<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
            
            #if not $prefixLoop_selector == 'keep':
                 --chrPrefixLoops $prefixLoop_selector
            #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 name="prefixLoop_selector" type="select" label="Add, remove, or keep the chr-prefix of the loop/TAD data">
            <option value="keep" selected="True">Keep</option>
            <option value="add">Add</option>
            <option value="remove">Remove</option>
        </param>
        <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>