view PDAUG_Peptide_Ngrams/PDAUG_Peptide_Ngrams.xml @ 3:b2a7b957cd52 draft

"planemo upload for repository commit edb37634e419f75dd66292e712de51278746d883"
author jay
date Wed, 30 Dec 2020 03:06:50 +0000
parents 7557b48b2872
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<tool id="pdaug_peptide_ngrams" name="PDAUG Peptide Ngrams" version="0.1.0" python_template_version="2.7">
	<description>Counts n-grams in the entire sequence set and fitting their distribution with the power-law distribution (Zipf’s law)</description>
      <requirement type="package" version="2.7.18">python</requirement>
      <requirement type="package" version="1.4.6">powerlaw</requirement>
      <requirement type="package" version="0.2.4">quantiprot</requirement>

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

        python2 '$__tool_directory__/' -f1 '$fasta1' -f2 '$fasta2'  --OutFile 'out.png'

      <param name="fasta1" type="data" format="fasta" label="First fasta file" argument= "--fasta1" help="First fasta file"/>
      <param name="fasta2" type="data" format="fasta" label="Second fasta file" argument= "--fasta2" help="First fasta file"/>

        <data name='output2' format='png' label="${} on $on_string - (PNG)" from_work_dir="out.png"/>
            <param name="fasta1" value="test1.fasta"/>
            <param name="fasta2" value="test2.fasta"/>
            <output name="output2" file="out.png"/>

.. class:: infomark

**What it does**

This tool counts n-grams in the entire  peptide sequence set and fitting their distribution with the power-law distribution (Zipf’s law) and plot the results.


    * **--InFile** Takes fasta file as input with peptide sequences. 


    * Returns html report file.]]></help>
  <citation type="bibtex">
      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 =
  <citation type="bibtex">
       title={Quantiprot - a Python package for quantitative analysis of protein sequences}, 
       journal={BMC Bioinformatics},
       author={Konopka, Bogumił M. and Marciniak, Marta and Dyrka, Witold},