Mercurial > repos > iuc > schicexplorer_schiccluster

annotate scHicCluster.xml @ 1:36e26166034d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
author iuc
date Tue, 10 Mar 2020 15:06:22 -0400
parents a532cbac217a
children baa3ae7ac42c
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1 <tool id="schicexplorer_schiccluster" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>clusters single-cell Hi-C interaction matrices on the raw data</description>
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3 <macros>
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4 <token name="@BINARY@">scHicCluster</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 @BINARY@
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11 --matrix '$matrix_scooler'
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13 --numberOfClusters $numberOfClusters
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15 --clusterMethod $clusterMethod_selector
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17 #if $chromosomes:
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18 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
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19 --chromosomes $chromosome
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20 #end if
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22 --dimensionReductionMethod $dimensionReductionMethod_selector
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23 --numberOfNearestNeighbors $numberOfNearestNeighbors
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24 --outFileName cluster_list.txt
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26 --threads @THREADS@
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30 ]]></command>
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31 <inputs>
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32
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33 <expand macro="matrix_scooler_macro"/>
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34 <param name="clusterMethod_selector" type="select" label="Cluster method:">
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35 <option value="kmeans" selected="True">K-means</option>
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36 <option value="spectral" >Spectral clustering</option>
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37 </param>
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38 <param name="dimensionReductionMethod_selector" type="select" label="Apply dimension reduction:">
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39 <option value="none" selected="True">No dimension reduction</option>
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40 <option value="knn" >Exact k-nearest neighbors</option>
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41 <option value="pca" >Principal components</option>
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42 </param>
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43 <param name="numberOfClusters" type="integer" value="7" label="Number of clusters" help='How many clusters should be computed by kmeans or spectral clustering' />
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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?' />
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46 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
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47 </inputs>
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48 <outputs>
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49 <data name="outFileName" from_work_dir="cluster_list.txt" format="txt" label="${tool.name} on ${on_string}: Cluster results"/>
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50 </outputs>
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51 <tests>
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52 <test>
1
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53 <param name='matrix_scooler' value='test_matrix.scool' />
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54 <param name='clusterMethod_selector' value='kmeans' />
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55 <param name='dimensionReductionMethod_selector' value='none' />
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56 <param name='numberOfClusters' value='7' />
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57 <output name="outFileName" file="scHicCluster/cluster_kmeans.txt" ftype="txt" compare="sim_size" delta="4000"/>
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58 </test>
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59 <test>
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60 <param name='matrix_scooler' value='test_matrix.scool' />
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61 <param name='clusterMethod_selector' value='kmeans' />
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62 <param name='dimensionReductionMethod_selector' value='none' />
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63 <param name='numberOfClusters' value='7' />
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64 <param name='chromosomes' value='chr1 chr2' />
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65
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66 <output name="outFileName" file="scHicCluster/cluster_kmeans_chromosomes.txt" ftype="txt" compare="sim_size" delta="4000"/>
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67 </test>
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68 <test>
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69 <param name='matrix_scooler' value='test_matrix.scool' />
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70 <param name='clusterMethod_selector' value='spectral' />
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71 <param name='dimensionReductionMethod_selector' value='knn' />
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72 <param name='numberOfClusters' value='7' />
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73 <output name="outFileName" file="scHicCluster/cluster_spectral_knn.txt" ftype="txt" compare="sim_size" delta="4000"/>
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74 </test>
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75 <test>
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76 <param name='matrix_scooler' value='test_matrix.scool' />
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77 <param name='clusterMethod_selector' value='spectral' />
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78 <param name='dimensionReductionMethod_selector' value='pca' />
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79 <param name='numberOfClusters' value='7' />
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80 <output name="outFileName" file="scHicCluster/cluster_spectral_pca.txt" ftype="txt" compare="sim_size" delta="4000"/>
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81 </test>
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82 </tests>
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83 <help><![CDATA[
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84
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85 Clustering on raw data
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86 ======================
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87
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88 scHicCluster uses kmeans or spectral clustering to associate each cell to a cluster and therefore to its cell cycle.
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89 The clustering can be run on the raw data, on a kNN computed via the exact euclidean distance or via PCA.
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90 Please consider also the other clustering and dimension reduction approaches of the scHicExplorer suite such as `scHicCluster`, `scHicClusterMinHash` and `scHicClusterSVL`.
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91 They can give you better results, can be faster or less memory demanding.
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92
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93 For more information about scHiCExplorer please consider our documentation on readthedocs.io_
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94
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95 .. _readthedocs.io: http://schicexplorer.readthedocs.io/
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96 ]]></help>
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97 <expand macro="citations" />
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98
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99 </tool>