comparison scHicClusterCompartments.xml @ 1:0bc84d7d94d4 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
author iuc
date Tue, 10 Mar 2020 15:08:15 -0400
parents 5426f006d7ed
children 54b6cef88a7f
comparison
equal deleted inserted replaced
0:5426f006d7ed 1:0bc84d7d94d4
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 @BINARY@ 9 @BINARY@
10 10
11 --matrix '$matrix_mcooler' 11 --matrix '$matrix_scooler'
12 12
13 --numberOfClusters $numberOfClusters 13 --numberOfClusters $numberOfClusters
14 14
15 --clusterMethod $clusterMethod_selector 15 --clusterMethod $clusterMethod_selector
16 16
39 39
40 40
41 ]]></command> 41 ]]></command>
42 <inputs> 42 <inputs>
43 43
44 <expand macro="matrix_mcooler_macro"/> 44 <expand macro="matrix_scooler_macro"/>
45 <param name="clusterMethod_selector" type="select" label="Cluster method:"> 45 <param name="clusterMethod_selector" type="select" label="Cluster method:">
46 <option value="kmeans" selected="True">K-means</option> 46 <option value="kmeans" selected="True">K-means</option>
47 <option value="spectral" >Spectral clustering</option> 47 <option value="spectral" >Spectral clustering</option>
48 </param> 48 </param>
49 <param name="numberOfClusters" type="integer" value="7" label="Number of clusters" help='How many clusters should be computed by kmeans or spectral clustering' /> 49 <param name="numberOfClusters" type="integer" value="7" label="Number of clusters" help='How many clusters should be computed by kmeans or spectral clustering' />
71 <outputs> 71 <outputs>
72 <data name="outFileName" from_work_dir="cluster_list.txt" format="txt" label="${tool.name} on ${on_string}: Cluster results"/> 72 <data name="outFileName" from_work_dir="cluster_list.txt" format="txt" label="${tool.name} on ${on_string}: Cluster results"/>
73 </outputs> 73 </outputs>
74 <tests> 74 <tests>
75 <test> 75 <test>
76 <param name='matrix_mcooler' value='test_matrix.mcool' /> 76 <param name='matrix_scooler' value='test_matrix.scool' />
77 <param name='clusterMethod_selector' value='kmeans' /> 77 <param name='clusterMethod_selector' value='kmeans' />
78 <param name='numberOfClusters' value='3' /> 78 <param name='numberOfClusters' value='3' />
79 <output name="outFileName" file="scHicClusterCompartments/cluster_kmeans.txt" ftype="txt" compare="sim_size" delta="4000"/> 79 <output name="outFileName" file="scHicClusterCompartments/cluster_kmeans.txt" ftype="txt" compare="sim_size" delta="4000"/>
80 </test> 80 </test>
81 <test> 81 <test>
82 <param name='matrix_mcooler' value='test_matrix.mcool' /> 82 <param name='matrix_scooler' value='test_matrix.scool' />
83 <param name='clusterMethod_selector' value='spectral' /> 83 <param name='clusterMethod_selector' value='spectral' />
84 <param name='numberOfClusters' value='3' /> 84 <param name='numberOfClusters' value='3' />
85 <output name="outFileName" file="scHicClusterCompartments/cluster_spectral.txt" ftype="txt" compare="sim_size" delta="4000"/> 85 <output name="outFileName" file="scHicClusterCompartments/cluster_spectral.txt" ftype="txt" compare="sim_size" delta="4000"/>
86 </test> 86 </test>
87 <test> 87 <test>
88 <param name='matrix_mcooler' value='test_matrix.mcool' /> 88 <param name='matrix_scooler' value='test_matrix.scool' />
89 <param name='clusterMethod_selector' value='kmeans' /> 89 <param name='clusterMethod_selector' value='kmeans' />
90 <param name='numberOfClusters' value='3' /> 90 <param name='numberOfClusters' value='3' />
91 <param name='binarization' value='True'/> 91 <param name='binarization' value='True'/>
92 <param name='norm' value='True'/> 92 <param name='norm' value='True'/>
93 <conditional name="extra_track_conditional"> 93 <conditional name="extra_track_conditional">
95 <param name="histonMarkType" value="scHicClusterCompartments/mm9_H3K36me3.bed.gz" /> 95 <param name="histonMarkType" value="scHicClusterCompartments/mm9_H3K36me3.bed.gz" />
96 </conditional> 96 </conditional>
97 <output name="outFileName" file="scHicClusterCompartments/cluster_kmeans_binarization_norm_histone_track.txt" ftype="txt" compare="sim_size" delta="4000"/> 97 <output name="outFileName" file="scHicClusterCompartments/cluster_kmeans_binarization_norm_histone_track.txt" ftype="txt" compare="sim_size" delta="4000"/>
98 </test> 98 </test>
99 <test> 99 <test>
100 <param name='matrix_mcooler' value='test_matrix.mcool' /> 100 <param name='matrix_scooler' value='test_matrix.scool' />
101 <param name='clusterMethod_selector' value='kmeans' /> 101 <param name='clusterMethod_selector' value='kmeans' />
102 <param name='numberOfClusters' value='3' /> 102 <param name='numberOfClusters' value='3' />
103 <param name='binarization' value='True'/> 103 <param name='binarization' value='True'/>
104 <param name='norm' value='True'/> 104 <param name='norm' value='True'/>
105 <conditional name="extra_track_conditional"> 105 <conditional name="extra_track_conditional">
114 Clustering with dimension reduction via A/B compartments 114 Clustering with dimension reduction via A/B compartments
115 ======================================================== 115 ========================================================
116 116
117 scHicClusterCompartments uses kmeans or spectral clustering to associate each cell to a cluster and therefore to its cell cycle. 117 scHicClusterCompartments uses kmeans or spectral clustering to associate each cell to a cluster and therefore to its cell cycle.
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). 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).
119 Please consider also the other clustering and dimension reduction approaches of the scHicExplorer suite. They can give you better results, 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,
120 can be faster or less memory demanding. 120 can be faster or less memory demanding.
121 121
122 For more information about scHiCExplorer please consider our documentation on readthedocs.io_ 122 For more information about scHiCExplorer please consider our documentation on readthedocs.io_
123 123
124 .. _readthedocs.io: http://schicexplorer.readthedocs.io/ 124 .. _readthedocs.io: http://schicexplorer.readthedocs.io/