<tool id="nucDyn_stats" name="Nucleosome Dynamics Statistics" version="0.1">
 <description>: statistics on Nucleosome Dynamics analysis</description>     
 <requirements>
 <requirement type="binary">docker</requirement>
 </requirements>
 <command>
<![CDATA[
    ln -f -s $output_gw_png_file $output_gw_png_file\.png;	  
    docker run -v $__root_dir__/database/files:$__root_dir__/database/files -v /data:/data  -v /tmp:/tmp -u `id -u`:`id -g` mmbirb/nucldyn nucDyn_stats --input $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
	--out_genes $output_genes_csv_file  --out_gw $output_gw_png_file\.png;
	rm $output_gw_png_file\.png 
]]>
  </command>
  <inputs>
    <param name="gff_file" type="data" format="gff" label="Input Nucleosome Calls"/>
    <conditional name="assembly">
            <param name="source" type="select" label="Select a built-in reference genome or use one from your history" help="Taking from each assembly their chromosome sizes and their annotated genes.">
                <option value="buildin" selected="True">Use a built-in genome</option>
                <option value="history">Use a genome from the history</option>
            </param>
            <when value="buildin">
                <param name="ref_genome_gff_buildin" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
                    <options from_file="nucldyn_publicdata.loc">
                        <column name="name" index="2"/>
                        <column name="value" index="4"/>
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="ref_genome_gff_history" type="data" format="gff" label="Select gene annotations for your reference genome" help="Check below the documentation for lerning about the file format."/>
            </when>
       </conditional>   
</inputs>
  <outputs>
    <data format="csv" name="output_genes_csv_file" label="ND__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.genes.csv" />
    <data format="png" name="output_gw_png_file" label="ND__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gw.png" />
  </outputs>
<tests>
	<test>
		<param name="gff_file" value="ND__cellcycleG2_chrII_cellcycleM_chrII.gff" />
		<param name="ref_genome_gff_buildin" value="genes.gff" />
		<output name="output_genes_csv_file" file="ND__stats__cellcycleG2_chrII_cellcycleM_chrII.genes.csv" />
		<output name="output_gw_png_file" file="ND__stats__cellcycleG2_chrII_cellcycleM_chrII.gw.png" />
	</test>
</tests>
     <help>
.. class:: warningmark


Check the documentation for setting the tool parameters at the source code repository: http://mmb.irbbarcelona.org/gitlab/NuclDynamics/docker 

-----

.. image:: ${static_path}/images/NucleosomeDynamicsLogo.png 
    :height: 80 
    :width: 200

**http://mmb.irbbarcelona.org/NucleosomeDynamics**
   </help>
   <citations>
        <citation type="bibtex">
@misc{github,
  author = {Buitrago D},
  year = {2019},
  title = {Nucleosome Dynamics suite: containerized installation},
  publisher = {GitLab},
  journal = {GitLab repository},
  url = {http://mmb.irbbarcelona.org/gitlab/NuclDynamics/docker},
}</citation>
 </citations>
</tool>