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1 <tool id="minfi_dmp" name="Minfi DMP" version="@MINFI_VERSION@">
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2 <description>to find differentially methylated positions</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 Rscript '$minfi_dmp_script'
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9 ]]></command>
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10 <configfiles>
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11 <configfile name="minfi_dmp_script"><![CDATA[
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12 require("minfi", quietly = TRUE)
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13
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14 set <- get(load('$grset'))
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15
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16 genomeranges <- as.data.frame(ranges(set))
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17
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18 beta <- getBeta(set)
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19
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20 pheno <- read.table('$phenotype_table',skip=1)
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21
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22 type <- '$phenotype'
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23
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24 qCutoff <- as.numeric('$q_cutoff')
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25
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26 shrinkVar <- '$variance_shrinkage'
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27
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28 tab <- read.table('$ucsc_genome')
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29
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30 tab <- tab[,-(11:14),drop=FALSE]
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31
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32 colnames(tab) <- c("seqname","source","feature","start","end","score","strand", "frame","attributes", "names")
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33
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34 tab[,"source"] <- NULL
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35
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36 tab[,"frame"] <- NULL
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37
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38 tab[,"attributes"] <- NULL
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39
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40 dmp <- dmpFinder(beta, pheno[,"V2"], type = type, qCutoff = qCutoff, shrinkVar = shrinkVar)
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41
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42 dmp[,"names"] <- rownames(dmp)
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43
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44 data <- merge(dmp, tab, by="names",sort = TRUE)
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45
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46 data <- data[c("seqname","start","end","names","score","strand", "feature","intercept", "f", "pval","qval")]
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47
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48 write.table(data, file= '$dmp', quote = FALSE,col.names = FALSE, row.names = FALSE, sep = "\t")
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49 ]]>
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50 </configfile>
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51 </configfiles>
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52 <inputs>
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53 <param type="data" name="grset" format="rdata" label="Input Set" help="MethylSet, RatioSet or GenomicRatioSet" />
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54 <param type="data" name="phenotype_table" format="tabular" label="Phenotype Table"/>
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55 <param name="phenotype" type="select" label="Phenotype Type">
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56 <option value="categorical">categorical</option>
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57 <option value="continuous">continuous</option>
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58 </param>
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59 <param name="q_cutoff" type="integer" value="1" label="qCutoff Size" help="DMPs with an FDR q-value greater than this will not be returned."/>
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60 <param name="variance_shrinkage" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Variance Shrinkage"
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61 help="Enable variance shrinkage is recommended when sample sizes are small"/>
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62 <param type="data" name="ucsc_genome" format="gtf" label="Genome Table" help="UCSC genome data Methyl450"/>
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63 </inputs>
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64 <outputs>
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65 <data name="dmp" format="interval" label="Differentially Methylated Positions"/>
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66 </outputs>
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67 <tests>
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68 <test>
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69 <param name="grset" value="GRSet_without_SNPs.rdata"/>
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70 <param name="phenotype_table" value="phenotypeTable.txt"/>
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71 <param name="phenotype" value="categorical"/>
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72 <param name="q_cutoff" value="1"/>
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73 <param name="variance_shrinkage" value="FALSE"/>
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74 <param name="ucsc_genome" value="ucsc.gtf"/>
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75 <output name="dmp" file="Differentially_Methylated_Positions.interval"/>
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76 </test>
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77 </tests>
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78 <help><![CDATA[
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79 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).
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80
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81 The output is an interval file with the following columns:
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82
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83 - seqnames
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84 - start
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85 - end
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86 - cpg
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87 - names
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88 - score
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89 - strand
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90 - feature
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91 - intercept
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92 - f pval
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93 - qval
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94
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95 ]]></help>
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96 <expand macro="citations" />
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97 </tool>
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