# HG changeset patch
# User kpbioteam
# Date 1550841231 18000
# Node ID 1e048d0cda1de088a908b5a68d639ba8a57a3c36
# Parent  7e6f943984b06536057d7165ba79939ca933af1a
Uploaded

diff -r 7e6f943984b0 -r 1e048d0cda1d minfi_getm.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_getm.xml	Fri Feb 22 08:13:51 2019 -0500
@@ -0,0 +1,41 @@
+<tool id="minfi_getM" name="minfi Get M" version="@MINFI_VERSION@">
+    <description>returns the Fisher information corresponding to a model and a design</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code">
+    <![CDATA[
+     Rscript '$minfi_m_script'
+    ]]>
+    </command>
+    <configfiles>
+    <configfile name="minfi_m_script"><![CDATA[
+require("minfi", quietly = TRUE)
+MSet <- get(load('$mset'))
+
+m <- getM(MSet)
+
+write.table(m, '$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="M Value Matrix"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="mset" value="MethylSet.rdata"/>
+            <output name="matrix" file="M_Value_Matrix.txt"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        This tool output M value the logit representation of methylation level ratio based on intensities between methylated and unmethylated alleles in each probed CpG site.
+    ]]></help>
+    <expand macro="citations" />
+</tool>
+