--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/stiffness_stats.xml	Fri Apr 12 05:28:43 2019 -0400
@@ -0,0 +1,77 @@
+<tool id="stiffness_stats" name="Stiffness Statistics" version="0.1">
+ <description>: gather gene and genome-wide statistics on nucleosome position stiffness</description>
+ <requirements>
+ <requirement type="binary">docker</requirement>
+ </requirements>
+ <command>
+<![CDATA[
+    ln -f -s $output_gw2_png_file $output_gw2_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 stiffness_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_csv_file --out_gw2 $output_gw2_png_file\.png;
+    rm $output_gw2_png_file\.png
+    ]]>
+ </command>
+  <inputs>
+    <param name="gff_file" type="data" format="gff" label="Stiffness (GFF)" help="Stiffness as annotated by Stiffness tool." />
+      <conditional name="assembly">
+            <param name="source" type="select" label="Select a built-in reference genome or use one from your history" help="Taking from each assembly their annotated genes.">
+                <option value="buildin" selected="True">Use a built-in genome</option>
+                <option value="history">Use a genome from the history</option>
+            </param>
+            <when value="buildin">
+                <param name="ref_genome_gff_buildin" type="select" label="Select reference genome (Genes)" help="Select gene annotations for your reference genome. If your genome of interest is not listed, contact the Galaxy team.">
+                    <options from_file="nucldyn_publicdata.loc">
+                        <column name="name" index="2"/>
+                        <column name="value" index="4"/>
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="ref_genome_gff_history" type="data" format="gff" label="Reference genome (Genes)" help="Upload gene annotations for your reference genome. Check below the documentation for learning about the file format."/>
+            </when>
+       </conditional>
+</inputs>
+  <outputs>
+    <data format="csv" name="output_genes_csv_file" label="STF__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.genes.csv" />
+    <data format="csv" name="output_gw_csv_file" label="STF__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gw.csv" />
+    <data format="png" name="output_gw2_png_file" label="STF__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gw2.png" />
+  </outputs>
+  <tests>
+	  <test>
+		  <param name="gff_file" value="STF__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="STF__stats__cellcycleM_chrII.genes.csv" />
+		  <output name="output_gw_csv_file" file="STF__stats__cellcycleM_chrII.gw.csv" />
+		  <output name="output_gw2_png_file" file="STF__stats__cellcycleM_chrII.gw2.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>