# HG changeset patch
# User kpbioteam
# Date 1518355729 18000
# Node ID a003221d59ccb09e0d8ebc67922463a351842431

planemo upload for repository https://github.com/kpbioteam/minfi_ppnoob commit 3301cca8b83e0539831cc8639f451e0a58018890-dirty

diff -r 000000000000 -r a003221d59cc RGSet.rdata
Binary file RGSet.rdata has changed
diff -r 000000000000 -r a003221d59cc minfi_ppnoob.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_ppnoob.R	Sun Feb 11 08:28:49 2018 -0500
@@ -0,0 +1,12 @@
+require("minfi", quietly = TRUE)
+
+args <- commandArgs(trailingOnly = TRUE)
+
+input = args[1]
+output = args[2]
+
+RGSet <- get(load(input))
+
+MSet <- preprocessNoob(RGSet)
+
+save(MSet,file = output)
diff -r 000000000000 -r a003221d59cc minfi_ppnoob.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_ppnoob.xml	Sun Feb 11 08:28:49 2018 -0500
@@ -0,0 +1,29 @@
+<tool id="minfi_ppnoob" name="minfi_ppnoob" version="0.1.0">
+    <description>implements the noob background subtraction method with dye-bias normalization</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 ${__tool_directory__}/minfi_ppnoob.R "$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="noob.rdata"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Background subtraction method estimates background noise from the out-of-band probes and remove it for each sample separately, while the dye-bias normalization utilizes a subset of the control probes to estimate the dye bias.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btu049</citation>
+    </citations>
+</tool>
\ No newline at end of file
diff -r 000000000000 -r a003221d59cc noob.rdata
Binary file noob.rdata has changed
diff -r 000000000000 -r a003221d59cc test-data/RGSet.rdata
Binary file test-data/RGSet.rdata has changed
diff -r 000000000000 -r a003221d59cc test-data/noob.rdata
Binary file test-data/noob.rdata has changed