annotate hicPlotAverageRegions.xml @ 2:0dff8b5011c0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"

<tool id="hicexplorer_hicplotaverageregions" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>plot the average regions from hicAverageRegions</description>
    <macros>
        <token name="@BINARY@">hicPlotAverageRegions</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive"><![CDATA[

        @BINARY@
            --matrix '$matrix'
            #if $colormap:
                --colorMap $colormap
            #end if

            #if $vMin:
                --vMin $vMin
            #end if

            #if $vMax:
                --vMax $vMax
            #end if

            #if $dpi:
                --dpi $dpi
            #end if

            $log1p $log
            --outputFile plot.$image_file_format

        && mv plot.$image_file_format plot
]]>
    </command>
    <inputs>
        <param argument="--matrix" type="data" format='zip' label="Average regions matrix computed by hicAverageRegions"/>
        <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" checked="false" label="Plot the log1p of the matrix values (log(Hi-C contacts+1)). This option is recommended."/>
        <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the log of the matrix values. (log(Hi-C contacts))"/>

        <expand macro="colormap" />

        <param argument="--vMin" type="float" optional="true" label="vMin" help="Minimum value of the plotted score."/>
        <param argument="--vMax" type="float" optional="true" label="vMax" help="Maximum value of the plotted score."/>

        <param name="image_file_format" type="select" label="Image output format">
            <option value="png" selected="True">png</option>
            <option value="svg">svg</option>
            <option value="pdf">pdf</option>
        </param>
        <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>

    </inputs>
    <outputs>
        <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} [${on_string}]: Plot">
            <change_format>
                <when input="image_file_format" value="svg" format="svg" />
                <when input="image_file_format" value="pdf" format="pdf" />
            </change_format>
        </data>

    </outputs>
    <tests>
        <test>
            <param name="matrix" value="hicAverageRegions/result_range_100000.npz" ftype="zip"/>
            <param name="colormap" value="RdYlBu_r"/>
            <param name='dpi' value='10' />
            <output name="outFileName" file="hicPlotAverageRegions/defaults.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <param name="matrix" value="hicAverageRegions/result_range_100000.npz" ftype="zip"/>
            <param name="colormap" value="RdYlBu_r"/>
            <param name="log" value="True"/>
            <param name='dpi' value='10' />


            <output name="outFileName" file="hicPlotAverageRegions/defaults_log.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <param name="matrix" value="hicAverageRegions/result_range_100000.npz" ftype="zip"/>
            <param name="colormap" value="RdYlBu_r"/>
            <param name="log1p" value="True"/>
            <param name='dpi' value='10' />


            <output name="outFileName" file="hicPlotAverageRegions/defaults_log1p.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <param name="matrix" value="hicAverageRegions/result_range_100000.npz" ftype="zip"/>
            <param name="colormap" value="plasma"/>
            <param name="vMax" value="20"/>
            <param name="vMin" value="10"/>
            <param name='dpi' value='10' />

            <output name="outFileName" file="hicPlotAverageRegions/defaults_log_vmin_vmax.png" ftype="png" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
Plot of hicAverageRegions matrix
================================
hicPlotAverage regions plots the data computed by hicAverageRegions. It shows the summed up and averaged regions around all given reference points. This is useful to determine the difference between samples if the TAD configuration is equal or changed.


| For more information about HiCExplorer please consider our documentation on readthedocs.io_

.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
]]></help>
    <expand macro="citations" />
</tool>