<tool id="hicexplorer_hichyperoptDetectLoops" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>optimizes parameters for hicDetectLoops</description>
    <macros>
        <token name="@BINARY@">hicHyperoptDetectLoops</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
        @BINARY@

            --matrix  'matrix.$matrix_h5_cooler.ext'

            #if '$proteinFile':
                --proteinFile '$proteinFile'
            #end if

            #if '$maximumNumberOfLoops':
                --maximumNumberOfLoops '$maximumNumberOfLoops'
            #end if

            #if '$resolution':
                --resolution '$resolution'
            #end if

            #if '$runs':
                --runs '$runs'
            #end if

            --outputFileName hyperopt_result.txt

            --threads @THREADS@
]]>
    </command>
    <inputs>
        <expand macro="matrix_h5_cooler_macro" />
        <param argument="--proteinFile" type='data' format="bed" label="Protein peak file in bed format" help= "The protein file to validate the detected loops." />
        <param argument="--maximumNumberOfLoops" type="integer" min='0' max='100000' label="Maximum number of loops" help= "The maximum number of loops that should be used for optimization computation." value='10000' />
        <param argument="--resolution" type="integer" min='0' max='100000000' label="Resolution of the matrix" help="The matrix resolution of the Hi-C interaction matrix." value='10000' />
        <param argument="--runs" type="integer" min='2' max='10000' label="Hyperopt runs" help= "The number of iterations hyperopt uses to search for a result" value='100' />
    </inputs>
    <outputs>
        <data name='hyperopt_result' from_work_dir='hyperopt_result.txt' format='txt' label='Computed parameters for hicDetectLoops' />
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
            <param name="proteinFile" value="hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak" />
            <param name="maximumNumberOfLoops" value="5" />
            <param name="resolution" value="2" />
            <param name="runs" value="5" />
            <output name="hyperopt_result" file="hicHyperoptDetectLoops/loops.bedgraph" ftype="txt" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[

Hyperopt parameter optimization loop detection
==============================================

Compute with a protein peak data file (bed format) optimal parameters for the loop calling. Useful proteins are e.g. CTCF or cohesin.

_________________

Usage
-----

A command line example is available below (easily matchable in Galaxy using each field information):

̀`$ hicHyperoptDetectLoops -m matrix.cool -o hyperopt_result.txt --maximumNumberOfLoops 10000 --resolution 10000 --runs 100`


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>