| Previous changeset 55:ca52f81202eb (2019-02-22) Next changeset 57:a63802ce1d26 (2019-02-22) |
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minfi_getcn.xml |
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| diff -r ca52f81202eb -r ef70ed848cce minfi_getcn.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/minfi_getcn.xml Fri Feb 22 11:14:02 2019 -0500 |
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| @@ -0,0 +1,40 @@ +<tool id="minfi_getcn" name="Minfi Get CN" version="@MINFI_VERSION@"> + <description>get the coordinating node associated with this D1Client object</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"> + <![CDATA[ + Rscript '$minfi_mset_script' + ]]> + </command> + <configfiles> + <configfile name="minfi_mset_script"><![CDATA[ +require("minfi", quietly = TRUE) +MSet <- get(load('$mset')) + +CN <- getCN(MSet) + +write.table(CN, '$matrix') +]]> + </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="matrix" format="txt" label="CN Value Matrix" /> + </outputs> + <tests> + <test> + <param name="mset" value="MethylSet.rdata"/> + <output name="matrix" file="CN_Value_Matrix.txt"/> + </test> + </tests> + <help><![CDATA[ + This tool output copy number of the values defined as the sum of the methylation and unmethylation channel for each probed CpG site. + ]]></help> + <expand macro="citations" /> +</tool> |