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<tool id="txstart" name="TSS classification" version="0.1">
  <description>: classify nucleosomes at Transcription Start Sites (TSS)</description>    
  <requirements>
  <requirement type="binary">docker</requirement>
  </requirements>
  <command>
	<![CDATA[
	docker run -v $__root_dir__/database/files:$__root_dir__/database/files -v /data:/data -v /tmp:/tmp -u `id -u`:`id -g`  mmbirb/nucleosome-dynamics txstart --calls $gff_file 
		#if $assembly.source == "buildin":
                	--genome ${assembly.ref_genome_gff_buildin}
        	#else if $assembly.source == "history":
                	--genome ${assembly.ref_genome_gff_history}
        	#end if
		--output $output_gff_file --window $window --open_thres $open_thres 
	]]>
  </command>
  <inputs>
    <param name="gff_file" type="data" format="gff" label="Nucleosome calls (GFF)" help="Nucleosome calls in GFF format as obtained from nucleR."/>
    <conditional name="assembly">
            <param name="source" type="select" label="Select a built-in reference genome or use one from your history" help="Taking from each assembly their annotated genes.">
                <option value="buildin" selected="True">Use a built-in genome</option>
                <option value="history">Use a genome from the history</option>
            </param>
            <when value="buildin">
                <param name="ref_genome_gff_buildin" type="select" label="Select reference genome (Genes)" help="Select gene annotations for your reference genome. If your genome of interest is not listed, contact the Galaxy team.">
                    <options from_file="nucldyn_publicdata.loc">
                        <column name="name" index="2"/>
                        <column name="value" index="4"/>
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="ref_genome_gff_history" type="data" format="gff" label="Reference genome (Genes)" help="Upload gene annotations for your reference genome. Check below the documentation for learning about the file format."/>
            </when>
    </conditional>    
    <param name="window" size="4" type="integer" value="300" label="Window" help="Number of nucleotides on each side of the TSS where -1 and +1 nucleosome are search for." />  
    <param name="open_thres" size="4" type="integer" value="215" label="Open threshold" help="Distance between nucleosomes -1 and +1 to discriminate between 'open' and 'close' classes." />  
</inputs>
  <outputs>
    <data format="gff" name="output_gff_file" label="TSS__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gff" />
  </outputs>
<tests>
	<test>
		<param name="gff_file" value="NR__cellcycleM_chrII.gff" />
		<param name="ref_genome_gff_buildin" value="/data/nucldyn_publicdata/refGenomes/R64-1-1/genes.gff" />
		<param name="window" value="300" />
		<param name="open_thres" value="215" />
		<output name="output_gff_file" file="TSS__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>