annotate chicDifferentialTest.xml @ 8:9d42a6133690 draft

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

<tool id="hicexplorer_chicdifferentialtest" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>computes differential interactions of viewpoints</description>
    <macros>
        <token name="@BINARY@">chicDifferentialTest</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        #import re
        @BINARY@
            --aggregatedFile $aggregatedFile
            --statisticTest $statisticTest_selector
            --alpha $alpha
            --outFileName differentialFile.hdf5
            --threads @THREADS@

    ]]>    </command>
    <inputs>
        <param name="aggregatedFile" type="data" format="h5" label="The aggregated data file created by chicAggregateStatistic" />
        <param name="alpha" type="float" value="2.0" label="Alpha" help="Accept all samples to significance level alpha." />
        <param name="statisticTest_selector" type="select" label="Statistical test">
            <option value="fisher" selected="True">Fisher exact</option>
            <option value="chi2">Chi2 contingency</option>
        </param>
    </inputs>
    <outputs>
        <data name="differentialFile" from_work_dir="differentialFile.hdf5" format="h5" label="Differential test file" />
    </outputs>
    <tests>
        <test>
            <param name="aggregatedFile" value="cHi-C/chicAggregateStatistic/aggregate.hdf5" />
            <param name="statisticTest_selector" value="chi2" />
            <param name="alpha" value="0.5" />
            <output name="differentialFile" ftype="h5">
                <assert_contents>
                    <has_h5_attribute key="type" value="differential" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

Differential testing of two viewpoints
======================================

chicDifferentialTest tests if two locations under consideration of the reference point have a different interaction count. Either Fisher's test or chi2 contingency test can be used.
Input files for this test can be created with `chicAggregateStatistic`. H0 is assuming the interactions are not different. Therefore the differential interaction counts are all where H0 was rejected.


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>