--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nucDyn_stats.xml	Fri Apr 12 05:28:43 2019 -0400
@@ -0,0 +1,75 @@
+<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/nucleosome-dynamics 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 $output_gw_png_file\.png 
+]]>
+  </command>
+  <inputs>
+    <param name="gff_file" type="data" format="gff" label="Nucleosome Architecture (GFF)" help="Annotation of nucleosome changes as produced by Nucleosome Dynamics"/>
+    <conditional name="assembly">
+            <param name="source" type="select" label="Select a built-in reference genome or use one from your history" help="Taking from each assembly their annotated genes.">
+                <option value="buildin" selected="True">Use a built-in genome</option>
+                <option value="history">Use a genome from the history</option>
+            </param>
+            <when value="buildin">
+                <param name="ref_genome_gff_buildin" type="select" label="Select reference genome (Genes)" help="Select gene annotations for your reference genome. If your genome of interest is not listed, contact the Galaxy team.">
+                    <options from_file="nucldyn_publicdata.loc">
+                        <column name="name" index="2"/>
+                        <column name="value" index="4"/>
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="ref_genome_gff_history" type="data" format="gff" label="Reference genome (Genes)" help="Upload gene annotations for your reference genome. Check below the documentation for learning about the file format."/>
+            </when>
+       </conditional>   
+</inputs>
+  <outputs>
+    <data format="csv" name="output_genes_csv_file" label="ND__stats__${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="/data/nucldyn_publicdata/refGenomes/R64-1-1/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>
+ .. 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>