Mercurial > repos > iuc > schicexplorer_schicclustercompartments
view scHicClusterCompartments.xml @ 2:54b6cef88a7f draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d
author | iuc |
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date | Fri, 14 Apr 2023 14:25:07 +0000 |
parents | 0bc84d7d94d4 |
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<tool id="schicexplorer_schicclustercompartments" name="@BINARY@" version="@TOOL_VERSION@.1" profile="@PROFILE@"> <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_scooler' --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_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="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_scooler' value='test_matrix.scool' /> <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_scooler' value='test_matrix.scool' /> <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_scooler' value='test_matrix.scool' /> <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_scooler' value='test_matrix.scool' /> <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 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> <expand macro="citations" /> </tool>