comparison scHicClusterSVL.xml @ 0:7cbd84a1f985 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
author iuc
date Thu, 23 Jan 2020 16:01:20 -0500
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children eeb26f378f34
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-1:000000000000 0:7cbd84a1f985
1 <tool id="schicexplorer_schicclustersvl" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>clusters single-cell Hi-C interaction matrices with svl dimension reduction</description>
3 <macros>
4 <token name="@BINARY@">scHicClusterSVL</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 --distanceShortRange $distanceShortRange
15 --distanceLongRange $distanceLongRange
16
17 --clusterMethod $clusterMethod_selector
18
19 #if $chromosomes:
20 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
21 --chromosomes $chromosome
22 #end if
23
24 --outFileName cluster_list.txt
25
26 --threads @THREADS@
27 ]]></command>
28 <inputs>
29
30 <expand macro="matrix_mcooler_macro"/>
31 <param name="clusterMethod_selector" type="select" label="Cluster method:">
32 <option value="kmeans" selected="True">K-means</option>
33 <option value="spectral" >Spectral clustering</option>
34 </param>
35
36 <param name="numberOfClusters" type="integer" value="7" label="Number of clusters" help='How many clusters should be computed by kmeans or spectral clustering' />
37 <param name="distanceShortRange" type="integer" value="2000000" label="Distance short range" help='Distance for the short range to compute the ratio of sum (short range interactions) / sum (long range interactions)' />
38 <param name="distanceLongRange" type="integer" value="12000000" label="Distance long range" help='Distance for the long range to compute the ratio of sum (short range interactions) / sum (long range interactions)' />
39
40 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
41 </inputs>
42 <outputs>
43 <data name="outFileName" from_work_dir="cluster_list.txt" format="txt" label="${tool.name} on ${on_string}: Cluster results"/>
44 </outputs>
45 <tests>
46 <test>
47 <param name='matrix_mcooler' value='test_matrix.mcool' />
48 <param name='clusterMethod_selector' value='kmeans' />
49 <param name='numberOfClusters' value='3' />
50 <param name='distanceShortRange' value='2000000' />
51 <param name='distanceLongRange' value='12000000' />
52
53 <output name="outFileName" file="scHicClusterSVL/cluster_kmeans.txt" ftype="txt" compare="sim_size" delta="4000"/>
54 </test>
55
56 <test>
57 <param name='matrix_mcooler' value='test_matrix.mcool' />
58 <param name='clusterMethod_selector' value='spectral' />
59 <param name='numberOfClusters' value='3' />
60 <param name='distanceShortRange' value='2000000' />
61 <param name='distanceLongRange' value='12000000' />
62
63 <output name="outFileName" file="scHicClusterSVL/cluster_spectral.txt" ftype="txt" compare="sim_size" delta="4000"/>
64 </test>
65
66 </tests>
67 <help><![CDATA[
68
69 Clustering with dimension reduction via short vs long range ratio
70 =================================================================
71
72 scHicClusterSVL uses kmeans or spectral clustering to associate each cell to a cluster and therefore to its cell cycle.
73 The clustering is applied on dimension reduced data based on the ratio of short vs long range contacts per chromosome. This approach reduces the number of dimensions from samples * (number of bins)^2 to samples * (number of chromosomes).
74 Please consider also the other clustering and dimension reduction approaches of the scHicExplorer suite. They can give you better results,
75 can be faster or less memory demanding.
76
77 For more information about scHiCExplorer please consider our documentation on readthedocs.io_
78
79 .. _readthedocs.io: http://schicexplorer.readthedocs.io/
80 ]]></help>
81 <expand macro="citations" />
82
83 </tool>