Mercurial > repos > iuc > schicexplorer_schicclustercompartments

annotate scHicClusterCompartments.xml @ 2:54b6cef88a7f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d
author iuc
date Fri, 14 Apr 2023 14:25:07 +0000
parents 0bc84d7d94d4
children
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54b6cef88a7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d
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1 <tool id="schicexplorer_schicclustercompartments" name="@BINARY@" version="@TOOL_VERSION@.1" profile="@PROFILE@">
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2 <description>clusters single-cell Hi-C interaction matrices with A/B compartments dimension reduction</description>
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3 <macros>
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4 <token name="@BINARY@">scHicClusterCompartments</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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11 --matrix '$matrix_scooler'
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13 --numberOfClusters $numberOfClusters
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15 --clusterMethod $clusterMethod_selector
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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 $norm:
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23 $norm
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24 #end if
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25 #if $binarization:
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26 $binarization
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27 #end if
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29 #if $extra_track_conditional.extra_track_selection == 'gene_density':
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30 --extraTrack '$extra_track_conditional.extraTrack'
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31 #elif $extra_track_conditional.extra_track_selection == 'histon_mark':
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32 --histonMarkType '$extra_track_conditional.histonMarkType'
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33 #end if
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35 --outFileName cluster_list.txt
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37 --threads @THREADS@
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41 ]]></command>
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42 <inputs>
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43
1
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44 <expand macro="matrix_scooler_macro"/>
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45 <param name="clusterMethod_selector" type="select" label="Cluster method:">
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46 <option value="kmeans" selected="True">K-means</option>
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47 <option value="spectral" >Spectral clustering</option>
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48 </param>
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49 <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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50
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51 <param name='norm' type='boolean' truevalue='--norm' label='Use different expected value computation'/>
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52 <param name='binarization' type='boolean' truevalue='--binarization' label='Convert positive values to 1 and all negative to -1.'/>
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54
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55 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
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56 <conditional name="extra_track_conditional">
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57 <param name='extra_track_selection' label='Extra track type' type='select'>
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58 <option value='' selected='true'>No track</option>
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59 <option value='gene_density'>Gene density</option>
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60 <option value='histon_mark'>Histone mark coverage</option>
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61 </param>
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62 <when value='gene_density' >
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63 <param name='extraTrack' type='data' format='bed' label='Correlate PCA with e.g. gene density or histone marks to flip sign'/>
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64 </when>
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65 <when value='histon_mark'>
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66 <param name='histonMarkType' type='data' format='bed' label='Correlate PCA with e.g. gene density or histone marks to flip sign'/>
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67 </when>
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68 <when value='' />
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69 </conditional>
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70 </inputs>
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71 <outputs>
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72 <data name="outFileName" from_work_dir="cluster_list.txt" format="txt" label="${tool.name} on ${on_string}: Cluster results"/>
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73 </outputs>
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74 <tests>
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75 <test>
1
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76 <param name='matrix_scooler' value='test_matrix.scool' />
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77 <param name='clusterMethod_selector' value='kmeans' />
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78 <param name='numberOfClusters' value='3' />
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79 <output name="outFileName" file="scHicClusterCompartments/cluster_kmeans.txt" ftype="txt" compare="sim_size" delta="4000"/>
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80 </test>
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81 <test>
1
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82 <param name='matrix_scooler' value='test_matrix.scool' />
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83 <param name='clusterMethod_selector' value='spectral' />
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84 <param name='numberOfClusters' value='3' />
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85 <output name="outFileName" file="scHicClusterCompartments/cluster_spectral.txt" ftype="txt" compare="sim_size" delta="4000"/>
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86 </test>
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87 <test>
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88 <param name='matrix_scooler' value='test_matrix.scool' />
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89 <param name='clusterMethod_selector' value='kmeans' />
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90 <param name='numberOfClusters' value='3' />
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91 <param name='binarization' value='True'/>
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92 <param name='norm' value='True'/>
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93 <conditional name="extra_track_conditional">
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94 <param name="extra_track_selection" value="histon_mark"/>
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95 <param name="histonMarkType" value="scHicClusterCompartments/mm9_H3K36me3.bed.gz" />
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96 </conditional>
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97 <output name="outFileName" file="scHicClusterCompartments/cluster_kmeans_binarization_norm_histone_track.txt" ftype="txt" compare="sim_size" delta="4000"/>
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98 </test>
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99 <test>
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100 <param name='matrix_scooler' value='test_matrix.scool' />
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101 <param name='clusterMethod_selector' value='kmeans' />
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102 <param name='numberOfClusters' value='3' />
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103 <param name='binarization' value='True'/>
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104 <param name='norm' value='True'/>
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105 <conditional name="extra_track_conditional">
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106 <param name="extra_track_selection" value="gene_density"/>
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107 <param name="extraTrack" value="scHicClusterCompartments/mm9_gene.bed.gz" />
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108 </conditional>
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109 <output name="outFileName" file="scHicClusterCompartments/cluster_spectral_binarization_norm_gene_track.txt" ftype="txt" compare="sim_size" delta="4000"/>
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110 </test>
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111 </tests>
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112 <help><![CDATA[
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113
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114 Clustering with dimension reduction via A/B compartments
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115 ========================================================
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116
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117 scHicClusterCompartments uses kmeans or spectral clustering to associate each cell to a cluster and therefore to its cell cycle.
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118 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).
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119 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,
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120 can be faster or less memory demanding.
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121
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122 For more information about scHiCExplorer please consider our documentation on readthedocs.io_
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123
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124 .. _readthedocs.io: http://schicexplorer.readthedocs.io/
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125 ]]></help>
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126 <expand macro="citations" />
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127
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128 </tool>