comparison chipeakanno_annopeaks.xml @ 4:104882a2de00 draft default tip

"planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit 3af73b895c2dac2b8d87d1dec15204e5d30c709a-dirty"

3:6f52c0dc56d4

<tool id="chipeakanno_annopeaks" name="ChIPpeakAnno annoPeaks" version="0.1.0">
    <description>annotate peaks by annoGR object in the given range</description>
    <requirements>
        <requirement type="package" version="3.16.0-0">bioconductor-chippeakanno</requirement>
        <requirement type="package" version="2.99.0-3">bioconductor-ensdb.hsapiens.v75</requirement>
        <requirement type="package" version="1.42.1-1">bioconductor-rtracklayer</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$chipeakanno_annopeaks_script'
    ]]></command>
    <configfiles>
        <configfile name="chipeakanno_annopeaks_script"><![CDATA[
require("ChIPpeakAnno", quietly = TRUE)
require("EnsDb.Hsapiens.v75", quietly = TRUE)
require("rtracklayer", quietly = TRUE)

options(warn = -1)

data <-  read.table('$dmp')

peaks <- GRanges(seqnames = data[, 1],
                 ranges = IRanges
                 (start = data[, 2], end = data[, 3]),score=data[, as.numeric('$score')])

db <- toGRanges(EnsDb.Hsapiens.v75)
seqlevelsStyle(peaks) <- seqlevelsStyle(db)

start <- as.numeric('$start')
end <- as.numeric('$end')

write.table(anno, file= '$tab', quote = FALSE, row.names = FALSE, sep = "\t")
]]>
        </configfile>
    </configfiles> 
    <inputs>
        <param type="data" name="dmp" format="interval" label="Differentially Methylated Positions"/>
        <param name="type" type="select" label="bindingType" help="Specifying the criteria to associate peaks with annotation e.g. startSite start position of the feature strand">
                        <option value="startSite">startSite</option>
                        <option value="endSite">endSite</option>
                        <option value="fullRange">fullRange</option>
                        <option value="nearestBiDirectionalPromoters">nearestBiDirectionalPromoters</option>

    <outputs>
        <data name="tab" format="tabular" label="Table of Annotated Peaks"/>
    </outputs>
    <tests>
        <test>
            <param name="dmp" value="Differentially_Methylated_Regions.interval"/>
            <param name="type" value="startSite"/>
            <param name="start" value="-5000"/>
            <param name="end" value="5000"/>
            <param name="score" value="5"/>
            <output name="tab" file="annoTab.tabular"/>

4:104882a2de00

<tool id="chipeakanno_annopeaks" name="ChIPpeakAnno annoPeaks" version="0.1.0">
    <description>annotate peaks by annoGR object in the given range</description>
    <requirements>
        <requirement type="package" version="3.20.0">bioconductor-chippeakanno</requirement>
        <requirement type="package" version="2.99.0">bioconductor-ensdb.hsapiens.v75</requirement>
        <requirement type="package" version="1.46.0">bioconductor-rtracklayer</requirement>
        <requirement type="package" version="1.2.2">bioconductor-genomeinfodbdata</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$chipeakanno_annopeaks_script'
    ]]></command>
    <configfiles>
        <configfile name="chipeakanno_annopeaks_script"><![CDATA[
require("ChIPpeakAnno", quietly = TRUE)
require("EnsDb.Hsapiens.v75", quietly = TRUE)
require("rtracklayer", quietly = TRUE)
require("GenomeInfoDbData", quietly = TRUE) 

options(warn = -1)

data <-  read.table('$dmp',header=FALSE)

peaks <- GRanges(seqnames = data[, 1],
                 ranges = IRanges
                 (start = as.numeric(data[, 2]), end = as.numeric(data[, 3]), score = data[, as.numeric('$score')]))

db <- toGRanges(EnsDb.Hsapiens.v75, feature="gene")
seqlevelsStyle(peaks) <- seqlevelsStyle(db)

start <- as.numeric('$start')
end <- as.numeric('$end')

write.table(anno, file= '$tab', quote = FALSE, row.names = FALSE, sep = "\t")
]]>
        </configfile>
    </configfiles> 
    <inputs>
        <param type="data" name="dmp" format="bed" label="Differentially Methylated Positions"/>
        <param name="type" type="select" label="bindingType" help="Specifying the criteria to associate peaks with annotation e.g. startSite start position of the feature strand">
                        <option value="startSite">startSite</option>
                        <option value="endSite">endSite</option>
                        <option value="fullRange">fullRange</option>
                        <option value="nearestBiDirectionalPromoters">nearestBiDirectionalPromoters</option>

    <outputs>
        <data name="tab" format="tabular" label="Table of Annotated Peaks"/>
    </outputs>
    <tests>
        <test>
            <param name="dmp" value="Differentially_Methylated_Positions.bed"/>
            <param name="type" value="startSite"/>
            <param name="start" value="-5000"/>
            <param name="end" value="5000"/>
            <param name="score" value="5"/>
            <output name="tab" file="annoTab.tabular"/>