comparison hicCompareMatrices.xml @ 13:3ee5332bf57c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9

12:826a6ac07f93

    @BINARY@
    --matrices 'matrix1.$matrix1.ext' 'matrix2.$matrix2.ext'
    --operation $operation
    --outFileName 'matrix.$matrix1.ext'

    && mv 'matrix.$matrix1.ext' matrix
]]>
    </command>
    <inputs>
        <param name='matrix1' type="data" format="h5,cool" label="First matrix" />
        <param name='matrix2' type="data" format="h5,cool" label="Second matrix to compare against the first" />

        <param name='operation' type='select' label="Operation to be used for the comparison">
            <option value='diff'>diff</option>
            <option value="ratio">ratio</option>
            <option value="log2ratio">log2ratio</option>
        </param>
    </inputs>
    <outputs>
        <data name="outFileName" from_work_dir="matrix" format="cool" label="${tool.name} MATRIX on ${on_string}">
            <change_format>
                <when input_dataset="matrix1" attribute="ext" value="h5" format="h5" />

    </outputs>
    <tests>
        <test>
            <param name="matrix1" value="small_test_matrix.h5" />
            <param name="matrix2" value="small_test_matrix.h5" />
            <param name="operation" value='log2ratio' />
            <output name="outFileName" ftype="h5">
                <assert_contents>
                    <has_h5_keys keys='intervals,matrix' />
                </assert_contents>
            </output>
        </test>

    </tests>

13:3ee5332bf57c

    @BINARY@
    --matrices 'matrix1.$matrix1.ext' 'matrix2.$matrix2.ext'
    --operation $operation
    --outFileName 'matrix.$matrix1.ext'
    $noNorm
    && mv 'matrix.$matrix1.ext' matrix
]]>
    </command>
    <inputs>
        <param name="matrix1" type="data" format="h5,cool" label="First matrix" />
        <param name="matrix2" type="data" format="h5,cool" label="Second matrix to compare against the first" />

        <param name="operation" type="select" label="Operation to be used for the comparison">
            <option value="diff">diff</option>
            <option value="ratio">ratio</option>
            <option value="log2ratio">log2ratio</option>
        </param>
        <param name="noNorm" type="boolean" truevalue="--noNorm" falsevalue="" checked="False" label="No normalization" help="Do not apply normalisation before computing the operation" />

    </inputs>
    <outputs>
        <data name="outFileName" from_work_dir="matrix" format="cool" label="${tool.name} MATRIX on ${on_string}">
            <change_format>
                <when input_dataset="matrix1" attribute="ext" value="h5" format="h5" />

    </outputs>
    <tests>
        <test>
            <param name="matrix1" value="small_test_matrix.h5" />
            <param name="matrix2" value="small_test_matrix.h5" />
            <param name="operation" value="log2ratio" />
            <output name="outFileName" ftype="h5">
                <assert_contents>
                    <has_h5_keys keys="intervals,matrix" />
                </assert_contents>
            </output>
        </test>

    </tests>