annotate biobb_apply_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_apply_mdae" name="ApplyMdae" version="@TOOL_VERSION@" profile="22.05">
    <description>Apply 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 '$input_data_npy_path' ./input_data_npy_path.$input_data_npy_path.ext &&
      ln -s '$input_model_pth_path' ./input_model_pth_path.pth &&

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

      apply_mdae

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

      --input_data_npy_path ./input_data_npy_path.$input_data_npy_path.ext
      --input_model_pth_path ./input_model_pth_path.pth
      #if $output_latent_space_npy_path:
      --output_latent_space_npy_path ./output_latent_space_npy_path.npy
      #end if
      --output_reconstructed_data_npy_path ./output_reconstructed_data_npy_path.npy
      ;
      ]]>
    </command>

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

    <outputs>
      <data format="npy" name="output_reconstructed_data_npy_path" from_work_dir="output_reconstructed_data_npy_path.npy" label="output_reconstructed_data_npy_path" />
      <data format="npy" name="output_latent_space_npy_path" from_work_dir="output_latent_space_npy_path.npy" label="output_latent_space_npy_path" />
    </outputs>

    <tests>
        <test>
          <param name="config_json" value="config_apply_mdae.json" ftype="json" />
          <param name="input_data_npy_path"  value="train_mdae_traj.npy" ftype="npy" />
          <param name="input_model_pth_path" value="ref_output_model.pth" />
          <output name="output_reconstructed_data_npy_path" ftype="npy">
            <assert_contents>
              <has_size value="123k" delta="50k"/>
            </assert_contents>
          </output>
          <output name="output_latent_space_npy_path" ftype="npy">
            <assert_contents>
              <has_size value="928" delta="200"/>
            </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>