<tool id="NFR" name="Nucleosome Free Regions" version="0.1">
<description>: determine Nucleosome Free Regions from nucleR nucleosome calls</description>
    <requirements>
        <requirement type="binary">docker</requirement>
    </requirements>
    <command>
<![CDATA[
	docker run -v $__root_dir__/database/files:$__root_dir__/database/files -v /tmp:/tmp -u `id -u`:`id -g`  mmbirb/nucleosome-dynamics NFR --input $gff_file --output $output_gff_file --minwidth $minwidth --threshold $threshold  
]]>
  </command>
  <inputs>
    <param name="gff_file" type="data" format="gff" label="Nucleosome Calls (GFF)" help="Nucleosome calls in GFF format as obtained from nucleR."/>
    <param name="minwidth" size="4" type="integer" value="110" label="Minimum Width" help="Minimum width for a linker fragment to be considered a nucleosome-free region." />  
    <param name="threshold" size="4" type="integer" value="140" label="Maximum Width" help="Maximum width for a linker fragment to be considered a nucleosome-free region." />  
</inputs>
  <outputs>
     <data format="gff" name="output_gff_file" label="NFR__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gff" />
  </outputs>
  <tests>
	  <test>
		  <param name="gff_file" value="NR__cellcycleM_chrII.gff"/>
		  <param name="minwidth" value="110" />
		  <param name="threshold" value="400" />
		  <output name="output_gff_file" file="NFR__cellcycleM_chrII.gff" />
	  </test>
  </tests>
     <help>
 .. image:: ${static_path}/images/NucleosomeDynamicsLogo.png
    :height: 80
    :width: 200

-----

Nucleosome Dynamics is a set of tools that take MNase-seq and ATAC-seq aligned reads and performs a serie of nucleosome-related analyses on them.

.. class:: infomark

Visit the  documentation of the original application for learning more about the accepted values and formats. http://mmb.irbbarcelona.org/NucleosomeDynamics/help/usage/nucleosome-dynamics
   </help>
   <citations>
        <citation type="bibtex">
@misc{github,
  author = {Buitrago D},
  year = {2019},
  title = {Nucleosome Dynamics suite: containerized installation},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics},
}</citation>
 </citations>
</tool>