changeset 11:7e6f943984b0 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/minfi_getsnp.xml	Fri Feb 22 08:13:32 2019 -0500
@@ -0,0 +1,44 @@
+<tool id="minfi_getsnp" name="Minfi Get SNP" version="@MINFI_VERSION@">
+    <description>retrieve the chromosome and the position of each SNP</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'))
+
+snps <- getSnpInfo(GRSet)
+
+write.table(snps, '$table')
+  ]]> 
+    </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="table" format="txt" label="SNPInfo Table"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="grset" value="GRSet.rdata"/>
+            <output name="table" file="SNPInfo_Table.txt"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        This tool is a version of the getSnpInfo adapted to retrieve the chromosome and the position of each SNP on a given Affymetrix SNP Array.
+    ]]></help>
+    <expand macro="citations" />
+</tool>
+