annotate hicDifferentialTAD.xml @ 3:5dfba24d7bdd draft default tip

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

<tool id="hicexplorer_hicdifferentialtad" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>searches for differential TADs</description>
    <macros>
        <token name="@BINARY@">hicDifferentialTAD</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$matrix_h5_cooler_target' 'matrix_target.$matrix_h5_cooler_target.ext' &&
        ln -s '$matrix_h5_cooler_control' 'matrix_control.$matrix_h5_cooler_control.ext' &&

        @BINARY@

            --targetMatrix  'matrix_target.$matrix_h5_cooler_target.ext'
            --controlMatrix  'matrix_control.$matrix_h5_cooler_control.ext'

            #if $tadDomains:
                --tadDomains '$tadDomains'
            #end if

            #if $pValue:
                --pValue $pValue
            #end if
       
            --mode $mode_selector
            --modeReject $modeReject
            --outFileNamePrefix galaxy_differential_tad
            --threads @THREADS@

]]>
    </command>
    <inputs>
        <param name="matrix_h5_cooler_target" type="data" format="h5,cool" label="Target matrix to compute on" />
        <param name="matrix_h5_cooler_control" type="data" format="h5,cool" label="Control matrix to compute on" />

        <param argument="--tadDomains" type="data" format="bed" optional="false" label="TAD domains file" help= "The TADs domain file computed by hicFindTADs." />
        <param argument="--pValue" type="float" label="P-value" min="0.0" max="1.0" help= "H0 is considered as \'two regions are identical.\' i.e. all regions with a test result of smaller p-value are rejected and considered as differential." value="0.05" />
        <param name="mode_selector" type="select" label="Method to compute the differentail TAD expression">
            <option value="intra-TAD">intra-TAD</option>
            <option value="left-inter-TAD">left-inter-TAD</option>
            <option value="right-inter-TAD">right-inter-TAD</option>
            <option value="all" selected="True">all</option>
        </param>

        <param name="modeReject" type="select" label="Method to compute the differentail TAD expression">
            <option value="one" selected="True">one</option>
            <option value="all">all</option>
        </param>
    </inputs>
    <outputs>
        <data name="acceptedTADs" from_work_dir="galaxy_differential_tad_accepted.diff_tad" format="txt" label="Accepted TADs" />
        <data name="rejectedTADs" from_work_dir="galaxy_differential_tad_rejected.diff_tad" format="txt" label="Rejected TADs" />
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler_target" value="small_test_matrix.cool" />
            <param name="matrix_h5_cooler_control" value="small_test_matrix.cool" />

            <param name="tadDomains" ftype="bed" value="hicDifferentialTAD/multiNone_domains.bed" />
            <param name="pValue" value="1.0" />
            <param name="mode_selector" value="all" />
            <param name="modeReject" value="one" />
            <output name="acceptedTADs" file="hicDifferentialTAD/accepted.txt" ftype="txt" />
            <!-- TODO remove lines_diff when updating to >=3.7 where" a multicore issue was solved that led to skipping data at the start and end of chromosomes-->
            <output name="rejectedTADs" file="hicDifferentialTAD/rejected.txt" ftype="txt" lines_diff="4"/>
        </test>
    </tests>
    <help><![CDATA[

Differential TAD detection
==========================

Computes if precomputed TADs are differentially expressed between two samples.


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>