comparison minfi_getcn.xml @ 56:ef70ed848cce draft

Uploaded
author kpbioteam
date Fri, 22 Feb 2019 11:14:02 -0500
parents db44217b3c5d
children 9c6fbb7d5a2a
comparison
equal deleted inserted replaced
55:ca52f81202eb 56:ef70ed848cce
1 <tool id="minfi_getcn" name="Minfi Get CN" version="@MINFI_VERSION@">
2 <description>get the coordinating node associated with this D1Client object</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code">
8 <![CDATA[
9 Rscript '$minfi_mset_script'
10 ]]>
11 </command>
12 <configfiles>
13 <configfile name="minfi_mset_script"><![CDATA[
14 require("minfi", quietly = TRUE)
15 MSet <- get(load('$mset'))
16
17 CN <- getCN(MSet)
18
19 write.table(CN, '$matrix')
20 ]]>
21 </configfile>
22 </configfiles>
23 <inputs>
24 <param type="data" name="mset" format="rdata" label="MethylSet" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic
25 location."/>
26 </inputs>
27 <outputs>
28 <data name="matrix" format="txt" label="CN Value Matrix" />
29 </outputs>
30 <tests>
31 <test>
32 <param name="mset" value="MethylSet.rdata"/>
33 <output name="matrix" file="CN_Value_Matrix.txt"/>
34 </test>
35 </tests>
36 <help><![CDATA[
37 This tool output copy number of the values defined as the sum of the methylation and unmethylation channel for each probed CpG site.
38 ]]></help>
39 <expand macro="citations" />
40 </tool>