comparison scHicCluster.xml @ 1:36e26166034d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"

0:a532cbac217a

    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        @BINARY@

        --matrix '$matrix_mcooler'

        --numberOfClusters $numberOfClusters

        --clusterMethod $clusterMethod_selector

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

        --dimensionReductionMethod $dimensionReductionMethod_selector

        --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="dimensionReductionMethod_selector" type="select" label="Apply dimension reduction:">
                <option value="none" selected="True">No dimension reduction</option>
                <option value="knn" >Exact k-nearest neighbors</option>
                <option value="pca" >Principal components</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='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
    </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='dimensionReductionMethod_selector' value='none' />
            <param name='numberOfClusters' value='7' />
            <output name="outFileName" file="scHicCluster/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='kmeans' />
            <param name='dimensionReductionMethod_selector' value='none' />
            <param name='numberOfClusters' value='7' />
            <param name='chromosomes' value='chr1 chr2' />

            <output name="outFileName" file="scHicCluster/cluster_kmeans_chromosomes.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='dimensionReductionMethod_selector' value='knn' />
            <param name='numberOfClusters' value='7' />
            <output name="outFileName" file="scHicCluster/cluster_spectral_knn.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='dimensionReductionMethod_selector' value='pca' />
            <param name='numberOfClusters' value='7' />
            <output name="outFileName" file="scHicCluster/cluster_spectral_pca.txt" ftype="txt" compare="sim_size" delta="4000"/>
        </test>

Clustering on raw data
======================

scHicCluster uses kmeans or spectral clustering to associate each cell to a cluster and therefore to its cell cycle. 
The clustering can be run on the raw data, on a kNN computed via the exact euclidean distance or via PCA. 
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>

1:36e26166034d

    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        @BINARY@

        --matrix '$matrix_scooler'

        --numberOfClusters $numberOfClusters

        --clusterMethod $clusterMethod_selector

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

        --dimensionReductionMethod $dimensionReductionMethod_selector
        --numberOfNearestNeighbors $numberOfNearestNeighbors
        --outFileName cluster_list.txt

        --threads @THREADS@



    ]]></command>
    <inputs>
        
        <expand macro="matrix_scooler_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="dimensionReductionMethod_selector" type="select" label="Apply dimension reduction:">
                <option value="none" selected="True">No dimension reduction</option>
                <option value="knn" >Exact k-nearest neighbors</option>
                <option value="pca" >Principal components</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="numberOfNearestNeighbors" type="integer" value="100"  label="Number of nearest neighbors" help='How many nearest neighbors should be computed for the k-nn graph?' />   

        <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
    </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_scooler' value='test_matrix.scool' />
            <param name='clusterMethod_selector' value='kmeans' />
            <param name='dimensionReductionMethod_selector' value='none' />
            <param name='numberOfClusters' value='7' />
            <output name="outFileName" file="scHicCluster/cluster_kmeans.txt" ftype="txt" compare="sim_size" delta="4000"/>
        </test>
        <test>
            <param name='matrix_scooler' value='test_matrix.scool' />
            <param name='clusterMethod_selector' value='kmeans' />
            <param name='dimensionReductionMethod_selector' value='none' />
            <param name='numberOfClusters' value='7' />
            <param name='chromosomes' value='chr1 chr2' />

            <output name="outFileName" file="scHicCluster/cluster_kmeans_chromosomes.txt" ftype="txt" compare="sim_size" delta="4000"/>
        </test>
        <test>
            <param name='matrix_scooler' value='test_matrix.scool' />
            <param name='clusterMethod_selector' value='spectral' />
            <param name='dimensionReductionMethod_selector' value='knn' />
            <param name='numberOfClusters' value='7' />
            <output name="outFileName" file="scHicCluster/cluster_spectral_knn.txt" ftype="txt" compare="sim_size" delta="4000"/>
        </test>
        <test>
            <param name='matrix_scooler' value='test_matrix.scool' />
            <param name='clusterMethod_selector' value='spectral' />
            <param name='dimensionReductionMethod_selector' value='pca' />
            <param name='numberOfClusters' value='7' />
            <output name="outFileName" file="scHicCluster/cluster_spectral_pca.txt" ftype="txt" compare="sim_size" delta="4000"/>
        </test>

Clustering on raw data
======================

scHicCluster uses kmeans or spectral clustering to associate each cell to a cluster and therefore to its cell cycle. 
The clustering can be run on the raw data, on a kNN computed via the exact euclidean distance or via PCA. 
Please consider also the other clustering and dimension reduction approaches of the scHicExplorer suite such as `scHicCluster`, `scHicClusterMinHash` and `scHicClusterSVL`. 
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>