Mercurial > repos > iuc > schicexplorer_schicclusterminhash
comparison scHicClusterMinHash.xml @ 1:68648299ffc4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
author | iuc |
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date | Tue, 10 Mar 2020 15:11:23 -0400 |
parents | 1c2e79e9311a |
children | 3048283ee054 |
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0:1c2e79e9311a | 1:68648299ffc4 |
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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 --numberOfHashFunctions $numberOfHashFunctions | 16 --numberOfHashFunctions $numberOfHashFunctions |
22 #if $exactModeMinhash: | 22 #if $exactModeMinhash: |
23 $exactModeMinhash | 23 $exactModeMinhash |
24 #end if | 24 #end if |
25 | 25 |
26 --outFileName cluster_list.txt | 26 --outFileName cluster_list.txt |
27 --numberOfNearestNeighbors $numberOfNearestNeighbors | |
27 | 28 |
28 --threads @THREADS@ | 29 --threads @THREADS@ |
29 | 30 |
30 | 31 |
31 | 32 |
32 ]]></command> | 33 ]]></command> |
33 <inputs> | 34 <inputs> |
34 | 35 |
35 <expand macro="matrix_mcooler_macro"/> | 36 <expand macro="matrix_scooler_macro"/> |
36 <param name="clusterMethod_selector" type="select" label="Cluster method:"> | 37 <param name="clusterMethod_selector" type="select" label="Cluster method:"> |
37 <option value="kmeans" selected="True">K-means</option> | 38 <option value="kmeans" selected="True">K-means</option> |
38 <option value="spectral" >Spectral clustering</option> | 39 <option value="spectral" >Spectral clustering</option> |
39 </param> | 40 </param> |
40 | 41 |
41 <param name="numberOfClusters" type="integer" value="7" label="Number of clusters" help='How many clusters should be computed by kmeans or spectral clustering' /> | 42 <param name="numberOfClusters" type="integer" value="7" label="Number of clusters" help='How many clusters should be computed by kmeans or spectral clustering' /> |
42 <param name="numberOfHashFunctions" type="integer" value="800" label="Number of hash functions" help='How many hash functions the minHash algorithm uses.' /> | 43 <param name="numberOfHashFunctions" type="integer" value="800" label="Number of hash functions" help='How many hash functions the minHash algorithm uses.' /> |
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?' /> | |
43 | 45 |
44 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/> | 46 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/> |
45 <param name='exactModeMinhash' type='boolean' truevalue='--exactModeMinHash' label='The MinHash algorithm computes additional the exact euclidean distance.'/> | 47 <param name='exactModeMinhash' type='boolean' truevalue='--exactModeMinHash' label='The MinHash algorithm computes additional the exact euclidean distance.'/> |
46 | 48 |
47 </inputs> | 49 </inputs> |
48 <outputs> | 50 <outputs> |
49 <data name="outFileName" from_work_dir="cluster_list.txt" format="txt" label="${tool.name} on ${on_string}: Cluster results"/> | 51 <data name="outFileName" from_work_dir="cluster_list.txt" format="txt" label="${tool.name} on ${on_string}: Cluster results"/> |
50 </outputs> | 52 </outputs> |
51 <tests> | 53 <tests> |
52 <test> | 54 <test> |
53 <param name='matrix_mcooler' value='test_matrix.mcool' /> | 55 <param name='matrix_scooler' value='test_matrix.scool' /> |
54 <param name='clusterMethod_selector' value='kmeans' /> | 56 <param name='clusterMethod_selector' value='kmeans' /> |
55 <param name='numberOfClusters' value='3' /> | 57 <param name='numberOfClusters' value='3' /> |
56 <param name='numberOfHashFunctions' value='800' /> | 58 <param name='numberOfHashFunctions' value='800' /> |
57 | 59 |
58 <output name="outFileName" file="scHicClusterMinHash/cluster_kmeans.txt" ftype="txt" compare="sim_size" delta="4000"/> | 60 <output name="outFileName" file="scHicClusterMinHash/cluster_kmeans.txt" ftype="txt" compare="sim_size" delta="4000"/> |
59 </test> | 61 </test> |
60 <test> | 62 <test> |
61 <param name='matrix_mcooler' value='test_matrix.mcool' /> | 63 <param name='matrix_scooler' value='test_matrix.scool' /> |
62 <param name='clusterMethod_selector' value='spectral' /> | 64 <param name='clusterMethod_selector' value='spectral' /> |
63 <param name='numberOfClusters' value='3' /> | 65 <param name='numberOfClusters' value='3' /> |
64 <param name='numberOfHashFunctions' value='800' /> | 66 <param name='numberOfHashFunctions' value='800' /> |
65 | 67 |
66 <output name="outFileName" file="scHicClusterMinHash/cluster_spectral.txt" ftype="txt" compare="sim_size" delta="4000"/> | 68 <output name="outFileName" file="scHicClusterMinHash/cluster_spectral.txt" ftype="txt" compare="sim_size" delta="4000"/> |
67 </test> | 69 </test> |
68 <test> | 70 <test> |
69 <param name='matrix_mcooler' value='test_matrix.mcool' /> | 71 <param name='matrix_scooler' value='test_matrix.scool' /> |
70 <param name='clusterMethod_selector' value='kmeans' /> | 72 <param name='clusterMethod_selector' value='kmeans' /> |
71 <param name='numberOfClusters' value='3' /> | 73 <param name='numberOfClusters' value='3' /> |
72 <param name='numberOfHashFunctions' value='800' /> | 74 <param name='numberOfHashFunctions' value='800' /> |
73 <param name='exactModeMinhash' value='true' /> | 75 <param name='exactModeMinhash' value='true' /> |
74 | 76 |
75 <output name="outFileName" file="scHicClusterMinHash/cluster_kmeans_exact.txt" ftype="txt" compare="sim_size" delta="4000"/> | 77 <output name="outFileName" file="scHicClusterMinHash/cluster_kmeans_exact.txt" ftype="txt" compare="sim_size" delta="4000"/> |
76 </test> | 78 </test> |
77 <test> | 79 <test> |
78 <param name='matrix_mcooler' value='test_matrix.mcool' /> | 80 <param name='matrix_scooler' value='test_matrix.scool' /> |
79 <param name='clusterMethod_selector' value='spectral' /> | 81 <param name='clusterMethod_selector' value='spectral' /> |
80 <param name='numberOfClusters' value='3' /> | 82 <param name='numberOfClusters' value='3' /> |
81 <param name='numberOfHashFunctions' value='800' /> | 83 <param name='numberOfHashFunctions' value='800' /> |
82 <param name='chromosomes' value='chr1 chr2' /> | 84 <param name='chromosomes' value='chr1 chr2' /> |
83 | 85 |
90 <help><![CDATA[ | 92 <help><![CDATA[ |
91 | 93 |
92 Clustering with dimension reduction via MinHash | 94 Clustering with dimension reduction via MinHash |
93 =============================================== | 95 =============================================== |
94 | 96 |
95 scHicClusterMinHash uses kmeans or spectral clustering to associate each cell to a cluster and therefore to its cell cycle. | 97 scHicClusterMinHash uses kmeans or spectral clustering to associate each cell to a cluster and therefore to its cell cycle. |
96 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. | 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. |
97 Please consider also the other clustering and dimension reduction approaches of the scHicExplorer suite. They can give you better results, | 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, |
98 can be faster or less memory demanding. | 100 can be faster or less memory demanding. can be faster or less memory demanding. |
99 | 101 |
100 For more information about scHiCExplorer please consider our documentation on readthedocs.io_ | 102 For more information about scHiCExplorer please consider our documentation on readthedocs.io_ |
101 | 103 |
102 .. _readthedocs.io: http://schicexplorer.readthedocs.io/ | 104 .. _readthedocs.io: http://schicexplorer.readthedocs.io/ |
103 ]]></help> | 105 ]]></help> |