Mercurial > repos > iuc > schicexplorer_schicclustercomparments

comparison scHicClusterCompartments.xml @ 0:442a40229460 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
author iuc
date Thu, 23 Jan 2020 16:00:33 -0500
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1 <tool id="schicexplorer_schicclustercomparments" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>clusters single-cell Hi-C interaction matrices with A/B compartments dimension reduction</description>
3 <macros>
4 <token name="@BINARY@">scHicClusterCompartments</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 #if $norm:
23 $norm
24 #end if
25 #if $binarization:
26 $binarization
27 #end if
28
29 #if $extra_track_conditional.extra_track_selection == 'gene_density':
30 --extraTrack '$extra_track_conditional.extraTrack'
31 #elif $extra_track_conditional.extra_track_selection == 'histon_mark':
32 --histonMarkType '$extra_track_conditional.histonMarkType'
33 #end if
34
35 --outFileName cluster_list.txt
36
37 --threads @THREADS@
38
39
40
41 ]]></command>
42 <inputs>
43
44 <expand macro="matrix_mcooler_macro"/>
45 <param name="clusterMethod_selector" type="select" label="Cluster method:">
46 <option value="kmeans" selected="True">K-means</option>
47 <option value="spectral" >Spectral clustering</option>
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' />
50
51 <param name='norm' type='boolean' truevalue='--norm' label='Use different expected value computation'/>
52 <param name='binarization' type='boolean' truevalue='--binarization' label='Convert positive values to 1 and all negative to -1.'/>
53
54
55 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
56 <conditional name="extra_track_conditional">
57 <param name='extra_track_selection' label='Extra track type' type='select'>
58 <option value='' selected='true'>No track</option>
59 <option value='gene_density'>Gene density</option>
60 <option value='histon_mark'>Histone mark coverage</option>
61 </param>
62 <when value='gene_density' >
63 <param name='extraTrack' type='data' format='bed' label='Correlate PCA with e.g. gene density or histone marks to flip sign'/>
64 </when>
65 <when value='histon_mark'>
66 <param name='histonMarkType' type='data' format='bed' label='Correlate PCA with e.g. gene density or histone marks to flip sign'/>
67 </when>
68 <when value='' />
69 </conditional>
70 </inputs>
71 <outputs>
72 <data name="outFileName" from_work_dir="cluster_list.txt" format="txt" label="${tool.name} on ${on_string}: Cluster results"/>
73 </outputs>
74 <tests>
75 <test>
76 <param name='matrix_mcooler' value='test_matrix.mcool' />
77 <param name='clusterMethod_selector' value='kmeans' />
78 <param name='numberOfClusters' value='3' />
79 <output name="outFileName" file="scHicClusterCompartments/cluster_kmeans.txt" ftype="txt" compare="sim_size" delta="4000"/>
80 </test>
81 <test>
82 <param name='matrix_mcooler' value='test_matrix.mcool' />
83 <param name='clusterMethod_selector' value='spectral' />
84 <param name='numberOfClusters' value='3' />
85 <output name="outFileName" file="scHicClusterCompartments/cluster_spectral.txt" ftype="txt" compare="sim_size" delta="4000"/>
86 </test>
87 <test>
88 <param name='matrix_mcooler' value='test_matrix.mcool' />
89 <param name='clusterMethod_selector' value='kmeans' />
90 <param name='numberOfClusters' value='3' />
91 <param name='binarization' value='True'/>
92 <param name='norm' value='True'/>
93 <conditional name="extra_track_conditional">
94 <param name="extra_track_selection" value="histon_mark"/>
95 <param name="histonMarkType" value="scHicClusterCompartments/mm9_H3K36me3.bed.gz" />
96 </conditional>
97 <output name="outFileName" file="scHicClusterCompartments/cluster_kmeans_binarization_norm_histone_track.txt" ftype="txt" compare="sim_size" delta="4000"/>
98 </test>
99 <test>
100 <param name='matrix_mcooler' value='test_matrix.mcool' />
101 <param name='clusterMethod_selector' value='kmeans' />
102 <param name='numberOfClusters' value='3' />
103 <param name='binarization' value='True'/>
104 <param name='norm' value='True'/>
105 <conditional name="extra_track_conditional">
106 <param name="extra_track_selection" value="gene_density"/>
107 <param name="extraTrack" value="scHicClusterCompartments/mm9_gene.bed.gz" />
108 </conditional>
109 <output name="outFileName" file="scHicClusterCompartments/cluster_spectral_binarization_norm_gene_track.txt" ftype="txt" compare="sim_size" delta="4000"/>
110 </test>
111 </tests>
112 <help><![CDATA[
113
114 Clustering with dimension reduction via A/B compartments
115 ========================================================
116
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).
119 Please consider also the other clustering and dimension reduction approaches of the scHicExplorer suite. They can give you better results,
120 can be faster or less memory demanding.
121
122 For more information about scHiCExplorer please consider our documentation on readthedocs.io_
123
124 .. _readthedocs.io: http://schicexplorer.readthedocs.io/
125 ]]></help>
126 <expand macro="citations" />
127
128 </tool>