<tool id="readBAM" name="readBAM" version="0.1">
  <description>: convert aligned BAM files to RData format for NucleosomeDynamics</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 readBAM --input $bam_file --output $rdata_file --type $seq_type
]]>
  </command>
  <inputs>
    <param name="bam_file" type="data" format="bam" label="MNase-seq / ATAC-seq BAM file" help="Upload your MNase-seq or ATAC-seq reads file in BAM format. Access sample data at 'Shared Data -> Data libraries" />
    <param name="seq_type" type="select" label="Type of sequence reads">
      <option value="paired">Paired</option>
      <option value="single">Single</option>
    </param>
  </inputs>
  <outputs>
    <data format="rdata" name="rdata_file" label="readBAM__${os.path.splitext(os.path.basename($bam_file.name))[0]}.rdata" />
  </outputs>
  <tests>
      <test>   
	  <param  name="bam_file" value="cellcycleM_chrII.bam"/>
          <param  name="seq_type" value="paired" />
	  <output name="rdata_file" file="readBAM__cellcycleM_chrII.RData"/>
       </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>