changeset 53:5cab527307f9 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_maptogenome.xml	Fri Feb 22 11:12:57 2019 -0500
@@ -0,0 +1,43 @@
+<tool id="minfi_maptogenome" name="Minfi map to genome" version="@MINFI_VERSION@">
+    <description>mapping Ilumina methylation array data to the genome</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+  <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement>
+    </expand>
+    <command detect_errors="exit_code">
+    <![CDATA[
+     Rscript '$minfi_mtg_script'
+    ]]>
+    </command>
+    <configfiles>
+    <configfile name="minfi_mtg_script"><![CDATA[ 
+require("minfi", quietly = TRUE)
+require("IlluminaHumanMethylation450kanno.ilmn12.hg19", quietly = TRUE)
+
+RSet <- get(load('$rset'))
+
+GRSet <- mapToGenome(RSet)
+
+save(GRSet,file = '$grset')
+    ]]>
+    </configfile>
+    </configfiles>
+    <inputs>
+        <param type="data" name="rset" format="rdata" label="Methylation Data to Map" help="This class holds preprocessed data for Illumina methylation microarrays." />
+    </inputs>
+    <outputs>
+        <data name="grset" format="rdata" from_work_dir="GRSet.rdata" label= "Data Mapped To The Genome" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="rset" value="RatioSet.rdata"/>
+            <output name="grset" file="GRSet.rdata"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        This tool is mapping Ilumina methylation array data to the genome using 450k annotation package. Depending on the genome, not all methylation loci may have a genomic position. The output is an a GenomicRatioSet object.
+    ]]></help>
+    <expand macro="citations" />
+</tool>