diff minfi_mset.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_mset.xml	Fri Jun 07 14:14:49 2019 -0400
@@ -0,0 +1,42 @@
+<tool id="minfi_mset" name="Minfi Mset" version="@MINFI_VERSION@">
+    <description>Create objects contains CpGs signals</description>
+     <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code">
+    <![CDATA[
+     Rscript '$minfi_mset_script'
+    ]]>
+    </command>
+    <configfiles>
+    <configfile name="minfi_mset_script"><![CDATA[
+require("minfi", quietly = TRUE)
+
+RGSet <- get(load('$RGChannelSet'))
+
+MSet <- preprocessRaw(RGSet)
+
+save(MSet,file = '$MethylSet')
+
+     ]]> 
+    </configfile>
+    </configfiles>
+    <inputs>
+        <param type="data" name="RGChannelSet" format="rdata" label="RGChannelSet"
+            help="These classes represents raw (unprocessed) data from a two color micro array; specifically an Illumina methylation array."/>
+    </inputs>
+    <outputs>
+        <data name="MethylSet" format="rdata" label="MethylSet" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="RGChannelSet" value="RGChannelSet.rdata"/>
+            <output name="MethylSet" file="MethylSet.rdata"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        This tool is transforming a class representing raw (unprocessed) data from a two color micro array - RGChannelSet into a class holding preprocessed data for Illumina methylation microarrays, mapped to genomic location - MethylSet. 
+    ]]></help>
+    <expand macro="citations" />
+</tool>