comparison chipseeker.xml @ 7:1b9a9409831d draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker commit e07ee851144e07fde91877727d6a39a1906f7639

6:b418a1d3585d

<tool id="chipseeker" name="ChIPseeker" version="1.18.0">
    <description>for ChIP peak annotation and visualization</description>
    <requirements>
        <requirement type="package" version="1.18.0">bioconductor-chipseeker</requirement>
        <requirement type="package" version="1.6.1">r-optparse</requirement>
    </requirements>

        #end if

        Rscript '$__tool_directory__/chipseeker.R'

        -i '$peaks'
        -G '$gtf'
        -u $adv.upstream
        -d $adv.downstream

        #if $adv.flankgeneinfo:

        -r $rdata
    ]]>
    </command>
    <inputs>
        <param name="peaks" type="data" format="bed,interval,tabular" label="Peaks file" help="A peaks file in BED format." />
        <conditional name="gtf_source">
            <param name="gtf_source_select" type="select" label="Annotation source" help="Select a GTF to use for annotation source.">
                <option value="cached" selected="true">Use a built-in GTF</option>
                <option value="history">Use a GTF from history</option>
            </param>

-----

**Inputs**

A peaks file in BED, Interval or Tabular format e.g from MACS2 or DiffBind.

Example:

    =====  ======  ======  ========  =====  ======
    Chrom  Start   End     Name      Score  Strand

**Outputs**

This tool outputs

    * a file of annotated peaks in Interval or Tabular format
    * a PDF of plots (plotAnnoPie, vennpie, upsetplot)

Optionally, you can choose to output

    * the R script used by this tool
    * an RData file

7:1b9a9409831d

<tool id="chipseeker" name="ChIPseeker" version="1.18.0+galaxy1">
    <description>for ChIP peak annotation and visualization</description>
    <requirements>
        <requirement type="package" version="1.18.0">bioconductor-chipseeker</requirement>
        <requirement type="package" version="1.6.1">r-optparse</requirement>
    </requirements>

        #end if

        Rscript '$__tool_directory__/chipseeker.R'

        -i '$peaks'
        -H $header
        -G '$gtf'
        -u $adv.upstream
        -d $adv.downstream

        #if $adv.flankgeneinfo:

        -r $rdata
    ]]>
    </command>
    <inputs>
        <param name="peaks" type="data" format="bed,interval,tabular" label="Peaks file" help="A peaks file in BED format." />
        <param name="header" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Peaks file has header?" help="If this option is set to Yes, the tool will assume that the peak file has column headers in the first row. Default: No" />
        <conditional name="gtf_source">
            <param name="gtf_source_select" type="select" label="Annotation source" help="Select a GTF to use for annotation source.">
                <option value="cached" selected="true">Use a built-in GTF</option>
                <option value="history">Use a GTF from history</option>
            </param>

-----

**Inputs**

A peaks file in BED, Interval or Tabular format e.g from MACS2 or DiffBind. Note that there is an option to specify if the input peaks file has a header row. No header row is assumed by default, which is usually the case for BED format e.g. MACS narrowpeak, however other formats e.g. MACS tabular format, may contain a header row.

Example:

    =====  ======  ======  ========  =====  ======
    Chrom  Start   End     Name      Score  Strand

**Outputs**

This tool outputs

    * a file of annotated peaks in Interval or Tabular format
    * a PDF of plots (plotAnnoPie, plotAnnoBar, vennpie, upsetplot, plotDistToTSS)

Optionally, you can choose to output

    * the R script used by this tool
    * an RData file