<tool id="schicexplorer_schicclustercomparments" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>clusters single-cell Hi-C interaction matrices with A/B compartments dimension reduction</description>
    <macros>
        <token name="@BINARY@">scHicClusterCompartments</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        @BINARY@

        --matrix '$matrix_mcooler'

        --numberOfClusters $numberOfClusters

        --clusterMethod $clusterMethod_selector

        #if $chromosomes:
            #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
            --chromosomes $chromosome
        #end if

        #if $norm:
            $norm
        #end if
        #if $binarization:
            $binarization
        #end if

        #if $extra_track_conditional.extra_track_selection == 'gene_density':
            --extraTrack '$extra_track_conditional.extraTrack'
        #elif $extra_track_conditional.extra_track_selection == 'histon_mark':
            --histonMarkType '$extra_track_conditional.histonMarkType'
        #end if

        --outFileName cluster_list.txt

        --threads @THREADS@



    ]]></command>
    <inputs>
        
        <expand macro="matrix_mcooler_macro"/>
        <param name="clusterMethod_selector" type="select" label="Cluster method:">
                <option value="kmeans" selected="True">K-means</option>
                <option value="spectral" >Spectral clustering</option>
        </param>
        <param name="numberOfClusters" type="integer" value="7"  label="Number of clusters" help='How many clusters should be computed by kmeans or spectral clustering' />   

        <param name='norm' type='boolean' truevalue='--norm' label='Use different expected value computation'/>
        <param name='binarization' type='boolean' truevalue='--binarization' label='Convert positive values to 1 and all negative to -1.'/>
        

        <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
        <conditional name="extra_track_conditional">
            <param name='extra_track_selection' label='Extra track type' type='select'>
                <option value='' selected='true'>No track</option>
                <option value='gene_density'>Gene density</option>
                <option value='histon_mark'>Histone mark coverage</option>
            </param>
            <when value='gene_density' >
                <param name='extraTrack' type='data' format='bed' label='Correlate PCA with e.g. gene density or histone marks to flip sign'/>
            </when>
            <when value='histon_mark'>
                <param name='histonMarkType' type='data' format='bed' label='Correlate PCA with e.g. gene density or histone marks to flip sign'/>
            </when>
            <when value='' />
        </conditional>
    </inputs>
    <outputs>
        <data name="outFileName" from_work_dir="cluster_list.txt" format="txt" label="${tool.name} on ${on_string}: Cluster results"/>
    </outputs>
    <tests>
        <test>
            <param name='matrix_mcooler' value='test_matrix.mcool' />
            <param name='clusterMethod_selector' value='kmeans' />
            <param name='numberOfClusters' value='3' />
            <output name="outFileName" file="scHicClusterCompartments/cluster_kmeans.txt" ftype="txt" compare="sim_size" delta="4000"/>
        </test>
        <test>
            <param name='matrix_mcooler' value='test_matrix.mcool' />
            <param name='clusterMethod_selector' value='spectral' />
            <param name='numberOfClusters' value='3' />
            <output name="outFileName" file="scHicClusterCompartments/cluster_spectral.txt" ftype="txt" compare="sim_size" delta="4000"/>
        </test>
        <test>
            <param name='matrix_mcooler' value='test_matrix.mcool' />
            <param name='clusterMethod_selector' value='kmeans' />
            <param name='numberOfClusters' value='3' />
            <param name='binarization' value='True'/>
            <param name='norm' value='True'/>
            <conditional name="extra_track_conditional">
                <param name="extra_track_selection" value="histon_mark"/>
                <param name="histonMarkType" value="scHicClusterCompartments/mm9_H3K36me3.bed.gz" />
            </conditional>
            <output name="outFileName" file="scHicClusterCompartments/cluster_kmeans_binarization_norm_histone_track.txt" ftype="txt" compare="sim_size" delta="4000"/>
        </test>
       <test>
            <param name='matrix_mcooler' value='test_matrix.mcool' />
            <param name='clusterMethod_selector' value='kmeans' />
            <param name='numberOfClusters' value='3' />
            <param name='binarization' value='True'/>
            <param name='norm' value='True'/>
            <conditional name="extra_track_conditional">
                <param name="extra_track_selection" value="gene_density"/>
                <param name="extraTrack" value="scHicClusterCompartments/mm9_gene.bed.gz" />
            </conditional>
            <output name="outFileName" file="scHicClusterCompartments/cluster_spectral_binarization_norm_gene_track.txt" ftype="txt" compare="sim_size" delta="4000"/>
        </test>
    </tests>
    <help><![CDATA[

Clustering with dimension reduction via A/B compartments
========================================================

scHicClusterCompartments uses kmeans or spectral clustering to associate each cell to a cluster and therefore to its cell cycle. 
The clustering is applied on dimension reduced data based on the A/B compartments track. This approach reduces the number of dimensions from samples * (number of bins)^2 to samples * (number of bins). 
Please consider also the other clustering and dimension reduction approaches of the scHicExplorer suite. They can give you better results, 
can be faster or less memory demanding.

For more information about scHiCExplorer please consider our documentation on readthedocs.io_

.. _readthedocs.io: http://schicexplorer.readthedocs.io/
]]></help>
    <expand macro="citations" />

</tool>