start Training:\n2024-06-28 11:00:56,521 [MainThread ] [INFO ] Device: cpu\n2024-06-28 11:00:56,521 [MainThread ] [INFO ] Train input file: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/input_train_npy_path.npy\n2024-06-28 11:00:56,521 [MainThread ] [INFO ] File size: 119.66 KB\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Number of atoms: 102\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Number of frames for training: 80 Total number of frames: 100\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Number of epochs: 50\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Partition: 0.8\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Batch size: 1\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Learning rate: 0.0001\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Learning rate step size: 100\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Learning rate gamma: 0.1\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Number of layers: 4\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Input dimensions: 306\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Latent dimensions: 2\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Loss function: MSELoss\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Optimizer: Adam \n2024-06-28 11:00:56,523 [MainThread ] [INFO ] Seed: 1\n2024-06-28 11:00:56,523 [MainThread ] [INFO ] Checkpoint interval: 25\n2024-06-28 11:00:56,523 [MainThread ] [INFO ] Log interval: 10\n\n2024-06-28 11:00:56,871 [MainThread ] [INFO ] Epoch 1/50, Train Loss: 0.042, Validation Loss: 0.040, LR: 0.00010, Duration: 00s, ETA: 17s\n2024-06-28 11:00:56,871 [MainThread ] [INFO ] Saving: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/checkpoint_epoch__0.pth\n2024-06-28 11:00:59,230 [MainThread ] [INFO ] Epoch 11/50, Train Loss: 0.026, Validation Loss: 0.025, LR: 0.00010, Duration: 00s, ETA: 11s\n2024-06-28 11:01:01,832 [MainThread ] [INFO ] Epoch 21/50, Train Loss: 0.024, Validation Loss: 0.024, LR: 0.00010, Duration: 00s, ETA: 07s\n2024-06-28 11:01:03,209 [MainThread ] [INFO ] Saving: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/checkpoint_epoch__25.pth\n2024-06-28 11:01:04,644 [MainThread ] [INFO ] Epoch 31/50, Train Loss: 0.023, Validation Loss: 0.023, LR: 0.00010, Duration: 00s, ETA: 04s\n2024-06-28 11:01:07,345 [MainThread ] [INFO ] Epoch 41/50, Train Loss: 0.023, Validation Loss: 0.023, LR: 0.00010, Duration: 00s, ETA: 02s\n2024-06-28 11:01:09,770 [MainThread ] [INFO ] Epoch 50/50, Train Loss: 0.022, Validation Loss: 0.022, LR: 0.00010, Duration: 00s, ETA: 00s\n2024-06-28 11:01:09,771 [MainThread ] [INFO ] Saving: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/checkpoint_epoch__49.pth\n2024-06-28 11:01:09,775 [MainThread ] [INFO ] End Training, total time: 13s\n2024-06-28 11:01:09,782 [MainThread ] [INFO ] Saving train data to: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/output_train_data.npz\n2024-06-28 11:01:09,782 [MainThread ] [INFO ] File size: 1.31 KB\n2024-06-28 11:01:09,821 [MainThread ] [INFO ] Saving evaluation data to: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/output_performance.npz\n2024-06-28 11:01:09,821 [MainThread ] [INFO ] File size: 121.13 KB\n2024-06-28 11:01:09,825 [MainThread ] [INFO ] Saving best model to: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/output_model.pth\n2024-06-28 11:01:09,826 [MainThread ] [INFO ] Best model epoch: 49\n2024-06-28 11:01:09,826 [MainThread ] [INFO ] File size: 931.57 KB\n2024-06-28 11:01:09,829 [MainThread ] [INFO ] Removed: []\n",
+ "tool_id": "biobb_pytorch_train_mdae",
+ "tool_stderr": "",
+ "tool_stdout": "2024-06-28 11:00:56,519 [MainThread ] [INFO ] Executing biobb_pytorch.mdae.train_mdae Version: 4.2.1\n2024-06-28 11:00:56,520 [MainThread ] [INFO ] Copy: ./input_train_npy_path.npy to /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a\n2024-06-28 11:00:56,520 [MainThread ] [INFO ] Start Training:\n2024-06-28 11:00:56,521 [MainThread ] [INFO ] Device: cpu\n2024-06-28 11:00:56,521 [MainThread ] [INFO ] Train input file: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/input_train_npy_path.npy\n2024-06-28 11:00:56,521 [MainThread ] [INFO ] File size: 119.66 KB\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Number of atoms: 102\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Number of frames for training: 80 Total number of frames: 100\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Number of epochs: 50\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Partition: 0.8\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Batch size: 1\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Learning rate: 0.0001\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Learning rate step size: 100\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Learning rate gamma: 0.1\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Number of layers: 4\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Input dimensions: 306\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Latent dimensions: 2\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Loss function: MSELoss\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Optimizer: Adam \n2024-06-28 11:00:56,523 [MainThread ] [INFO ] Seed: 1\n2024-06-28 11:00:56,523 [MainThread ] [INFO ] Checkpoint interval: 25\n2024-06-28 11:00:56,523 [MainThread ] [INFO ] Log interval: 10\n\n2024-06-28 11:00:56,871 [MainThread ] [INFO ] Epoch 1/50, Train Loss: 0.042, Validation Loss: 0.040, LR: 0.00010, Duration: 00s, ETA: 17s\n2024-06-28 11:00:56,871 [MainThread ] [INFO ] Saving: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/checkpoint_epoch__0.pth\n2024-06-28 11:00:59,230 [MainThread ] [INFO ] Epoch 11/50, Train Loss: 0.026, Validation Loss: 0.025, LR: 0.00010, Duration: 00s, ETA: 11s\n2024-06-28 11:01:01,832 [MainThread ] [INFO ] Epoch 21/50, Train Loss: 0.024, Validation Loss: 0.024, LR: 0.00010, Duration: 00s, ETA: 07s\n2024-06-28 11:01:03,209 [MainThread ] [INFO ] Saving: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/checkpoint_epoch__25.pth\n2024-06-28 11:01:04,644 [MainThread ] [INFO ] Epoch 31/50, Train Loss: 0.023, Validation Loss: 0.023, LR: 0.00010, Duration: 00s, ETA: 04s\n2024-06-28 11:01:07,345 [MainThread ] [INFO ] Epoch 41/50, Train Loss: 0.023, Validation Loss: 0.023, LR: 0.00010, Duration: 00s, ETA: 02s\n2024-06-28 11:01:09,770 [MainThread ] [INFO ] Epoch 50/50, Train Loss: 0.022, Validation Loss: 0.022, LR: 0.00010, Duration: 00s, ETA: 00s\n2024-06-28 11:01:09,771 [MainThread ] [INFO ] Saving: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/checkpoint_epoch__49.pth\n2024-06-28 11:01:09,775 [MainThread ] [INFO ] End Training, total time: 13s\n2024-06-28 11:01:09,782 [MainThread ] [INFO ] Saving train data to: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/output_train_data.npz\n2024-06-28 11:01:09,782 [MainThread ] [INFO ] File size: 1.31 KB\n2024-06-28 11:01:09,821 [MainThread ] [INFO ] Saving evaluation data to: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/output_performance.npz\n2024-06-28 11:01:09,821 [MainThread ] [INFO ] File size: 121.13 KB\n2024-06-28 11:01:09,825 [MainThread ] [INFO ] Saving best model to: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/output_model.pth\n2024-06-28 11:01:09,826 [MainThread ] [INFO ] Best model epoch: 49\n2024-06-28 11:01:09,826 [MainThread ] [INFO ] File size: 931.57 KB\n2024-06-28 11:01:09,829 [MainThread ] [INFO ] Removed: []\n",
+ "update_time": "2024-06-28T09:01:16.128563",
+ "user_email": "planemo@galaxyproject.org"
+ },
+ "status": "success",
+ "test_index": 0,
+ "time_seconds": 37.86598777770996,
+ "tool_id": "biobb_pytorch_train_mdae",
+ "tool_version": "4.2.1"
+ },
+ "has_data": true,
+ "id": "biobb_pytorch_train_mdae-0"
+ }
+ ],
+ "version": "0.1"
+}
\ No newline at end of file
diff --git a/tools/biobb_pytorch/.DS_Store b/tools/biobb_pytorch/.DS_Store
new file mode 100644
index 00000000..281b83a5
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diff --git a/tools/biobb_pytorch/.shed.yml b/tools/biobb_pytorch/.shed.yml
index 27bc89b3..e1f9744b 100644
--- a/tools/biobb_pytorch/.shed.yml
+++ b/tools/biobb_pytorch/.shed.yml
@@ -1,5 +1,5 @@
name: biobb_pytorch
-owner: "Biobb team"
+owner: chemteam
description: "biobb_pytorch is the Biobb module collection to create and train ML & DL models using the popular [PyTorch](https://pytorch.org/) Python library."
homepage_url: https://github.com/bioexcel/biobb_pytorch
long_description: |
@@ -20,6 +20,6 @@ categories:
- Biobb
- Autoencoders
maintainers:
- - Pau Andrio
- - Genis Bayarri
- - Adam Hospital
\ No newline at end of file
+ - PauAndrio
+ - gbayarri
+ - adamhospital
\ No newline at end of file
diff --git a/tools/biobb_pytorch/biobb_apply_mdae.xml b/tools/biobb_pytorch/biobb_apply_mdae.xml
index 25b5d71f..ab3c44d7 100644
--- a/tools/biobb_pytorch/biobb_apply_mdae.xml
+++ b/tools/biobb_pytorch/biobb_apply_mdae.xml
@@ -1,8 +1,11 @@
-
+
Apply a Molecular Dynamics AutoEncoder (MDAE) PyTorch model.
+
+ 4.2.1
+
- biobb_pytorch
+ biobb_pytorch
@@ -53,8 +56,16 @@
-
-
+
+
diff --git a/tools/biobb_pytorch/biobb_train_mdae.xml b/tools/biobb_pytorch/biobb_train_mdae.xml
index 68dba544..9cd98fca 100644
--- a/tools/biobb_pytorch/biobb_train_mdae.xml
+++ b/tools/biobb_pytorch/biobb_train_mdae.xml
@@ -1,39 +1,42 @@
-
+
: Train a Molecular Dynamics AutoEncoder (MDAE) PyTorch model.
+
+ 4.2.1
+
- biobb_pytorch
+ biobb_pytorch
-
-
+
+
.. class:: infomark
-Check the syntax for the tool parameters at the original library documentation: https://biobb_pytorch.readthedocs.io/en/latest
+Check the syntax for the tool parameters at the original library documentation: https://biobb-pytorch.readthedocs.io/en/latest
-----
diff --git a/tools/biobb_pytorch/test-data/.DS_Store b/tools/biobb_pytorch/test-data/.DS_Store
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diff --git a/tools/biobb_pytorch/test-data/ref_output_latent_space.npy b/tools/biobb_pytorch/test-data/ref_output_latent_space.npy
deleted file mode 100644
index b877e25f..00000000
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diff --git a/tools/biobb_pytorch/test-data/ref_output_performance.npz b/tools/biobb_pytorch/test-data/ref_output_performance.npz
deleted file mode 100644
index f390e10f..00000000
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diff --git a/tools/biobb_pytorch/test-data/ref_output_reconstructed_data.npy b/tools/biobb_pytorch/test-data/ref_output_reconstructed_data.npy
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diff --git a/tools/biobb_pytorch/test-data/ref_output_train_data.npz b/tools/biobb_pytorch/test-data/ref_output_train_data.npz
deleted file mode 100644
index ef970888..00000000
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