changeset 56:ef70ed848cce draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_getcn.xml	Fri Feb 22 11:14:02 2019 -0500
@@ -0,0 +1,40 @@
+<tool id="minfi_getcn" name="Minfi Get CN" version="@MINFI_VERSION@">
+    <description>get the coordinating node associated with this D1Client object</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code">
+    <![CDATA[
+     Rscript '$minfi_mset_script'
+    ]]>
+    </command>
+    <configfiles>
+    <configfile name="minfi_mset_script"><![CDATA[
+require("minfi", quietly = TRUE)
+MSet <- get(load('$mset'))
+
+CN <- getCN(MSet)
+
+write.table(CN, '$matrix')
+]]> 
+    </configfile>
+    </configfiles> 
+    <inputs>
+        <param type="data" name="mset" format="rdata" label="MethylSet" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic
+location."/>
+    </inputs>
+    <outputs>
+        <data name="matrix" format="txt" label="CN Value Matrix" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="mset" value="MethylSet.rdata"/>
+            <output name="matrix" file="CN_Value_Matrix.txt"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        This tool output copy number of the values defined as the sum of the methylation and unmethylation channel for each probed CpG site.
+    ]]></help>
+    <expand macro="citations" />
+</tool>