comparison hicMergeMatrixBins.xml @ 17:03dd3c16ae4e draft

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

16:9e357a8b2ec3

<tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>merge adjacent bins from a Hi-C contact matrix to reduce its resolution</description>
    <macros>
        <token name="@BINARY@">hicMergeMatrixBins</token>
        <import>macros.xml</import>
    </macros>

            --matrix 'matrix.$matrix_h5_cooler.ext'
            --numBins $numBins
            $runningWindow
            --outFileName 'matrix.$matrix_h5_cooler.ext'
        && mv 'matrix.$matrix_h5_cooler.ext' matrix

]]>
    </command>
    <inputs>
        <expand macro='matrix_h5_cooler_macro' />

        <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" />
        <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Set to merge for using a running window of length --numBins. Usually not set." />
    </inputs>
    <outputs>
        <data name="outFileName" from_work_dir="matrix" format="cool">
              <change_format>
                <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5"/>
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
            <param name="numBins" value="5" />
            <output name="outFileName" ftype="h5">
                <assert_contents>
                    <has_h5_keys keys='intervals,matrix,nan_bins'/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

_________________

| 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>

17:03dd3c16ae4e

<tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>merge adjacent bins from a Hi-C contact matrix to reduce its resolution</description>
    <macros>
        <token name="@BINARY@">hicMergeMatrixBins</token>
        <import>macros.xml</import>
    </macros>

            --matrix 'matrix.$matrix_h5_cooler.ext'
            --numBins $numBins
            $runningWindow
            --outFileName 'matrix.$matrix_h5_cooler.ext'
        && mv 'matrix.$matrix_h5_cooler.ext' matrix
]]>
    </command>
    <inputs>
        <expand macro='matrix_h5_cooler_macro' />
        <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" />
        <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Set to merge for using a running window of length --numBins. Usually not set." />
    </inputs>
    <outputs>
        <data name="outFileName" from_work_dir="matrix" format="cool">
            <change_format>
                <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
            <param name="numBins" value="5" />
            <output name="outFileName" ftype="h5">
                <assert_contents>
                    <has_h5_keys keys='intervals,matrix,nan_bins' />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

_________________

| 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>