annotate PDAUG_Peptide_Structure_Builder/PDAUG_Peptide_Structure_Builder.xml @ 0:0118cc553f3b draft

"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"

<tool id="pdaug_peptide_structure_builder" name="PDAUG Peptide Structure Builder" version="0.1.0">
  <description>Builds 3D structures of peptide sequences up to 3 amino acid </description>

  <requirements>
    <requirement type="package" version="0.24.2">pandas</requirement>
    <requirement type="package" version="1.0.1">fragbuilder</requirement>
  </requirements>
  <stdio>
    <exit_code range="1" level="fatal" />
  </stdio>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/PDAUG_Peptide_Structure_Builder.py' -p '$input1'  

    ]]></command>

  <inputs>
    <param name="input1" type="data" format="fasta" argument= "--pep" label="Input file" help="Input fasta file with peptides"/>
  </inputs>

  <outputs>
    <collection name="output" type="list" label="${tool.name} on $on_string - (PDB)">
        <discover_datasets pattern="__name_and_ext__" format='pdb' directory="DataFile" />
    </collection>
  </outputs>  

  <tests>
    <test>
      <param name="input1" value="test.fasta"/>
      <output_collection name="output" type="list"  >
        <element name="GLF" file="DataFile/GLF.pdb" lines_diff="102" />
      </output_collection>
    </test>
  </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**

This tool generates 3D structures of peptide sequences up to three amino acids that can be utilized for peptide docking with macromolecules with tools such as Autodock Vina. 

-----

**Inputs**
    * **--InFile** A fasta file witth the peptide sequences.

-----

**Outputs**
    * Return collection of peptides with 3D structure.]]></help>
<citations>
  <citation type="bibtex">
    @misc{PDAUGGITHUB, 
      author = {Joshi, Jayadev  and Blankenberg, Daniel}, 
      year = {2020}, 
      title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling}, 
      publisher = {GitHub}, 
      journal = {GitHub repository}, 
      url =
      {https://github.com/jaidevjoshi83/pdaug.git}, 
    }
</citation>

<citation type="bibtex">
    @article{christensen_hamelryck_jensen_2013, 
      title={FragBuilder: An efficient Python library to setup quantum chemistry calculations on peptides models}, DOI={10.7287/peerj.preprints.169v2}, 
      author={Christensen, Anders Steen and Hamelryck, Thomas and Jensen, Jan H}, 
      year={2013}}
        }
  </citation>
</citations>
</tool>