comparison hicMergeMatrixBins.xml @ 21:08a76d7a4bdb draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788

20:9fb16042c466

<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>

        ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
        @BINARY@
            --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">

        <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[

21:08a76d7a4bdb

<tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <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>

        ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
        @BINARY@
            --matrix 'matrix.$matrix_h5_cooler.ext'
            --numBins $numBins
            $runningWindow
            --outFileName 'out_matrix.$matrix_h5_cooler.ext'
        && mv 'out_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">

        <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[