diff findSNPs/findSNPs.xml @ 2:15bb9a34d924 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/findSNPs/findSNPs.xml	Sun Jun 11 11:49:04 2017 -0400
@@ -0,0 +1,39 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="findSNPs" name="findSNPs" version="1.16.2">
+<requirements>
+<requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
+</requirements>
+<stdio>
+<exit_code range="1:" />
+</stdio>
+  <command> Rscript $__tool_directory__/findSNPs.R "$input" "$output" </command>
+  <inputs>
+     <param name="input" type="RDdata" value="" label="Genomic Ratio Set" help="e.g. 'GRsetFromGEO tool output'"/>
+  </inputs>
+  <outputs>
+    <data format="text" name="output" label="findSNPs.txt"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="test">
+      <element name="test-data">
+          <collection type="data">
+                <element name="input" format="RData"  name="output" label="test-data/out.RData"> </element>
+          </collection>
+        </element>
+        </param>
+        <output type="data" format="text"  name="output" label="test-data/findSNPs.txt"/>
+        </test>
+    </tests>
+  <help>
+**What it does**
+Function To Retrieve The Chromosome And The Position Of Each SNP On A Given Affymetrix SNP Array
+**Input**
+GenomicRatioSet object
+**Output**
+Text file containing information on which probes contains SNPs
+  </help>
+  <citations>
+<citation type="doi">10.1093/bioinformatics/btu049</citation>
+  </citations>
+</tool>