<tool id="nucDyn" name="Nucleosome Dynamics" version="0.1">
 <description>: detection of local changes in the position of nucleosomes, observed between two reference nucleosome maps </description>     
  <requirements>
  <requirement type="binary">docker</requirement>
  </requirements>
  <command>
<![CDATA[	  
    ln -f -s $output_bw_file $output_bw_file\.bw; 
    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 nucDyn --input1 $rdata_file --input2 $rdata_file2 --calls1 $gff_file --calls2 $gff_file2  --outputGff $output_gff_file --outputBigWig $output_bw_file\.bw 
    #if $assembly.source == "buildin":
	--genome ${assembly.ref_chrom_sizes_buildin}
    #else if $assembly.source == "history":
    	--genome ${assembly.ref_chrom_sizes}
    #end if

    #if $maxdiff
                --maxDiff $maxdiff
    #end if
    #if $maxlen
                --maxLen $maxlen
    #end if
    #if $minreads
                --shift_min_nreads $minreads
    #end if
    #if $threshold
    		--shift_threshold $threshold
    #end if
    #if $minread
                --indel_min_nreads $minread 
    #end if 
    #if $indthreshold
    		--indel_threshold $indthreshold
    #end if
	
    --range $range --equal_size $equal --readSize $readsize ;
    rm $output_bw_file\.bw 
]]>  
 </command>
  <inputs>
    <param name="rdata_file"  type="data" format="rdata" label="Condition 1: MNase-seq reference reads (Rdata)"     help="Input BAM from MNase-seq in RData format  for the initial state to be compared."/>
    <param name="gff_file"    type="data" format="gff"   label="Condition 1: MNase-seq reference nucleosomes (GFF)" help="Nucleosome calls in GFF format as obtained from nucleR for the initial state to be compared"/>
    <param name="rdata_file2" type="data" format="rdata" label="Condition 2: MNase-seq final reads (Rdata)"         help="Input BAM from MNase-seq in RData format  for the final state to be compared. "/>
    <param name="gff_file2"   type="data" format="gff"   label="Condition 2: MNase-seq final nucleosomes (GFF)"     help="Nucleosome calls in GFF format as obtained from nucleR for the final state to be compared."/>
    <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.">
	        <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_chrom_sizes_buildin" type="select" label="Select reference genome (Chrom sizes)" help="Select chromosome size 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="3"/>
		    </options>
		</param>
	    </when>
	    <when value="history">
    		<param name="ref_chrom_sizes" type="data" format="txt" label="Reference genome (Chrom sizes)" help="Upload chromosome size for your reference genome. Check below the documentation for learning about the file format."/> 
	    </when>
       </conditional>
    <param name="range"  type="text" value="All" label="Range" help="Genomic region to be analyzed: whole genome ('all'), entire chromosome (chromosome name i.e. 'chrX'), or region of a chromosome."/>  
    <param name="maxdiff" type="integer" value="70" label="Maximum Diff" optional="True" help="Maximum distance between the dyads of two reads that allows them to still be considered a *shift*. If unspecified but *readSize* is specified, it will be set to the half of readSize. If neither of them is specified, it will be set to 70."/>
    <param name="maxlen"  type="integer" value="140" label="Maximum Lenght" optional="True" help="Used in the preliminar filtering. Reads longer than this number will be filtered out."/>
    <param name="minreads"  type="integer" value="3" label="Shift minimum num. reads" optional="True" help="Minimum number of reads in a 'SHIFT +' or a 'SHIFT -' hotspot."/>
    <param name="threshold" type="float"    value="0.1" label="Shifts threshold" optional="True" help="Minimum score for a 'SHIFT +' or a 'SHIFT -' hotspot."/>
    <param name="minread"   type="integer" value="3" label="Indels minimum num. reads" optional="True" help="Minimum number of reads in an 'INCLUSION +' or a 'DELETION -' hotspot" />
    <param name="indthreshold"  type="float" value="0.05" label="Indels threshold" optional="True" help="Minimum score for an 'INCLUSION' or a 'DELETION' hotspot." />
    <param name="equal" type="boolean" checked="false" label="Use Equal Size" optional="True" help="Set all fragments to the same size."/>
    <param name="readsize" type="integer" value="140" label="Read Size" help="Length to which all reads will be set in case `equalSize` is `TRUE`. It is ignored when `equalSize` is set to `FALSE`." />
  </inputs>
  <outputs>
    <data format="gff" name="output_gff_file" label="ND__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}_${os.path.splitext(($gff_file2.name.split('__'))[1])[0]}.gff"/>
    <data format="bigwig" name="output_bw_file" label="ND__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}_${os.path.splitext(($gff_file2.name.split('__'))[1])[0]}.bw"/>
  </outputs>
 <tests>
	 <test>
		<param name="rdata_file" value="readBAM__cellcycleG2_chrII.RData" />
		<param name="rdata_file2" value="readBAM__cellcycleM_chrII.RData" />
		<param name="gff_file" value="NR__cellcycleG2_chrII.gff"  />
		<param name="gff_file2" value="NR__cellcycleM_chrII.gff" />
		<param name="ref_chrom_sizes_buildin" value="/data/nucldyn_publicdata/refGenomes/R64-1-1/R64-1-1.fa.chrom.sizes" />
		<param name="range" value="All" />
		<param name="maxdiff" value="70" />
		<param name="maxlen" value="140" />
		<param name="minreads" value="3" />
		<param name="threshold" value="0.1" />
		<param name="minread" value="3" />
		<param name="indthreshold" value="0.05" />
		<output name="output_gff_file" file="ND__cellcycleG2_chrII_cellcycleM_chrII.gff" />
		<output name="output_bw_file" file="ND__cellcycleG2_chrII_cellcycleM_chrII.bw" />
	</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>