annotate 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

<tool id="biobb_pytorch_train_mdae" name="TrainMdae" version="@TOOL_VERSION@" profile="22.05">
    <description>Train a Molecular Dynamics AutoEncoder (MDAE) PyTorch model</description>
    <macros>
      <token name="@TOOL_VERSION@">4.2.1</token>
    </macros>

    <requirements>
      <requirement type="package" version="@TOOL_VERSION@">biobb_pytorch</requirement>
    </requirements>

    <command detect_errors="exit_code"><![CDATA[

      ln -s '$input_train_npy_path' ./input_train_npy_path.$input_train_npy_path.ext &&

      #if $input_model_pth_path:
        ln -s '$input_model_pth_path' ./input_model_pth_path.$input_model_pth_path.ext &&
      #end if
      #if $config_json:
        ln -s '$config_json' ./config_json.$config_json.ext &&
      #end if

      train_mdae

      #if $config_json:
        --config ./config_json.$config_json.ext
      #end if

      --input_train_npy_path ./input_train_npy_path.$input_train_npy_path.ext
      #if $input_model_pth_path:
        --input_model_pth_path ./input_model_pth_path.$input_model_pth_path.ext
      #end if
      --output_model_pth_path ./output_model_pth_path.pth
      #if $output_train_data_npz_path:
        --output_train_data_npz_path ./output_train_data_npz_path.npz
      #end if
      #if $output_performance_npz_path:
        --output_performance_npz_path ./output_performance_npz_path.npz
      #end if
      ;
      ]]>
    </command>

    <inputs>
      <param name="input_train_npy_path" type="data" format="npy"  optional="False" label="Input NPY file" help="Input train NPY data file"/>
      <param name="input_model_pth_path" type="data" format="pth"  optional="True" label="Input PTH file" help="Input model PTH file"/>
      <param name="config_json" type="data" format="json" optional="True" label="Configuration file" help="File containing tool settings"/>
    </inputs>

    <outputs>
      <data format="pth" name="output_model_pth_path" from_work_dir="output_model_pth_path.pth" label="output_model_pth_path" />
      <data format="npz" name="output_train_data_npz_path" from_work_dir="output_train_data_npz_path.npz" label="output_train_data_npz_path" />
      <data format="npz" name="output_performance_npz_path" from_work_dir="output_performance_npz_path.npz" label="output_performance_npz_path" />
    </outputs>

    <tests>
      <test>
        <param name="config_json" value="config_train_mdae.json" ftype="json" />
        <param name="input_train_npy_path" value="train_mdae_traj.npy" ftype="npy" />
        <output name="output_model_pth_path"       file="ref_output_model.pth" compare="sim_size" />
        <output name="output_train_data_npz_path">
          <assert_contents>
            <has_size value="1k" delta="500"/>
          </assert_contents>
        </output>
        <output name="output_performance_npz_path">
          <assert_contents>
            <has_size value="124k" delta="50k"/>
          </assert_contents>
        </output>
      </test>
    </tests>

    <help>
.. class:: infomark

Check the syntax for the tool parameters at the original library documentation: https://biobb-pytorch.readthedocs.io/en/latest
   </help>

    <citations>
        <citation type="bibtex">
            @misc{githubbiobb,
            author = {Andrio P, Bayarri, G., Hospital A, Gelpi JL},
            year = {2019-21},
            title = {biobb: BioExcel building blocks },
            publisher = {GitHub},
            journal = {GitHub repository},
            url = {https://github.com/bioexcel/biobb_pytorch},
            }
        </citation>
        <citation type="doi">10.1038/s41597-019-0177-4</citation>
    </citations>
</tool>