changeset 58:3eae88629318 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_dropsnp.xml	Fri Feb 22 11:16:23 2019 -0500
@@ -0,0 +1,45 @@
+<tool id="minfi_dropsnp" name="Minfi drop SNPs" version="@MINFI_VERSION@">
+    <description>drop the probes that contain either a SNP at the CpG interrogation or at the single nucleotide extension</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 '$minfi_snp_script'
+    ]]>
+    </command>
+    <configfiles>
+    <configfile name="minfi_snp_script"><![CDATA[
+require("minfi", quietly = TRUE)
+
+GRSet <- get(load('$grset'))
+
+GRSet <- dropLociWithSnps(GRSet, snps=c("SBE","CpG"), maf=0)
+
+save(GRSet,file =  '$grsetwithoutsnp')
+    ]]>
+    </configfile>
+    </configfiles>
+    <inputs>
+        <param type="data" name="grset" format="rdata" label="Genomic Ratio Set" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic
+location."/>
+    </inputs>
+    <outputs>
+        <data name="grsetwithoutsnp" format="rdata" from_work_dir="dropsnpGRSet.rdata" label="GRSet without SNPs"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="grset" value="GRSet.rdata"/>
+            <output name="grsetwithoutsnp" file="GRSet_without_SNPs.rdata"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+This tool is a version of the dropLociWithSnps function adapted to drop the probes that contain either a SNP at the CpG interrogation or at the single nucleotide extension (recommend).
+
+The output is a GenomicRatioSet object without SNPs loci.
+    ]]></help>
+    <expand macro="citations" />
+</tool>