| Previous changeset 12:1e048d0cda1d (2019-02-22) Next changeset 14:8833eedd24fb (2019-02-22) |
|
Commit message:
Uploaded |
|
added:
minfi_getcn.xml |
| b |
| diff -r 1e048d0cda1d -r db44217b3c5d minfi_getcn.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/minfi_getcn.xml Fri Feb 22 08:14:12 2019 -0500 |
| [ |
| @@ -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> |