Mercurial > repos > kpbioteam > ewastools
comparison minfi_getcn.xml @ 13:db44217b3c5d draft
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| author | kpbioteam |
|---|---|
| date | Fri, 22 Feb 2019 08:14:12 -0500 |
| parents | |
| children | 9c6fbb7d5a2a |
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| 12:1e048d0cda1d | 13:db44217b3c5d |
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| 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> |