diff minfi_ppnoob.xml @ 0:a003221d59cc draft default tip

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_ppnoob.xml	Sun Feb 11 08:28:49 2018 -0500
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+<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>
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