<tool id="nucleR" name="NucleR" version="0.1">
  <description>: analyze aligned BAM files from MNAse (in RData format)</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 nucleR --input $rdata_file --output $output_gff_file --type $seq_type --width $width --minoverlap $minoverlap --dyad_length $dyad_length --hthresh $hthres --wthresh $wthres --pcKeepComp $pcKeepComp --fdrOverAmp $fdrOverAmp  --trim $trim --fragmentLen $fragmentLen 
	#if $threshold.is == "absolute":
        	--thresholdValue ${threshold.thresholdValue}
      	#else if $threshold.is == "percentage":
        	--thresholdPercentage ${threshold.thresholdPercentage}
	#end if
	#if $chr
        	--chr $chr
	#end if 
	#if $start
        	--start $start
	#end if 
	#if $end
        	--end $end
	#end if 
	#if $comp
                --components $comp
        #end if
]]>
  </command>
  <inputs>
    <param name="rdata_file" type="data" format="rdata" label="Input MNase-seq/ATAC-seq reads (RData)" help="Input BAM file in RData format as generated by readBAM."/>
    <param name="seq_type" type="select" label="Type of sequence reads">
      <option value="paired">Paired</option>
      <option value="single">Single</option>
    </param>
    <param name="width" size="4" type="integer" value="147" label="Width (bp)" help="Size of each nucleosome."/>  
    <param name="minoverlap"   type="integer" value="80" label="Minimum Overlap (bp)" help="Minimum overlap between two nucleosomes for merging them."/>
    <param name="dyad_length"  type="integer" value="50" label="Dyad length (bp)" help="Lenght of the reads that should be used for nucleosome calling to define the dyad of the nucleosomes keeping the number of bases around the center of the read."/>
    <param name="fragmentLen"  type="integer" value="170" label="Fragment Length (bp)" help="Maximum fragment length allowed (bp)" optional="True" />
    <param name="chr"          type="text"    value="" label="Chromosome"  optional="True" help="Chromosome to consider for the analysis in the given input file."/>
    <param name="start"        type="integer" value="" label="Start" optional="True" help="Start genomic position to consider for the analysis in the given input file."/>
    <param name="end"          type="integer" value="" label="End" optional="True" help="End genomic position to consider for the analysis in the given input file."/>
    <param name="comp"          type="integer" value="1" label="Components" optional="True" help="Number of negative binomials that will be used to filter duplicated reads."/>
    <conditional name="threshold">
            <param name="is" type="select" label="Background threshold" help="Minimum number of reads (Coverage) to call a nucleosome. Can be given as a percentage, or an absolute number of reads.">
                <option value="percentage" selected="True">use a percentage</option>
                <option value="absolute">use a number of reads</option>
            </param>
            <when value="absolute">
    		<param name="thresholdValue" type="integer" value="10" label="Bakground level (reads)" help="Absolute value to filter out nucleosome calls. It is the minimum number of reads (coverage) in a nucleosome call expressed as reads per million of mapped reads."/>
            </when>
            <when value="percentage">
		    <param name="thresholdPercentage" type="float" value="35" label="Background level (%)" help="Percentile of coverage in the experiment used as threshold to filter out nucleosome calls (i.e., 25% would mean that only peaks with coverage in the 1st quantile would be considered)"/>
            </when>
    </conditional>
    <param name="hthres"       type="float"   value="0.4" label="Height Threshold" help="Height threshold (between 0 and 1) to classify a nucleosome as fuzzy (class=F) or well-positioned ( class=W) according to the number of reads at the dyad. Nucleosomes below this value will be defined as fuzzy."/>
    <param name="wthres"       type="float"   value="0.6" label="Width Threshold" help="Width threshold (between 0 and 1) to classify a nucleosome as fuzzy (class=F) or well-positioned (class=W) according to the dispersion of the reads around the dyad."/>
    <param name="fdrOverAmp"   type="float"   value="0.05" label="fdrOverAmp" help="Threshold to filter over-amplified reads , as defined in filterDuplReads function of htSetqTools R package."/>
    <param name="pcKeepComp"   type="float"   value="0.02" label="Coverage Smoothing" help="Parameter used in the smoothing when Fourier transformation is applied. Number of components to select with respect to the total size of the sample. Allowed values are numeric (in range 0:1) for manual setting, or auto for automatic detection."/>
    <param name="trim"         type="integer" value="50" label="Trim" help="Number of basepairs to keep from each read (or to extend in case it is larger than the read width)."/>
  </inputs>
  <outputs>
    <data format="gff" name="output_gff_file" label="NR__${os.path.splitext(($rdata_file.name.split('__'))[1])[0]}.gff" />
</outputs>
  <tests>
      <test>
          <param name="rdata_file" value="readBAM__cellcycleM_chrII.RData" />
	  <param name="seq_type" value="paired" />
          <param name="width" value="147" />
	  <param name="minoverlap" value="80" />
	  <param name="dyad_length" value="50" />
	  <param name="thresholdPercentage" value="35" />
	  <param name="hthres" value="0.4" />
	  <param name="wthres" value="0.6" />
	  <param name="pcKeepComp" value="0.02" />	  
	  <output name="output_gff_file" file="NR__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>