annotate mummerplot.xml @ 1:c0cedc12fcc5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 96608e94742d17cb73d57201099ff5f5abbef276"

<tool id="mummer_mummerplot" name="Mummerplot" version="@MUMMER_VERSION@@WRAPPER_VERSION@">
    <description>Generate 2-D dotplot of aligned sequences</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <expand macro="gnuplot_requirement"/>
    </expand>
    <command detect_errors="exit_code">
        <![CDATA[
        ln -s $reference_sequence reference.fa &&
        ln -s $query_sequence query.fa &&
        mummerplot
            -b '$breaklen'
            $color
            $coverage
            $filter
            $fat
            #if str($labels.IDs) == 'yes':
                -IdR '$labels.ref_id'
                -IdQ '$labels.query_id'
            #end if
            #if str($sequences.seq_input) == 'yes':
                -R '$reference_sequence'
                -Q '$query_sequence'
                $sequences.layout
            #end if
            -s '$size'
            -terminal png
            -title '$title'
            $snp
            #if $range.custom == 'yes':
                -x [$range.min_x:$range.max_x]
                -y [$range.min_y:$range.max_y]
            #end if
            '$delta'
            @MUMMER_GNUPLOT_MANUAL@
        ]]>
    </command>
    <inputs>
        <param name="delta" type="data" format="tabular" label="Match File" />
        <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" />
        <param name="query_sequence" type="data" format="fasta" label="Query Sequence(s)" />
        <expand macro="mumplot_input" >
            <conditional name="sequences" >
                <param name="seq_input" type="select" label="Plot an ordered set of reference/query sequences?" >
                    <option value="no">NO</option>
                    <option value="yes">YES</option>
                </param>
                <when value="yes">
                    <param name="layout" type="boolean" argument="--layout" truevalue="--layout" falsevalue="" label="Layout" help="Layout a .delta multiplot in an intelligible fashion. (--layout)" />
                </when>
                <when value="no" />
            </conditional>
        </expand>
        <param name="extra_outs" type="select" label="Output files used to create the plot or just the plot?" >
            <option value="plot">Just the plot</option>
            <option value="all">All outputs</option>
        </param>
    </inputs>
    <outputs>
        <data name="gnuplot" format="txt" from_work_dir="out.gp" label="${tool.name} on ${on_string}: gnuplot" >
            <filter> extra_outs == 'all' </filter>
        </data>
        <data name="fplot" format="txt" from_work_dir="out.fplot" label="${tool.name} on ${on_string}: fplot" >
            <filter> extra_outs == 'all' </filter>
        </data>
        <data name="rplot" format="txt" from_work_dir="out.rplot" label="${tool.name} on ${on_string}: rplot" >
            <filter> extra_outs == 'all' </filter>
        </data>
        <data name="hplot" format="txt" from_work_dir="out.hplot" label="${tool.name} on ${on_string}: hplot" >
            <filter> extra_outs == 'all' </filter>
        </data>
        <data name="output_png" format="png" from_work_dir="out.png" label="${tool.name} on ${on_string}: plot" />
    </outputs>
    <tests>
        <test>
            <param name="delta" ftype="txt" value="nucmer.txt" />
            <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" />
            <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
            <param name="seq_input" value="no" />
            <param name="extra_outs" value="all" />
            <output name="gnuplot" ftype="txt" compare="diff" value="gnuplot.txt" />
            <output name="fplot" ftype="txt" compare="diff" value="fplot.txt" />
            <output name="rplot" ftype="txt" compare="diff" value="rplot.txt" />
            <output name="hplot" ftype="txt" compare="diff" value="hplot.txt" />
            <output name="output_png" ftype="png" compare="sim_size" value="plot.png" />
        </test>
    </tests>
    <help><![CDATA[
Mummerplot is a perl script that generates gnuplot scripts and data collections for plotting with the gnuplot utility. It can generate 2-d dotplots and 1-d coverage plots for the output of mummer or nucmer. It can also color dotplots with an identity color gradient.

**Outputs:**
    * gnuplot: The gnuplot script
    * fplot, rplot, hplot: The forward, reverse, and highlighted match information for plotting with gnuplot.
    * plot: The plotted image file

**Options:**::


    -b             Highlight alignments with breakpoints further than breaklen nucleotides from the nearest 
                   sequence end

    -color         Color plot lines with a percent similarity gradient or turn off all plot color (default 
                   color by match dir) If the plot is very sparse, edit the .gp script to plot with 
                   'linespoints' instead of 'lines'

    -c             Generate a reference coverage plot (default for .tiling)

    --filter       Only display .delta alignments which represent the "best" hit to any particular spot on 
                   either sequence, i.e. a one-to-one mapping of reference and query subsequences

    --fat          Layout sequences using fattest alignment only

    -IdR           Plot a particular reference sequence ID on the X-axis

    -IdQ           Plot a particular query sequence ID on the Y-axis

    -s             Set the output size to small, medium or large (--small) (--medium) (--large) (default 'small')

    --SNP          Highlight SNP locations in each alignment

    -title         Specify the gnuplot plot title (default none)

    -x             Set the xrange for the plot '[min:max]'

    -y             Set the yrange for the plot '[min:max]'

    -R             Plot an ordered set of reference sequences from Rfile

    -Q             Plot an ordered set of query sequences from Qfile

    --layout       Layout a .delta multiplot in an intelligible fashion, this option requires the -R -Q options

    ]]></help>
    <expand macro="citation" />
</tool>