annotate scHicClusterMinHash.xml @ 2:3048283ee054 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d
author iuc
date Fri, 14 Apr 2023 14:26:40 +0000
parents 68648299ffc4
children
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3048283ee054 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d
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1 <tool id="schicexplorer_schicclusterminhash" name="@BINARY@" version="@TOOL_VERSION@.1" profile="@PROFILE@">
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2 <description>clusters single-cell Hi-C interaction matrices with MinHash dimension reduction</description>
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3 <macros>
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4 <token name="@BINARY@">scHicClusterMinHash</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 @BINARY@
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10
1
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11 --matrix '$matrix_scooler'
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1c2e79e9311a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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13 --numberOfClusters $numberOfClusters
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1c2e79e9311a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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15 --clusterMethod $clusterMethod_selector
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16 --numberOfHashFunctions $numberOfHashFunctions
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17 #if $chromosomes:
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18 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
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19 --chromosomes $chromosome
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20 #end if
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22 #if $exactModeMinhash:
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23 $exactModeMinhash
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24 #end if
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25
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26 --outFileName cluster_list.txt
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27 --numberOfNearestNeighbors $numberOfNearestNeighbors
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29 --threads @THREADS@
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33 ]]></command>
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34 <inputs>
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35
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36 <expand macro="matrix_scooler_macro"/>
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37 <param name="clusterMethod_selector" type="select" label="Cluster method:">
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38 <option value="kmeans" selected="True">K-means</option>
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39 <option value="spectral" >Spectral clustering</option>
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40 </param>
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42 <param name="numberOfClusters" type="integer" value="7" label="Number of clusters" help='How many clusters should be computed by kmeans or spectral clustering' />
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43 <param name="numberOfHashFunctions" type="integer" value="800" label="Number of hash functions" help='How many hash functions the minHash algorithm uses.' />
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44 <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?' />
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46 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
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47 <param name='exactModeMinhash' type='boolean' truevalue='--exactModeMinHash' label='The MinHash algorithm computes additional the exact euclidean distance.'/>
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48
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49 </inputs>
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50 <outputs>
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51 <data name="outFileName" from_work_dir="cluster_list.txt" format="txt" label="${tool.name} on ${on_string}: Cluster results"/>
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name='matrix_scooler' value='test_matrix.scool' />
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56 <param name='clusterMethod_selector' value='kmeans' />
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57 <param name='numberOfClusters' value='3' />
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58 <param name='numberOfHashFunctions' value='800' />
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59
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60 <output name="outFileName" file="scHicClusterMinHash/cluster_kmeans.txt" ftype="txt" compare="sim_size" delta="4000"/>
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61 </test>
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62 <test>
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63 <param name='matrix_scooler' value='test_matrix.scool' />
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64 <param name='clusterMethod_selector' value='spectral' />
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65 <param name='numberOfClusters' value='3' />
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66 <param name='numberOfHashFunctions' value='800' />
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68 <output name="outFileName" file="scHicClusterMinHash/cluster_spectral.txt" ftype="txt" compare="sim_size" delta="4000"/>
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69 </test>
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70 <test>
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71 <param name='matrix_scooler' value='test_matrix.scool' />
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72 <param name='clusterMethod_selector' value='kmeans' />
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73 <param name='numberOfClusters' value='3' />
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74 <param name='numberOfHashFunctions' value='800' />
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75 <param name='exactModeMinhash' value='true' />
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77 <output name="outFileName" file="scHicClusterMinHash/cluster_kmeans_exact.txt" ftype="txt" compare="sim_size" delta="4000"/>
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78 </test>
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79 <test>
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80 <param name='matrix_scooler' value='test_matrix.scool' />
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81 <param name='clusterMethod_selector' value='spectral' />
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82 <param name='numberOfClusters' value='3' />
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83 <param name='numberOfHashFunctions' value='800' />
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84 <param name='chromosomes' value='chr1 chr2' />
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85
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86
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87 <output name="outFileName" file="scHicClusterMinHash/cluster_spectral_chromosomes.txt" ftype="txt" compare="sim_size" delta="4000"/>
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88 </test>
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89
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90
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91 </tests>
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92 <help><![CDATA[
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93
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94 Clustering with dimension reduction via MinHash
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95 ===============================================
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96
1
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97 scHicClusterMinHash uses kmeans or spectral clustering to associate each cell to a cluster and therefore to its cell cycle.
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98 The clustering is applied on dimension reduced data based on an approximate kNN search with the local sensitive hashing technique MinHash. This approach reduces the number of dimensions from samples * (number of bins)^2 to samples * samples. The clustering is applied on dimension reduced data based on an approximate kNN search with the local sensitive hashing technique MinHash. This approach reduces the number of dimensions from samples * (number of bins)^2 to samples * samples.
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99 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, Please consider also the other clustering and dimension reduction approaches of the scHicExplorer suite such as `scHicCluster`, `scHicClusterCompartments` and `scHicClusterSVL`. They can give you better results,
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100 can be faster or less memory demanding. can be faster or less memory demanding.
0
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101
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102 For more information about scHiCExplorer please consider our documentation on readthedocs.io_
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103
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104 .. _readthedocs.io: http://schicexplorer.readthedocs.io/
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105 ]]></help>
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106 <expand macro="citations" />
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107
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108 </tool>