Mercurial > repos > ebi-gxa > scanpy_find_cluster

annotate scanpy-find-cluster.xml @ 1:ee181563bae7 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
author ebi-gxa
date Mon, 16 Sep 2019 08:13:51 -0400
parents ce27ae8a36cd
children d5290f98fde4
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ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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1 <?xml version="1.0" encoding="utf-8"?>
ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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2 <tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy1">
ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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3 <description>based on community detection on KNN graph</description>
ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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4 <macros>
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ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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5 <import>scanpy_macros2.xml</import>
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ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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6 </macros>
ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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7 <expand macro="requirements"/>
ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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8 <command detect_errors="exit_code"><![CDATA[
ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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9 ln -s '${input_obj_file}' input.h5 &&
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ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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10 PYTHONIOENCODING=utf-8 scanpy-find-cluster
ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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11 ${method}
ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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12 #if $settings.default == "false"
ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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13 --use-graph '${settings.use_graph}'
ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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14 #if $settings.key_added
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ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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15 --key-added '${settings.key_added}'
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16 #end if
ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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17 #if $settings.resolution_file
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18 --resolution \$( cat $settings.resolution_file )
ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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19 #elif $settings.resolution
ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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20 --resolution '${settings.resolution}'
ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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21 #end if
ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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22 #if $settings.restrict_to
ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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23 --restrict-to '${settings.restrict_to}'
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24 #end if
1
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25 #if $settings.use_weights
ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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26 --use-weights
ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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27 #end if
ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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28 --random-state '${settings.random_seed}'
ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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29 ${settings.directed}
ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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30 #end if
ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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31 #if $output_cluster
ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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32 --export-cluster output.tsv
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33 #end if
ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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34 @INPUT_OPTS@
ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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35 @OUTPUT_OPTS@
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36 ]]></command>
ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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37
ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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38 <inputs>
ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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39 <expand macro="input_object_params"/>
ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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40 <expand macro="output_object_params"/>
ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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41 <param name="output_cluster" type="boolean" checked="true" label="Output cluster in two column text format"/>
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42
ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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43 <param name="method" type="select" label="Clustering algorithm">
ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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44 <option value="louvain" selected="true">Louvain</option>
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45 <option value="leiden">Leiden</option>
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46 </param>
ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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47
0
ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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48 <conditional name="settings">
ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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49 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
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50 <when value="true"/>
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51 <when value="false">
1
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52 <param name="use_graph" argument="--use-graph" value="neighbors" type="text"
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53 label="Name of the slot that holds the KNN graph"/>
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54 <param name="key_added" argument="--key-added" type="text" optional="true"
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55 label="Additional suffix to the name of the slot to save the calculated trajectory"/>
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56
ee181563bae7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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57 <param name="resolution" argument="--resolution" type="float" min="0.0" value="1.0"
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58 label="Resolution, high value for more and smaller clusters"/>
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59 <param name="resolution_file" argument="--resolution" type="data" format="txt,tsv" optional="true"
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60 label="File with resolution, use with parameter iterator. Overrides the resolution setting"/>
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61 <param name="restrict_to" argument="--restrict-to" type="text" optional="true"
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62 label="Restrict clustering to certain sample categories"/>
0
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63 <param name="use_weights" argument="--use-weights" type="boolean" checked="false" label="Use weights from knn graph"/>
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64 <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for random number generator"/>
1
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65 <param name="directed" argument="--directed" type="boolean" truevalue="--directed" falsevalue="--undirected" checked="true"
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66 label="Interpret the adjacency matrix as directed graph."/>
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67 </when>
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68 </conditional>
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69 </inputs>
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70
ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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71 <outputs>
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72 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Cluster object"/>
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73 <data name="output_txt" format="tsv" from_work_dir="output.tsv" label="${tool.name} on ${on_string}: Cluster table">
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74 <filter>output_cluster</filter>
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75 </data>
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76 </outputs>
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77
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78 <tests>
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79 <test>
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80 <param name="input_obj_file" value="compute_graph.h5"/>
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81 <param name="input_format" value="anndata"/>
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82 <param name="output_format" value="anndata"/>
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83 <param name="output_txt" value="true"/>
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84 <param name="default" value="false"/>
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85 <param name="resolution" value="1.0"/>
ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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86 <param name="random_seed" value="0"/>
ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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87 <output name="output_h5" file="find_cluster.h5" ftype="h5" compare="sim_size"/>
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88 <output name="output_txt" file="find_cluster.tsv" ftype="tsv"/>
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89 </test>
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90 </tests>
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91
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92 <help><![CDATA[
1
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93 ======================================================================
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94 Cluster cells into subgroups (`scanpy.tl.louvain`, `scanpy.tl.leiden`)
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95 ======================================================================
0
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96
1
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97 Cluster cells using the Louvain algorithm (Blondel et al, 2008) in the
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98 implementation of Traag et al, 2017, or the Leiden algorithm (Traag et al,
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99 2019). The Louvain algorithm has been proposed for single-cell analysis by
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100 Levine et al, 2015.
0
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101
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102 This requires to run `Scanpy ComputeGraph`, first.
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103
1
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104 It by default yields `louvain` or `leiden`, generated cluster label.
0
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105
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106 @HELP@
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107
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108 @VERSION_HISTORY@
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109 ]]></help>
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110 <expand macro="citations">
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111 <citation type="doi">10.1088/1742-5468/2008/10/P10008</citation>
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112 <citation type="doi">10.1016/j.cell.2015.05.047</citation>
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113 <citation type="doi">10.1038/s41598-019-41695-z</citation>
0
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114 <citation type="doi">10.5281/zenodo.35117</citation>
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115 </expand>
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116 </tool>