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annotate chipseeker.xml @ 0:313332cb7745 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
author rnateam
date Thu, 24 May 2018 18:22:53 -0400
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children 2019b4dd86a8
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313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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1 <tool id="chipseeker" name="ChIPseeker" version="1.14.2">
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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2 <description>for ChIP peak annotation and visualization</description>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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3 <requirements>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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4 <requirement type="package" version="1.14.2">bioconductor-chipseeker</requirement>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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5 <requirement type="package" version="3.4.0">bioconductor-txdb.hsapiens.ucsc.hg38.knowngene</requirement>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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6 <requirement type="package" version="3.2.2">bioconductor-txdb.hsapiens.ucsc.hg19.knowngene</requirement>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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7 <requirement type="package" version="3.4.0">bioconductor-txdb.Mmusculus.UCSC.mm10.knownGene</requirement>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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8 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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9 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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10 </requirements>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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11 <version_command><![CDATA[
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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12 echo $(R --version | grep version | grep -v GNU)", ChIPseeker version" $(R --vanilla --slave -e "library(ChIPseeker); cat(sessionInfo()\$otherPkgs\$ChIPseeker\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", TxDb.Hsapiens.UCSC.hg38.knownGene version" $(R --vanilla --slave -e "library(TxDb.Hsapiens.UCSC.hg38.knownGene); cat(sessionInfo()\$otherPkgs\$TxDb.Hsapiens.UCSC.hg38.knownGene\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", TxDb.Hsapiens.UCSC.hg19.knownGene version" $(R --vanilla --slave -e "library(TxDb.Hsapiens.UCSC.hg19.knownGene); cat(sessionInfo()\$otherPkgs\$TxDb.Hsapiens.UCSC.hg19.knownGene\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", TxDb.Mmusculus.UCSC.mm10.knownGene version" $(R --vanilla --slave -e "library(TxDb.Mmusculus.UCSC.mm10.knownGene); cat(sessionInfo()\$otherPkgs\$TxDb.Mmusculus.UCSC.mm10.knownGene\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Hs.eg.db version" $(R --vanilla --slave -e "library(org.Hs.eg.db); cat(sessionInfo()\$otherPkgs\$org.Hs.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Mm.eg.db version" $(R --vanilla --slave -e "library(org.Mm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Mm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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13 ]]></version_command>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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14 <command detect_errors="exit_code"><![CDATA[
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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15 #if $rscript:
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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16 cp '${chipseeker_script}' '${out_rscript}' &&
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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17 #end if
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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18 Rscript '${chipseeker_script}'
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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19 ]]>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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20 </command>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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21 <configfiles>
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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22 <configfile name="chipseeker_script"><![CDATA[
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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23 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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24
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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25 # we need that to not crash galaxy with an UTF8 error on German LC settings.
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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26 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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27
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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28 suppressPackageStartupMessages(library(ChIPseeker))
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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29
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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30 genome <- "${genome}"
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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31
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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32 if (genome == "hg38") {
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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33 suppressPackageStartupMessages({
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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34 library(TxDb.Hsapiens.UCSC.hg38.knownGene)
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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35 library(org.Hs.eg.db)
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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36 })
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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37 txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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38 annodb <- "org.Hs.eg.db"
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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39 } else if (genome == "hg19") {
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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40 suppressPackageStartupMessages({
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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41 library(TxDb.Hsapiens.UCSC.hg19.knownGene)
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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42 library(org.Hs.eg.db)
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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43 })
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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44 txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
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45 annodb <- "org.Hs.eg.db"
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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46 } else if (genome == "mm10") {
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47 suppressPackageStartupMessages({
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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48 library(TxDb.Mmusculus.UCSC.mm10.knownGene)
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49 library(org.Mm.eg.db)
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50 })
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51 txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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52 annodb <- "org.Mm.eg.db"
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53 } else {
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54 cat(paste("Genome not supported", genome))
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55 }
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56
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57 peaks <- readPeakFile('$peaks_file')
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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58 peakAnno <- annotatePeak(peaks, TxDb=txdb, annoDb=annodb)
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59 write.table(peakAnno, file='$out_tab', sep="\t", row.names=FALSE, quote=FALSE)
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60
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61 if (!is.null("${pdf}")) {
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62 pdf("out.pdf", width=14)
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63 plotAnnoPie(peakAnno)
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64 plotAnnoBar(peakAnno)
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65 vennpie(peakAnno)
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66 upsetplot(peakAnno)
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67 plotDistToTSS(peakAnno, title="Distribution of transcription factor-binding loci\nrelative to TSS")
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68 dev.off()
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69 }
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70 ]]></configfile>
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71 </configfiles>
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72
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73 <inputs>
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74 <param name="peaks_file" type="data" format="bed" label="Peaks file" help="A peaks file in BED format." />
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75 <param name="genome" type="select" label="Genome" help="Select the genome. Options are hg38, hg19 or mm10.">
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76 <option value="hg38">hg38</option>
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77 <option value="hg19">hg19</option>
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78 <option value="mm10">mm10</option>
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79 </param>
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80
313332cb7745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce
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81 <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="True" label="Output a PDF file of plots?" help="Default: Yes" />
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82 <param name="rscript" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used to annotate the IDs will be provided as a text file in the output. Default: No" />
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83 </inputs>
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84
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85 <outputs>
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86 <data name="out_tab" format="tabular" from_work_dir="out.tab" label="${tool.name} on ${on_string}: Annotated Peaks" />
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87 <data name="out_plots" format="pdf" from_work_dir="out.pdf" label="${tool.name} on ${on_string}: Plots">
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88 <filter>pdf</filter>
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89 </data>
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90 <data name="out_rscript" format="txt" from_work_dir="out_rscript.txt" label="${tool.name} on ${on_string}: Rscript">
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91 <filter>rscript</filter>
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92 </data>
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93 </outputs>
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94
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95 <tests>
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96 <!-- Ensure outputs work -->
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97 <test expect_num_outputs="3">
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98 <param name="peaks_file" value="in.diffbind" ftype="bed"/>
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99 <param name="genome" value="hg19"/>
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100 <param name="rscript" value="True"/>
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101 <output name="out_tab" file="out.tab" />
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102 <output name="out_plots" file="out.pdf" compare="sim_size"/>
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103 <output name="out_rscript" >
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104 <assert_contents>
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105 <has_text_matching expression="peakAnno.*annotatePeak" />
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106 </assert_contents>
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107 </output>
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108 </test>
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109 </tests>
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110 <help><![CDATA[
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111
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112 .. class:: infomark
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113
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114 **What it does**
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115
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116 ChIPseeker_ is a Bioconductor package for annotating ChIP-seq data analysis. See
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117 the `ChIPseeker vignette`_ for more information.
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118
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119 -----
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120
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121 **Inputs**
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122
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123 A peaks file in BED format e.g from MACS2 or DiffBind.
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124
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125 -----
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126
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127 **Outputs**
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128
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129 This tool outputs
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130
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131 * a table of annotated peaks
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132 * a PDF of plots
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133 * the R script used by this tool
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134
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135 .. _ChIPseeker: https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html
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136 .. _`ChIPseeker vignette`: http://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html
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137
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138 ]]></help>
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139 <citations>
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140 <citation type="doi">10.1093/bioinformatics/btv145</citation>
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141 </citations>
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142 </tool>