--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ChipSeqRatioDef.xml	Thu Sep 05 09:04:56 2019 -0400
@@ -0,0 +1,60 @@
+<tool id="chip_seq_ratio_1" name="Chip-Seq Mapper" version="0.1.1">
+  <stdio>
+    <exit_code range="1:" level="fatal" description="Error"/>
+  </stdio>
+    <description></description>
+    <requirements>
+      <requirement type="package">r-base64enc</requirement>
+      <requirement type="package">r-r2html</requirement>
+      <requirement type="package">blast</requirement>
+    </requirements>
+    <command interpreter="python3">
+	ChipSeqRatioAnalysis.py 
+	--ChipSeq=${ChipFile}
+	--InputSeq=${InputFile}
+	--Contigs=${ContigFile}
+	--output=${OutputFile}
+	--html=${ReportFile}
+	--max_cl=${MaxCl}
+  --bitscore=$bitscore
+  --nproc=16
+    </command>
+
+    <inputs>
+        <param name="ChipFile" label="Chip Sequences" type="data" format="fasta" help="NGS data in fasta format"/> 
+	<param name="InputFile" label="Input Sequences" type="data" format="fasta" help="NGS data in fasta format"/>
+	<param name="ContigFile" label="Reference - Contig Sequences" type="data" format="fasta"
+	       help="Contigs obtained from RepeatExplorer clustering pipeline in fasta file"/> 
+	<param name="MaxCl" label="Number of clusters to be shown in graph" type="integer" value="200"/>   
+	<param name="bitscore" label="Minimum bit score threshold" type="integer" value="30" help="All similarity hits with lower bit score will not be considered for ChIP/Input ratio calculation"/>   
+    </inputs>
+    <outputs>
+    	<data name="OutputFile" format="tabular"/>
+	<data name="ReportFile" format="html"/> 
+    </outputs>
+
+    <help>
+**What it does**
+
+Analysis of NGS sequences from Chromatin Imunoprecipitation. ChiP
+and Input reads are mapped to contigs obtained from graph based
+repetitive sequence clustering(`Novak et al. 2013`__) to enriched repeats. Reads from input
+and ChIP should be ideally short illumina reads with uniform length
+above 80 nt. It is sufficiant to use about 1 milion of reads for both Input and Chip.
+This method was first used in (`Neumann et al. 2012`__) for
+identification of repetitive sequences associated with cetromeric
+region. If you use this method, reference:
+
+
+`PLoS Genet. Epub 2012 Jun 21. Stretching the rules: monocentric chromosomes with multiple centromere domains. Neumann P, Navrátilová A, Schroeder-Reiter E, Koblížková A, Steinbauerová V, Chocholová E, Novák P, Wanner G, Macas J.`__.
+
+.. __: http://bioinformatics.oxfordjournals.org/content/29/6/792.full
+ 
+.. __: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002777
+.. __: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002777
+      
+    </help>
+
+</tool>
+
+