comparison hicTransform.xml @ 16:f36828ebdc54 draft

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

15:21b3ef2a6a80

        && mv 'matrix.$matrix_h5_cooler.ext' matrix
]]>
    </command>
    <inputs>
        <expand macro='matrix_h5_cooler_macro' />
        <param name="method_selector" type="select" label="Choose method to apply">
            <option value="obs_exp" selected="True">obs / exp</option>
            <option value="obs_exp_lieberman">obs / exp (Lieberman-Aiden 2009)</option>
            <option value="obs_exp_non_zero">obs / exp (exclude non-zero from exp)</option>
            <option value="pearson">pearson</option>
            <option value="covariance">covariance</option>
        </param>
        <param name='ligation_factor' type='boolean' truevalue='--ligation_factor' falsevalue="" checked="false" label='Multiplies a scaling factor to each entry of the expected matrix to take care of the proximity ligation' />
        <param argument="--perChromosome" type="boolean" truevalue="--perChromosome" falsevalue="" checked="false" label="Computation per chromosome" />
        <repeat name="chromosomeOrder" min="0" title="Chromosomes to include in the computation">
            <param name="chromosome" type="text">
                <validator type="empty_field" />
                <validator type="expression" message="Only alphanumeric characters and the underscore can be used in chromosome names">value.replace('_', '').isalnum()</validator>

        </data>
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
            <param name='method_selector' value='obs_exp_lieberman' />
            <output name="matrix_out" ftype="h5">
                <assert_contents>
                    <has_h5_keys keys='intervals,matrix' />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
            <param name='method_selector' value='obs_exp_lieberman' />
            <param name='ligation_factor' value='True' />
            <output name="matrix_out" ftype="h5">
                <assert_contents>
                    <has_h5_keys keys='intervals,matrix' />
                </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
.. _`Lieberman-Aiden et al. (2009)`: https://doi.org/10.1126/science.1181369
]]>    </help>
    <expand macro="citations" />
</tool>

16:f36828ebdc54

        && mv 'matrix.$matrix_h5_cooler.ext' matrix
]]>
    </command>
    <inputs>
        <expand macro="matrix_h5_cooler_macro" />
        <param name="method_selector" type="select" label="Choose method to apply">
            <option value="obs_exp" selected="True">obs / exp</option>
            <option value="obs_exp_lieberman">obs / exp (Lieberman-Aiden 2009)</option>
            <option value="obs_exp_non_zero">obs / exp (exclude non-zero from exp)</option>
            <option value="pearson">pearson</option>
            <option value="covariance">covariance</option>
        </param>
        <param name="ligation_factor" type="boolean" truevalue="--ligation_factor" falsevalue="" checked="false" label="Multiplies a scaling factor to each entry of the expected matrix to take care of the proximity ligation" />
        <param argument="--perChromosome" type="boolean" truevalue="--perChromosome" falsevalue="" checked="false" label="Computation per chromosome" />
        <repeat name="chromosomeOrder" min="0" title="Chromosomes to include in the computation">
            <param name="chromosome" type="text">
                <validator type="empty_field" />
                <validator type="expression" message="Only alphanumeric characters and the underscore can be used in chromosome names">value.replace('_', '').isalnum()</validator>

        </data>
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
            <param name="method_selector" value="obs_exp_lieberman" />
            <output name="matrix_out" ftype="h5">
                <assert_contents>
                    <has_h5_keys keys="intervals,matrix" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
            <param name="method_selector" value="obs_exp_lieberman" />
            <param name="ligation_factor" value="True" />
            <output name="matrix_out" ftype="h5">
                <assert_contents>
                    <has_h5_keys keys="intervals,matrix" />
                </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
.. _`Lieberman-Aiden et al. (2009)`: https://pubmed.ncbi.nlm.nih.gov/19815776/
]]>    </help>
    <expand macro="citations" />
</tool>