Mercurial > repos > kpbioteam > ewastools
annotate minfi_dmp.xml @ 74:53aaf097238c draft
planemo upload commit b4d745c28290bce5c7653886d70a63b001aaab19-dirty
author | kpbioteam |
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date | Thu, 16 May 2019 08:56:35 -0400 |
parents | 3d083550977f |
children |
rev | line source |
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17 | 1 <tool id="minfi_dmp" name="Minfi DMP" version="@MINFI_VERSION@"> |
2 <description>to find differentially methylated positions</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 Rscript '$minfi_dmp_script' | |
9 ]]></command> | |
10 <configfiles> | |
11 <configfile name="minfi_dmp_script"><![CDATA[ | |
12 require("minfi", quietly = TRUE) | |
13 | |
14 set <- get(load('$grset')) | |
15 | |
16 genomeranges <- as.data.frame(ranges(set)) | |
17 | |
18 beta <- getBeta(set) | |
19 | |
20 pheno <- read.table('$phenotype_table',skip=1) | |
21 | |
22 type <- '$phenotype' | |
23 | |
24 qCutoff <- as.numeric('$q_cutoff') | |
25 | |
26 shrinkVar <- '$variance_shrinkage' | |
27 | |
28 tab <- read.table('$ucsc_genome') | |
29 | |
30 tab <- tab[,-(11:14),drop=FALSE] | |
31 | |
64 | 32 tab <- tab[,c(1,4,5,10)] |
17 | 33 |
64 | 34 colnames(tab) <- c('chr','start','end','names') |
17 | 35 |
36 dmp <- dmpFinder(beta, pheno[,"V2"], type = type, qCutoff = qCutoff, shrinkVar = shrinkVar) | |
37 | |
38 dmp[,"names"] <- rownames(dmp) | |
39 | |
40 data <- merge(dmp, tab, by="names",sort = TRUE) | |
41 | |
64 | 42 data <- data[,c(6,7,8,1,4,5)] |
17 | 43 |
64 | 44 write.table(data, file= '$dmp', quote = FALSE,col.names = TRUE, row.names = FALSE, sep = "\t") |
45 ]]> | |
17 | 46 </configfile> |
47 </configfiles> | |
48 <inputs> | |
74
53aaf097238c
planemo upload commit b4d745c28290bce5c7653886d70a63b001aaab19-dirty
kpbioteam
parents:
64
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changeset
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49 <param type="data" name="grset" format="rdata" label="Data Mapped To The Genome" help="MethylSet, RatioSet or GenomicRatioSet" /> |
17 | 50 <param type="data" name="phenotype_table" format="tabular" label="Phenotype Table"/> |
51 <param name="phenotype" type="select" label="Phenotype Type"> | |
52 <option value="categorical">categorical</option> | |
53 <option value="continuous">continuous</option> | |
54 </param> | |
64 | 55 <param name="q_cutoff" type="float" value="1" label="qCutoff Size" help="DMPs with an FDR q-value greater than this will not be returned."/> |
17 | 56 <param name="variance_shrinkage" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Variance Shrinkage" |
57 help="Enable variance shrinkage is recommended when sample sizes are small"/> | |
58 <param type="data" name="ucsc_genome" format="gtf" label="Genome Table" help="UCSC genome data Methyl450"/> | |
59 </inputs> | |
60 <outputs> | |
64 | 61 <data name="dmp" format="interval" label="Differentially Methylated Positions"/> |
17 | 62 </outputs> |
63 <tests> | |
64 <test> | |
65 <param name="grset" value="GRSet_without_SNPs.rdata"/> | |
66 <param name="phenotype_table" value="phenotypeTable.txt"/> | |
67 <param name="phenotype" value="categorical"/> | |
68 <param name="q_cutoff" value="1"/> | |
69 <param name="variance_shrinkage" value="FALSE"/> | |
70 <param name="ucsc_genome" value="ucsc.gtf"/> | |
71 <output name="dmp" file="Differentially_Methylated_Positions.interval"/> | |
72 </test> | |
73 </tests> | |
74 <help><![CDATA[ | |
75 This tool creates differentially methylated positions (DMPs) with respect to a phenotype covariate. The phenotype may be categorical (e.g. cancer vs. normal) or continuous (e.g. blood pressure). | |
76 | |
77 The output is an interval file with the following columns: | |
78 | |
64 | 79 - chr |
17 | 80 - start |
81 - end | |
82 - names | |
64 | 83 - pvalue |
84 - qval | |
17 | 85 |
86 ]]></help> | |
87 <expand macro="citations" /> | |
88 </tool> |