changeset 57:a63802ce1d26 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_getbeta.xml	Fri Feb 22 11:15:28 2019 -0500
@@ -0,0 +1,41 @@
+<tool id="minfi_getbeta" name="Minfi Get Beta" version="@MINFI_VERSION@">
+    <description>obtain Beta value matrix</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code">
+    <![CDATA[
+     Rscript '$minfi_beta_script'
+    ]]>
+    </command>
+    <configfiles>
+    <configfile name="minfi_beta_script"><![CDATA[
+require("minfi", quietly = TRUE)
+
+MSet <- get(load('$mset'))
+
+beta <- getBeta(MSet)
+
+write.table(beta, file = '$matrix', quote = FALSE, sep = "\t")
+         ]]> 
+    </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="bedgraph" label="Beta Values Matrix"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="mset" value="MethylSet.rdata"/>
+            <output name="matrix" file="Beta_Values_Matrix.bedgraph"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        This tools outputs an interval file of methylation indices (beta values), which are continuous values between 0 and 1 representing the ratio/fraction of the intensity of the methylated-probe signal to the total signal intensity for each probed CpG site.
+    ]]></help>
+    <expand macro="citations" />
+</tool>