Mercurial > repos > kpbioteam > ewastools

annotate minfi_dmr.xml @ 0:bb6c8d38fad1 draft default tip

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planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
author kpbioteam
date Fri, 07 Jun 2019 14:14:49 -0400
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0
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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1 <tool id="minfi_dmr" name="Minfi DMR" version="@MINFI_VERSION@">
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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2 <description>to find differentially methylated regions</description>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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3 <macros>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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4 <import>macros.xml</import>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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5 </macros>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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6 <expand macro="requirements" />
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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7 <command detect_errors="exit_code">
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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8 <![CDATA[
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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9 Rscript '$minfi_dmr_script'
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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10 ]]>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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11 </command>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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12 <configfiles>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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13 <configfile name="minfi_dmr_script">
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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14 <![CDATA[
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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15 require("minfi", quietly = TRUE)
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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16 options(warn = -1)
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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18 GRSet <- get(load('$grset'))
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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20 pheno <- read.table('$phenotype_table',skip = 1)
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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22 group <- pheno\$V2
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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24 pair <- factor(pheno\$V3)
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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26 design.matrix <- model.matrix(~ group + pair)
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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28 maxGap <- as.numeric('$maxgap_size')
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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29
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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30 if(is.null(GRSet\$cluster)){
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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31 cluster = NULL
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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32 maxGap = maxGap
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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33 } else {
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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34 cluster = GRSet\$cluster
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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35 maxGap = NULL
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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36 }
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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37
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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38 cutoff <- as.numeric('$cutoff_size')
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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39 B <- as.numeric('$number_of_resamples')
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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40 nullMethod <- '$null_method'
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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41 coef <- 2
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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42
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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43 dmrs <- bumphunter(GRSet,
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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44 design = design.matrix,
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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45 cluster = cluster,
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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46 maxGap = maxGap,
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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47 cutoff = cutoff,
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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48 nullMethod = nullMethod,
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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49 B = B)
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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50
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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51 dmrGR <- dmrs\$table[,c(1,2,3)]
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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52 colnames(dmrGR) <- c("chr","start","end")
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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53
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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54 write.table(dmrGR, file= '$dmr', quote = FALSE,col.names = TRUE, row.names = FALSE, sep = "\t")
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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55 ]]>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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56 </configfile>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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57 </configfiles>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
kpbioteam
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58 <inputs>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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59 <param type="data" name="grset" format="rdata" label="Data Mapped To The Genome"
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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60 help="This class (GenomicRatioSet) holds preprocessed data for Illumina methylation microarrays, mapped to a genomic location." />
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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61 <param type="data" name="phenotype_table" format="tabular" label="Phenotype Table"
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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62 help="Phenotype Table must include the following information: sampleID, phenotype and paird or unpaired samples column"/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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63 <param name="maxgap_size" type="integer" value="250" label="maxGap Size"
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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64 help="If cluster is not provided this maximum location gap will be used to define cluster"/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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65 <param name="cutoff_size" type="float" value="0.1" label="Cutoff Size"
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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66 help="A numeric value. Values of the estimate of the genomic profile above the cutoff or below the negative of the cutoff will be used as candidate regions. It is possible to give two separate values (upper and lower bounds). If one value is given, the lower bound is minus the value."/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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67 <param name="number_of_resamples" type="integer" value="0" label="Number of Resamples"
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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68 help="An integer denoting the number of resamples to use when computing null distributions. This defaults to 0. If permutations is supplied that defines the number of permutations/bootstraps and B is ignored."/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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69 <param name="null_method" type="select" label="null Method" help="Method used to generate null candidate regions.">
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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70 <option value="permutation" selected="True">permutation</option>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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71 <option value="bootstrap">bootstrap</option>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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72 </param>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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73 </inputs>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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74 <outputs>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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75 <data name="dmr" format="interval" label="Differentially Methylated Regions"/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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76 </outputs>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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77 <tests>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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78 <test>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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79 <param name="grset" value="GRSet_without_SNPs.rdata"/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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80 <param name="phenotype_table" value="phenotypeTable.txt"/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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81 <param name="maxgap_size" value="250"/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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82 <param name="cutoff_size" value="0.1"/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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83 <param name="number_of_resamples" value="0"/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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84 <param name="null_method" value="permutation"/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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85 <output name="dmr" file="Differentially_Methylated_Regions.interval"/>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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86 </test>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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87 </tests>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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88 <help><![CDATA[
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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89 Genomic Ratio Set should contain 450k arrays reads for each sample listed in Phenotype Table: sampleID phenotype paired e.g. GSM1588708 sensitive 1
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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90
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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91 This tool is a version of the bump hunting algorithm (Andrew E Jaffe et al. 2012) adapted to the 450k array finding find differentially methylated regions DMR.
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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93 The output is an interval file with the following columns:
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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94
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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95 - chr
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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96 - start
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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97 - end
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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99 ]]></help>
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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100 <expand macro="citations" />
bb6c8d38fad1 planemo upload for repository https://github.com/kpbioteam/ewas_galaxy commit 945cecdba6528d35c6dfa866f785f182c5dd22ed
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101 </tool>