Mercurial > repos > kpbioteam > ewastools
annotate minfi_getcn.xml @ 76:fef50103f6b3 draft
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
author | kpbioteam |
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date | Fri, 07 Jun 2019 08:57:26 -0400 |
parents | 9c6fbb7d5a2a |
children |
rev | line source |
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13 | 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> | |
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9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
13
diff
changeset
|
24 <param type="data" name="mset" format="rdata" label="MethylSet" |
9c6fbb7d5a2a
planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 9ce5c86f66f4a0cb64a1b8f48a2a937268b62064-dirty
kpbioteam
parents:
13
diff
changeset
|
25 help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic location."/> |
13 | 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> |