--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/findSNP/findSNPs.xml	Sun Jun 11 10:00:48 2017 -0400
@@ -0,0 +1,38 @@
+<tool id="SNPs" name="SNPs" version="1.16.2">
+  <requirements>
+   <requirement name="package_r_3_2_1" type="package" version="3.2.1">R</requirement>
+</requirements>
+<stdio>
+   <exit_code range="1:" />
+</stdio>
+  <command> Rscript $__tool_directory__/findSNPs.R "$input" "$output" </command>
+  <inputs>
+    <param name="input" format="Rdata"label="GenomicRatioSet.Rdata" help="e.g. 'GSE51547'"/>
+  </inputs>
+  <outputs>
+    <data format="txt" name="output" label="SNPs.txt"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="test">
+      <element name="test-data">
+           <collection type="data">
+                <element format="Rdata" name="input" label="test-data/GenomicRatioSet.Rdata"/>
+          </collection>
+        </element>
+        </param>
+        <output format="txt" name="output" label="test-data/findSNP.txt"/>
+        </test>
+    </tests>
+  <help>
+**What it does**
+SNPs inside the probe body or at the nucleotide extension can have important consequences on the downstream analysis, these tool offers the possibility to remove such probes
+**Input**
+GenomicRatioSet object e.g. output from getGRsetFromGEO tool
+**Output**
+Text file with columns containing the SNP information about the probes
+</help>
+<citations>
+<citation type="doi">10.1093/bioinformatics/btu049</citation>
+</citations>
+</tool>