<tool id="pdaug_peptide_core_descriptors" name="PDAUG Peptide Core Descriptors" version="0.1.0">
  <description>Calculates core descriptors of peptide sequences</description>

  <requirements>
    <requirement type="package" version="0.24.2">pandas</requirement>
    <requirement type="package" version="4.2.1">modlamp</requirement> 
  </requirements>
  <stdio>
    <exit_code range="1" level="fatal" />
  </stdio>
    <command detect_errors="exit_code"><![CDATA[

        python '$__tool_directory__/PDAUG_Peptide_Core_Descriptors.py'  -I '$input1' -N '$ngrams' -O '$output1'              

    ]]></command>

  <inputs>
    <param name="input1" type="data" label="Input file" format="fasta" argument= "--InFile1" help="Input fasta file with peptides"/>
    <param name="ngrams"  type="integer" label="ngram size" value="3" help="ngram size"/>
  </inputs>

  <outputs>
        <data name='output1' format='tabular' label="${tool.name} on $on_string - n-grams (tabular)" />    
  </outputs>
  <tests>
    <test>
      <param name="input1" value="test.fasta"/>
      <param name="ngrams" value="3" />
      <output name="output1" file="Out.tsv"/>
    </test>
  </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**

Calculates the frequency of ngrames in peptide sequences.

-----

**Inputs**
    * **--InFile** Fasta file with peptide sequences as Input File.
    * **--Ngrams** Integer value of Ngrams frequency to be calculated.  
    
-----

**Outputs**
    * **--OutFile** Returns tabular data file. ]]></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{müller_gabernet_hiss_schneider_2017, 
      title={modlAMP: Python for antimicrobial peptides}, 
      volume={33}, 
      DOI={10.1093/bioinformatics/btx285}, 
      number={17}, 
      journal={Bioinformatics}, 
      author={Müller, Alex T and Gabernet, Gisela and Hiss, Jan A and Schneider, Gisbert}, 
      year={2017}, 
      pages={2753–2755}
    }
  </citation>
</citations>
</tool>