# HG changeset patch
# User kpbioteam
# Date 1550851838 18000
# Node ID 9f6e5d00629be99b7bf366c184e1f502feaf95a4
# Parent  0d296a6a18d3dd727af270b7d6379573116af05a
Uploaded

diff -r 0d296a6a18d3 -r 9f6e5d00629b minfi_qc.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_qc.xml	Fri Feb 22 11:10:38 2019 -0500
@@ -0,0 +1,48 @@
+<tool id="minfi_qc" name="Minfi qc" version="@MINFI_VERSION@">
+    <description>provides a simple quality control matrix and plot</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+     <expand macro="requirements" />
+    <command detect_errors="exit_code">
+    <![CDATA[
+        Rscript '$read_qc_script'
+     ]]>
+    </command>
+    <configfiles>
+      <configfile name="read_qc_script">
+    <![CDATA[
+require("minfi", quietly = TRUE)
+
+MSet <- get(load('$MethylSet'))
+
+qc <- getQC(MSet)
+
+write.table(qc, '$qctab')
+
+png('$qcpng')
+plotQC(qc)
+dev.off()
+    ]]>
+     </configfile>
+        </configfiles>
+    <inputs>
+        <param type="data" name="MethylSet" format="rdata" label="MethylSet" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic
+location."/>
+    </inputs>
+    <outputs>
+        <data name="qctab" format="txt" label="Quality Control Report"/>
+        <data name="qcpng" format="png" label="Quality Control Plot"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="MethylSet" value="MethylSet.rdata"/>
+            <output name="qctab" file="Quality_Control_Report.txt"/>
+            <output name="qcpng" file="Quality_Control_Plot.png" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Quality Control (QC) outputs plot of the log median intensity in both the methylated (M) and unmethylated (U) channels. When plotting these two medians against each other the good samples cluster together, while failed samples tend to separate and have lower median intensities.
+    ]]></help>
+    <expand macro="citations" />
+</tool>