--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nucleosome_prediction.xml	Tue Sep 27 10:02:29 2016 -0400
@@ -0,0 +1,65 @@
+<tool id="Nucleosome" name="Nucleosome Predictions" version="3.0">
+    <requirements>
+        <requirement type="package" version="3.0">nucleosome_prediction</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+      nucleosome_prediction.pl
+        -t Example
+        -s '$input'
+        -p predition_output
+        -tab
+        -c $c
+        -temp $temp
+        $raw_binding
+    ]]></command>
+
+    <inputs>
+        <param type="data" name="input" label="Input sequence file (.fasta format)" format="fasta" />
+        <param argument="-c" type="float" value="0.1"
+            label="Nucleosomes Concentration" help="Nucleosomes concentration: the default value = 0.1"/>
+        <param argument="-temp" type="integer" value="1"
+            label="Temperature Scaling" help="Temperature scaling: the default value = 1"/>
+        <param argument="-raw_binding" type="boolean" truevalue="-raw_binding" falsevalue=""
+            label="Raw Binding" help="Raw Binding: When 'No' (default), then the output will be the default average occupancy probabilities. When 'yes', then the output will be  the raw nucleosome binding log-ratio per basepair"/>
+    </inputs>
+
+    <outputs>
+        <data name="output" format="tabular" from_work_dir="predition_output.tab" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input" value="input.fa" ftype="fasta"/>
+            <param name="raw_binding" value="True"/>
+            <output name="output" file="npresults.tab" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="input" value="input.fa" ftype="fasta"/>
+            <param name="c" value="0.1"/>
+            <param name="temp" value="1"/>
+            <output name="output" file="npresultsf.tab" ftype="tabular"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+
+    **What it does**
+    This tool allows you to submit a genomic sequence and to recieve a prediction of the nucleosomes positions on it, based on the nucleosome-DNA interaction model that we developed in these papers:
+    This version (version 3) is applicable to all species.
+
+    The tool takes a sequence .fasta file and finds all positions of the matrices above the background
+
+    ]]></help>
+
+    <citations>
+
+        <citation type="bibtex">
+          @MISC{10.1038/nature07667,
+                      DOI = {10.1038/nature07667},
+                      note = {The DNA-encoded nucleosome organization of a eukaryotic genome}
+                      year = "2009"
+                  }
+        </citation>
+    </citations>
+
+</tool>