Mercurial > repos > iuc > schicexplorer_schiccluster
comparison scHicCluster.xml @ 0:a532cbac217a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
author | iuc |
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date | Thu, 23 Jan 2020 15:57:55 -0500 |
parents | |
children | 36e26166034d |
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-1:000000000000 | 0:a532cbac217a |
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1 <tool id="schicexplorer_schiccluster" name="@BINARY@" version="@WRAPPER_VERSION@.0"> | |
2 <description>clusters single-cell Hi-C interaction matrices on the raw data</description> | |
3 <macros> | |
4 <token name="@BINARY@">scHicCluster</token> | |
5 <import>macros.xml</import> | |
6 </macros> | |
7 <expand macro="requirements" /> | |
8 <command detect_errors="exit_code"><![CDATA[ | |
9 @BINARY@ | |
10 | |
11 --matrix '$matrix_mcooler' | |
12 | |
13 --numberOfClusters $numberOfClusters | |
14 | |
15 --clusterMethod $clusterMethod_selector | |
16 | |
17 #if $chromosomes: | |
18 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ]) | |
19 --chromosomes $chromosome | |
20 #end if | |
21 | |
22 --dimensionReductionMethod $dimensionReductionMethod_selector | |
23 | |
24 --outFileName cluster_list.txt | |
25 | |
26 --threads @THREADS@ | |
27 | |
28 | |
29 | |
30 ]]></command> | |
31 <inputs> | |
32 | |
33 <expand macro="matrix_mcooler_macro"/> | |
34 <param name="clusterMethod_selector" type="select" label="Cluster method:"> | |
35 <option value="kmeans" selected="True">K-means</option> | |
36 <option value="spectral" >Spectral clustering</option> | |
37 </param> | |
38 <param name="dimensionReductionMethod_selector" type="select" label="Apply dimension reduction:"> | |
39 <option value="none" selected="True">No dimension reduction</option> | |
40 <option value="knn" >Exact k-nearest neighbors</option> | |
41 <option value="pca" >Principal components</option> | |
42 </param> | |
43 <param name="numberOfClusters" type="integer" value="7" label="Number of clusters" help='How many clusters should be computed by kmeans or spectral clustering' /> | |
44 | |
45 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/> | |
46 </inputs> | |
47 <outputs> | |
48 <data name="outFileName" from_work_dir="cluster_list.txt" format="txt" label="${tool.name} on ${on_string}: Cluster results"/> | |
49 </outputs> | |
50 <tests> | |
51 <test> | |
52 <param name='matrix_mcooler' value='test_matrix.mcool' /> | |
53 <param name='clusterMethod_selector' value='kmeans' /> | |
54 <param name='dimensionReductionMethod_selector' value='none' /> | |
55 <param name='numberOfClusters' value='7' /> | |
56 <output name="outFileName" file="scHicCluster/cluster_kmeans.txt" ftype="txt" compare="sim_size" delta="4000"/> | |
57 </test> | |
58 <test> | |
59 <param name='matrix_mcooler' value='test_matrix.mcool' /> | |
60 <param name='clusterMethod_selector' value='kmeans' /> | |
61 <param name='dimensionReductionMethod_selector' value='none' /> | |
62 <param name='numberOfClusters' value='7' /> | |
63 <param name='chromosomes' value='chr1 chr2' /> | |
64 | |
65 <output name="outFileName" file="scHicCluster/cluster_kmeans_chromosomes.txt" ftype="txt" compare="sim_size" delta="4000"/> | |
66 </test> | |
67 <test> | |
68 <param name='matrix_mcooler' value='test_matrix.mcool' /> | |
69 <param name='clusterMethod_selector' value='spectral' /> | |
70 <param name='dimensionReductionMethod_selector' value='knn' /> | |
71 <param name='numberOfClusters' value='7' /> | |
72 <output name="outFileName" file="scHicCluster/cluster_spectral_knn.txt" ftype="txt" compare="sim_size" delta="4000"/> | |
73 </test> | |
74 <test> | |
75 <param name='matrix_mcooler' value='test_matrix.mcool' /> | |
76 <param name='clusterMethod_selector' value='spectral' /> | |
77 <param name='dimensionReductionMethod_selector' value='pca' /> | |
78 <param name='numberOfClusters' value='7' /> | |
79 <output name="outFileName" file="scHicCluster/cluster_spectral_pca.txt" ftype="txt" compare="sim_size" delta="4000"/> | |
80 </test> | |
81 </tests> | |
82 <help><![CDATA[ | |
83 | |
84 Clustering on raw data | |
85 ====================== | |
86 | |
87 scHicCluster uses kmeans or spectral clustering to associate each cell to a cluster and therefore to its cell cycle. | |
88 The clustering can be run on the raw data, on a kNN computed via the exact euclidean distance or via PCA. | |
89 Please consider also the other clustering and dimension reduction approaches of the scHicExplorer suite. They can give you better results, | |
90 can be faster or less memory demanding. | |
91 | |
92 For more information about scHiCExplorer please consider our documentation on readthedocs.io_ | |
93 | |
94 .. _readthedocs.io: http://schicexplorer.readthedocs.io/ | |
95 ]]></help> | |
96 <expand macro="citations" /> | |
97 | |
98 </tool> |