annotate chipseeker.xml @ 1:95f779f4adb7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292

<tool id="chipseeker" name="ChIPseeker" version="1.14.2.1">
    <description>for ChIP peak annotation and visualization</description>
    <requirements>
        <requirement type="package" version="1.14.2">bioconductor-chipseeker</requirement>
        <requirement type="package" version="1.4.4">r-optparse</requirement>
    </requirements>
    <version_command><![CDATA[
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: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
    ]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
        #set gtf = "refgtf"
        #if $gtf_source.gtf_source_select == "history":
            ln -s '${gtf_source.gtf_hist}' $gtf &&
        #else if $gtf_source.gtf_source_select == "cached":
            ln -s '${gtf_source.gtf_builtin.fields.path}' $gtf &&
        #end if

        #if $rscript:
            cp '$__tool_directory__/chipseeker.R' '$out_rscript' &&
        #end if

        Rscript '$__tool_directory__/chipseeker.R'

        -i '$peaks'
        -G '$gtf'
        -u $upstream
        -d $downstream
        #if $flankgeneinfo:
            -F $flankgeneinfo
            -D $flankgenedist
        #end if
        -f $format
        -p $pdf
    ]]>
    </command>
    <inputs>
        <param name="peaks" type="data" format="bed,interval" 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>
            <when value="cached">
                 <param name="gtf_builtin" type="select" label="Select a built-in GTF" help="If the GTF file for your transcriptome of interest is not listed, contact your Galaxy administrator">
                     <options from_data_table="gene_sets">
                         <filter type="sort_by" column="2" />
                         <validator type="no_options" message="No GTF file is available." />
                     </options>
                 </param>
            </when>
            <when value="history">
                <param name="gtf_hist" type="data" format="gtf" label="Select a history GTF" />
            </when>
        </conditional>
        <param name="upstream" type="integer" min="0" value="3000" label="TSS upstream region" help="User can define TSS (transcription start site) region, by default TSS is defined from -3kb to +3kb." />
        <param name="downstream" type="integer" min="0" value="3000" label="TSS downstream region" help="User can define TSS (transcription start site) region, by default TSS is defined from -3kb to +3kb."/>
        <param name="flankgeneinfo" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Add flanking gene information?" help="If specified all genes within the flanking gene distance are reported for each peak. Default: No."/>
        <param name="flankgenedist" type="integer" min="0" value="5000" label="Flanking gene distance" help="If flanking gene info is turned on the flanking distance can be specified. Default: 5000."/>
        <param name="format" type="select" label="Output Format">
            <option value="interval" selected="True">Interval</option>
            <option value="tabular">Tabular (tab-separated)</option>
        </param>
        <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="True" label="Output PDF of plots?" help="Default: Yes" />
        <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" />
    </inputs>

        <outputs>
            <data name="out_tab" format="interval" from_work_dir="out.tab" label="${tool.name} on ${on_string}: Annotated Peaks" >
                <change_format>
                    <when input="format" value="tabular" format="tabular" />
                </change_format>
            </data>
            <data name="out_plots" format="pdf" from_work_dir="out.pdf" label="${tool.name} on ${on_string}: Plots">
                <filter>pdf</filter>
            </data>
            <data name="out_rscript" format="txt" from_work_dir="out_rscript.txt" label="${tool.name} on ${on_string}: Rscript">
                <filter>rscript</filter>
            </data>
        </outputs>

    <tests>
        <!-- Ensure bed and GTF inputs and all outputs work -->
        <test expect_num_outputs="3">
            <param name="peaks" value="in.bed" ftype="bed"/>
            <param name="gtf_source_select" value="history"/>
            <param name="gtf_hist" value="in.gtf"/>
            <param name="rscript" value="True"/>
            <output name="out_tab" ftype="interval" file="out.int" />
            <output name="out_plots" file="out.pdf" compare="sim_size"/>
            <output name="out_rscript" >
                <assert_contents>
                    <has_text_matching expression="peakAnno.*annotatePeak" />
                </assert_contents>
            </output>
        </test>
        <!-- Ensure built-in GTF works -->
        <test expect_num_outputs="2">
            <param name="peaks" value="in.interval" ftype="interval"/>
            <param name="gtf_source_select" value="cached"/>
            <output name="out_tab" ftype="interval" file="outint.int" />
            <output name="out_plots" file="out.pdf" compare="sim_size"/>
        </test>
        <!-- Ensure tabular output works -->
        <test expect_num_outputs="2">
            <param name="peaks" value="in.interval" ftype="interval"/>
            <param name="gtf_source_select" value="history"/>
            <param name="gtf_hist" value="in.gtf"/>
            <param name="format" value="tabular"/>
            <output name="out_tab" ftype="tabular" file="outint.tab" />
            <output name="out_plots" file="out.pdf" compare="sim_size"/>
        </test>
        <!-- Ensure TSS region specification works -->
        <test expect_num_outputs="2">
            <param name="peaks" value="in.interval" ftype="interval"/>
            <param name="gtf_source_select" value="history"/>
            <param name="gtf_hist" value="in.gtf"/>
            <param name="upstream" value="1000" />
            <param name="downstream" value="1000" />
            <param name="format" value="tabular"/>
            <output name="out_tab" ftype="tabular" file="outtss.tab" />
            <output name="out_plots" file="out.pdf" compare="sim_size"/>
        </test>
        <!-- Ensure flanking genes works -->
        <test expect_num_outputs="2">
            <param name="peaks" value="in.interval" ftype="interval"/>
            <param name="gtf_source_select" value="history"/>
            <param name="gtf_hist" value="in.gtf"/>
            <param name="flankgeneinfo" value="True" />
            <param name="format" value="tabular"/>
            <output name="out_tab" ftype="tabular" file="outflank.tab" />
            <output name="out_plots" file="out.pdf" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

ChIPseeker_ is a Bioconductor package for annotating ChIP-seq data analysis. See
the `ChIPseeker vignette`_ for more information.

-----

**Inputs**

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

Example:

    =====  ======  ======  ========  =====  ======
    Chrom  Start   End     Name      Score  Strand
    =====  ======  ======  ========  =====  ======
    18     394599  396513  DiffBind  0      .
    18     111566  112005  DiffBind  0      .
    18     346463  347342  DiffBind  0      .
    18     399013  400382  DiffBind  0      .
    18     371109  372102  DiffBind  0      .
    =====  ======  ======  ========  =====  ======

A GTF file for annotation.

-----

**Outputs**

This tool outputs

    * a file of annotated peaks in Interval or Tabular format
    * a PDF of plots
    * the R script used by this tool

**Annotated peaks**

Annotation similar to below will be added to the input file.

Example - **Interval format**:

    =====  ======  ======  =====================================================================================================================================================
    Chrom  Start   End     Comment
    =====  ======  ======  =====================================================================================================================================================
    18     394599  396513  DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256| 3869
    18     111566  112005  DiffBind|0|.|Promoter (<=1kb)|1|111568|112005|  438|1|ENSG00000263006|ENST00000608049|    0
    18     346463  347342  DiffBind|0|.|Exon (ENST00000400256/ENSG00000158270, exon 1 of 1)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256|53040
    18     399013  400382  DiffBind|0|.|Promoter (<=1kb)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256|    0
    18     371109  372102  DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256|28280
    =====  ======  ======  =====================================================================================================================================================

    Columns contain the following data:

* **Chrom**: Chromosome name
* **Start**: Start position of site
* **End**: End position of site
* **Comment**: The pipe ("|") separated values in this column correspond to:

    * *<Any additional input columns>*
    * *annotation* (Promoter, 5’ UTR, 3’ UTR, Exon, Intron, Downstream, Intergenic)
    * *geneChr*
    * *geneStart*
    * *geneEnd*
    * *geneLength*
    * *geneStrand*
    * *geneId*
    * *transcriptId*
    * *distanceToTSS*

Example - **Tabular format**:

    =====  ======  ======  ========  ====== ======  ===========================================  ======================================================= ======= ========= ======= ========== ========== =============== =============== =============
    Chrom  Start   End     Name      Score  Strand  Comment                                      annotation                                              geneChr geneStart geneEnd geneLength geneStrand geneId          transcriptId    distanceToTSS
    =====  ======  ======  ========  ====== ======  ===========================================  ======================================================= ======= ========= ======= ========== ========== =============== =============== =============
    18     394599  396513  DiffBind    0     .      1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21  Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)  1       346465    400382   53918      2        ENSG00000158270 ENST00000400256 3869
    18     111566  112005  DiffBind    0     .      439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06    Promoter (<=1kb)                                         1       111568    112005   438        1        ENSG00000263006 ENST00000608049 0
    18     346463  347342  DiffBind    0     .      879|5|5.77|3.24|2.52|6.51e-06|0.00303        Exon (ENST00000400256/ENSG00000158270, exon 1 of 1)      1       346465    400382   53918      2        ENSG00000158270 ENST00000400256 53040
    18     399013  400382  DiffBind    0     .      1369|7.62|7|8.05|-1.04|1.04e-05|0.00364      Promoter (<=1kb)                                         1       346465    400382   53918      2        ENSG00000158270 ENST00000400256 0
    18     371109  372102  DiffBind    0     .      993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226       Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)  1       346465    400382   53918      2        ENSG00000158270 ENST00000400256 28280
    =====  ======  ======  ========  ====== ======  ===========================================  ======================================================= ======= ========= ======= ========== ========== =============== =============== =============

.. _ChIPseeker: https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html
.. _`ChIPseeker vignette`: http://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html

]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btv145</citation>
    </citations>
</tool>