<tool id="pdaug_peptide_length_distribution" name="PDAUG Peptide Length Distribution" version="0.1.0" python_template_version="3.6">
	<description>Analyze peptides length distribution of a dataset</description>

    <requirements>
      <requirement type="package" version="3.2.2">matplotlib</requirement>
      <requirement type="package" version="1.76" >biopython</requirement>                       

    </requirements>

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

        python '$__tool_directory__/PDAUG_Peptide_Length_Distribution.py' --InFile '$input1'  --OutFile 'out.png'              
    ]]></command>

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

    <outputs>   
        <data name='output2' format='png' label="${tool.name} on $on_string - (PNG)" from_work_dir="out.png"/>
    </outputs>
 
    <tests>
        <test>
            <param name="input1" value="positive.fasta"/>
            <output name="output2" file="out.png"/>
        </test>
    </tests>

    <help><![CDATA[
.. class:: infomark

**What it does**

This tool calculates and plots the length distribution of peptide sequences in a peptide dataset. 

-----

**Inputs**
    * **--InFile** fasta file with peptide sequences. 
 
-----

**Outputs**
    * Return html report 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>
</citations>
</tool>