diff minfi_rset.xml @ 0:bb6c8d38fad1 draft default tip

planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_rset.xml	Fri Jun 07 14:14:49 2019 -0400
@@ -0,0 +1,40 @@
+<tool id="minfi_rset" name="Minfi Rset" version="@MINFI_VERSION@">
+    <description>store Beta values and/or M values</description>
+      <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code">
+    <![CDATA[
+        Rscript '$read_rset_script'
+     ]]>
+   </command>
+    <configfiles>
+        <configfile name="read_rset_script">
+<![CDATA[
+require("minfi", quietly = TRUE)
+MSet <- get(load('$mset'))
+
+RSet <- ratioConvert(MSet, what = "both", keepCN = TRUE)
+
+save(RSet,file = '$rset')  
+    ]]> </configfile>
+    </configfiles>
+    <inputs>
+        <param type="data" name="mset" format="rdata" label="MethylSet"
+            help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic location."/>
+    </inputs>
+    <outputs>
+        <data name="rset" format="rdata" label="RatioSet"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="mset" value="MethylSet.rdata"/>
+            <output name="rset" file="RatioSet.rdata"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        RSet class holds preprocessed data for Illumina methylation microarrays. It contains respectively the Beta value matrix, M value matrix and the Copy Number matrix.
+    ]]></help>
+    <expand macro="citations" />
+</tool>