# HG changeset patch
# User kpbioteam
# Date 1518352545 18000
# Node ID 41ab8ba3a9013671b7eb03d33e81f3ed003f9d39

planemo upload for repository https://github.com/kpbioteam/minfi_ppquantile commit 93ac44e4428f7560ef032adcf5749ada58d15f57-dirty

diff -r 000000000000 -r 41ab8ba3a901 RGSet.rdata
Binary file RGSet.rdata has changed
diff -r 000000000000 -r 41ab8ba3a901 minfi_ppquantile.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_ppquantile.R	Sun Feb 11 07:35:45 2018 -0500
@@ -0,0 +1,15 @@
+require("minfi", quietly = TRUE)
+
+args <- commandArgs(trailingOnly = TRUE)
+
+input = args[1]
+output = args[2]
+
+RGSet <- get(load(input))
+
+GRSet <- preprocessQuantile(RGSet, fixOutliers = TRUE,
+  removeBadSamples = TRUE, badSampleCutoff = 10.5,
+  quantileNormalize = TRUE, stratified = TRUE, 
+  mergeManifest = FALSE, sex = NULL)
+
+save(GRSet,file = output)
diff -r 000000000000 -r 41ab8ba3a901 minfi_ppquantile.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_ppquantile.xml	Sun Feb 11 07:35:45 2018 -0500
@@ -0,0 +1,29 @@
+<tool id="minfi_ppquantile" name="minfi_ppquantile" version="0.1.0">
+    <description>implements stratified quantile normalization preprocessing</description>
+    <requirements>
+        <requirement type="package" version="1.24.0">bioconductor-minfi</requirement>
+        <requirement type="package" version="0.4.0">bioconductor-illuminahumanmethylation450kmanifest</requirement>
+        <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript ${__tool_directory__}/minfi_ppquantile.R "$input1" "$output1"
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="rdata" />
+    </inputs>
+    <outputs>
+        <data name="output1" format="rdata" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="RGSet.rdata"/>
+            <output name="output1" file="quantile.rdata"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        The normalization procedure is applied to the Meth and Unmeth intensities separately. The distribution of type I and type II signals is forced to be the same by first quantile normalizing the type II probes across samples and then interpolating a reference distribution to which we normalize the type I probes. Since probe types and probe regions are confounded and we know that DNAm distributions vary across regions we stratify the probes by region before applying this interpolation.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btu049</citation>
+    </citations>
+</tool>
\ No newline at end of file
diff -r 000000000000 -r 41ab8ba3a901 quantile.rdata
Binary file quantile.rdata has changed
diff -r 000000000000 -r 41ab8ba3a901 test-data/RGSet.rdata
Binary file test-data/RGSet.rdata has changed
diff -r 000000000000 -r 41ab8ba3a901 test-data/quantile.rdata
Binary file test-data/quantile.rdata has changed