comparison hicPlotViewpoint.xml @ 13:b637a1e3cb14 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"

12:76ad9e40883d

<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>

]]>
    </command>
    <inputs>
        <expand macro='matrix_h5_cooler_multiple_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_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 format="bedgraph" name="interactionFile" >
            <filter>interactionOutFileName</filter>
            <discover_datasets pattern='__name_and_ext__' directory="interaction" visible="true"/>
        </data>

    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.cool"/>
            <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_multiple" value="Li_et_al_2015.cool"/>
            <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">
                <discovered_dataset designation="0_interactions" file="li_32-33mb_interactions.bedgraph" />
            </output>
        </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.

_________________

| 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>

13:b637a1e3cb14

<tool id="hicexplorer_hicplotviewpoint" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>plot interactions around a viewpoint</description>
    <macros>
        <token name="@BINARY@">hicPlotViewpoint</token>
        <import>macros.xml</import>
    </macros>

]]>
    </command>
    <inputs>
        <expand macro='matrix_h5_cooler_multiple_macro' />
        <expand macro="region" />
        <param name="referencePoint" type="text" label="Reference point" help="The format is chr:referencePoint or chr:regionStart-regionEnd.">
            <validator type="expression" message="Only alphanumeric characters, the colon or a dash are allowed.">not value or value.replace(':', '').replace('-', '').isalnum()</validator>
        </param>
        <param argument="--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_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 format="bedgraph" name="interactionFile">
            <filter>interactionOutFileName</filter>
            <discover_datasets pattern='__name_and_ext__' directory="interaction" visible="true" />
        </data>
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.cool" />
            <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_multiple" value="Li_et_al_2015.cool" />
            <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">
                <discovered_dataset designation="0_interactions" file="li_32-33mb_interactions.bedgraph" />
            </output>
        </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.

_________________

| 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>