Mercurial > repos > iuc > schicexplorer_schicclustersvl

annotate scHicClusterSVL.xml @ 0:7cbd84a1f985 draft

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