view hicPlotViewpoint.xml @ 4:c4f273c3c73f draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dddc0b9035b8edadfd45d74b01aeca245c2725d7

<tool id="hicexplorer_hicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>plot interactions around a viewpoint</description>
    <macros>
        <token name="@BINARY@">hicPlotViewpoint</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

        hicPlotViewpoint --matrix '$matrix_h5_cooler'
        #if $interactionOutFileName:
            $interactionOutFileName interactions.bedgraph
        #end if
        --outFileName plot.$image_file_format
        --region $region
        --referencePoint $referencePoint
        && mv plot.$image_file_format plot
]]>
    </command>
    <inputs>
        <expand macro='matrix_h5_cooler_macro' />
        <expand macro="region" />
        <param name="referencePoint" type="text" label="Reference point"
            help="The format is chr:referencePoint or chr:regionStart-regionEnd."/>

        <param name="interactionOutFileName" type="boolean" truevalue="--interactionOutFileName" falsevalue="" checked="false"
                            label="Create bedgraph file with interactions" />
        <param name="image_file_format" type="select" label="Image output format">
            <option value="png">png</option>
            <option value="svg">svg</option>
        </param>

    </inputs>
    <outputs>

        <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Plot">
            <change_format>
                <when input="image_file_format" value="png" format="png" />
                <when input="image_file_format" value="svg" format="svg" />
            </change_format>
        </data>
        <data name='interactionFile' from_work_dir='interactions.bedgraph' format='bedgraph' label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Bedgraph">
            <filter>interactionOutFileName</filter>
        </data>

    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
            <param name="image_file_format" value="png" />
            <param name='region' value='X:3000000-3500000' />
            <param name='referencePoint' value='X:3200000' />
            <output name="outFileName" file="li_viewpoint_32Mb.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
            <param name="image_file_format" value="png" />
            <param name='region' value='X:3000000-3500000' />
            <param name='referencePoint' value='X:3200000-3300000' />
            <param name='interactionOutFileName' value='True' />
            <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size"/>
            <output name="interactionFile" file="li_32-33mb_interactions.bedgraph" ftype="bedgraph" compare="sim_size"/>

        </test>
    </tests>
    <help><![CDATA[
Plot Viewpoint
==============

**hicPlotViewpoint** plots the number of interactions around a specific reference point or region in the genome like a 4C analysis using Hi-C data.
This plotting method allows to make long-range interactions more visible.

_________________

Usage
-----

This tool must be used on Hi-C contact matrices corrected using ``hicCorrectMatrix``.

_________________

Output
------

**hicPlotViewpoint** outputs an image with the plotted interactions around the reference point in png or svg format, an example plot can be found bellow. An option allows to also output the interactions as a bedgraph file.

.. image:: $PATH_TO_IMAGES/pulication_plots_viewpoint.png
   :width: 50 %

_________________

| 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>