# HG changeset patch
# User kpbioteam
# Date 1550841105 18000
# Node ID 4f34e3f73ebfd9154bb852743fa83c64b6573e3d
# Parent  ab6e72fdf3509d40ad4dedb8bf25d4a5fb0a7bc0
Uploaded

diff -r ab6e72fdf350 -r 4f34e3f73ebf minfi_qc.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_qc.xml	Fri Feb 22 08:11:45 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>