Mercurial > repos > ebi-gxa > scanpy_find_cluster

annotate scanpy-find-cluster.xml @ 18:15e8a4c60418 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 fda35ff3ea8609c4bb5e1fd9e58ba70cd5b5a997-dirty"
author ebi-gxa
date Wed, 30 Sep 2020 11:12:27 +0000
parents b45b85d5c7ec
children b531acda966c
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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"?>
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2 <tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@">
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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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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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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"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 #if $settings.resolution_file
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b45b85d5c7ec "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit c02d457c74016980672e64832e6cad31d703edcd-dirty"
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10 #set f = open($settings.resolution_file.__str__)
b45b85d5c7ec "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit c02d457c74016980672e64832e6cad31d703edcd-dirty"
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11 #set resolution = f.read().strip()
b45b85d5c7ec "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit c02d457c74016980672e64832e6cad31d703edcd-dirty"
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12 #silent f.close
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13 #elif $settings.resolution
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14 #set resolution = $settings.resolution.__str__.strip()
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15 #end if
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16
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ce27ae8a36cd planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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17 ln -s '${input_obj_file}' input.h5 &&
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18 PYTHONIOENCODING=utf-8 scanpy-find-cluster
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19 ${method}
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20 #if $settings.default == "false"
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21 --neighbors-key '${settings.neighbors_key}'
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22 #if $settings.key_added
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23 #set key_added = $settings.key_added.replace('METHOD', $method.__str__)
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24 #if $resolution
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25 #set key_added = $key_added.replace('RESOLUTION', $resolution.__str__)
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26 #end if
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27 --key-added '${key_added}'
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28 #end if
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29 #if $resolution
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30 --resolution '$resolution'
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31 #end if
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32 #if $settings.layer
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33 --layer '${settings.layer}'
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34 #end if
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35 #if $settings.restrict_to
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36 --restrict-to '${settings.restrict_to}'
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37 #end if
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38 #if $settings.use_weights
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39 --use-weights
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40 #end if
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41 --random-state '${settings.random_seed}'
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42 ${settings.directed}
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43 #end if
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44 #if $output_cluster
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45 --export-cluster output.tsv
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46 #end if
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47 @INPUT_OPTS@
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48 @OUTPUT_OPTS@
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49 ]]></command>
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50
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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51 <inputs>
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52 <expand macro="input_object_params"/>
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53 <expand macro="output_object_params"/>
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54 <param name="output_cluster" type="boolean" checked="true" label="Output cluster in two column text format"/>
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55
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56 <param name="method" type="select" label="Clustering algorithm">
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57 <option value="louvain" selected="true">Louvain</option>
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58 <option value="leiden">Leiden</option>
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59 </param>
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60
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61 <conditional name="settings">
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62 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
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63 <when value="true"/>
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64 <when value="false">
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65 <param name="neighbors_key" argument="--neighbors-key" value="neighbors" type="text"
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66 label="Name of the slot that holds the KNN graph"/>
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67 <param name="layer" argument="--layer" value="" type="text"
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68 label="Key from adata.layers whose value will be used to perform tests on. (Default: use .X)"/>
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69 <param name="key_added" argument="--key-added" type="text" optional="true"
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70 label="Additional suffix to the name of the slot to save the calculated clustering" help="If included, the keyword 'METHOD' will be substituted with the value of the method setting and 'RESOLUTION' with the value of that field."/>
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71 <param name="resolution" argument="--resolution" type="float" min="0.0" value="1.0"
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72 label="Resolution, high value for more and smaller clusters"/>
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73 <param name="resolution_file" argument="--resolution" type="data" format="txt,tsv" optional="true"
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74 label="File with resolution, use with parameter iterator. Overrides the resolution setting"/>
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75 <param name="restrict_to" argument="--restrict-to" type="text" optional="true"
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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76 label="Restrict clustering to certain sample categories"/>
0
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77 <param name="use_weights" argument="--use-weights" type="boolean" checked="false" label="Use weights from knn graph"/>
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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78 <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for random number generator"/>
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79 <param name="directed" argument="--directed" type="boolean" truevalue="--directed" falsevalue="--undirected" checked="true"
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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80 label="Interpret the adjacency matrix as directed graph."/>
0
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81 </when>
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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82 </conditional>
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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83 </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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84
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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85 <outputs>
5
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86 <expand macro="output_data_obj" description="Clusters"/>
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 <data name="output_txt" format="tsv" from_work_dir="output.tsv" label="${tool.name} on ${on_string}: Cluster table">
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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88 <filter>output_cluster</filter>
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89 </data>
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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90 </outputs>
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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91
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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92 <tests>
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93 <test>
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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94 <param name="input_obj_file" value="compute_graph.h5"/>
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95 <param name="input_format" value="anndata"/>
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96 <param name="output_format" value="anndata"/>
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97 <param name="output_txt" value="true"/>
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98 <param name="default" value="false"/>
17
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99 <param name="resolution_file" value="resolution.txt"/>
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100 <param name="random_seed" value="0"/>
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101 <output name="output_h5" file="find_cluster.h5" ftype="h5" compare="sim_size"/>
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102 <output name="output_txt" file="find_cluster.tsv" ftype="tsv"/>
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103 </test>
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104 <test>
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105 <param name="input_obj_file" value="compute_graph.h5"/>
b45b85d5c7ec "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit c02d457c74016980672e64832e6cad31d703edcd-dirty"
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106 <param name="input_format" value="anndata"/>
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107 <param name="output_format" value="anndata"/>
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108 <param name="output_txt" value="true"/>
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109 <param name="default" value="false"/>
0
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110 <param name="resolution" value="1.0"/>
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111 <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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112 <output name="output_h5" file="find_cluster.h5" ftype="h5" compare="sim_size"/>
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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113 <output name="output_txt" file="find_cluster.tsv" ftype="tsv"/>
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114 </test>
18
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115 <test>
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116 <param name="input_obj_file" value="compute_graph.h5"/>
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117 <param name="input_format" value="anndata"/>
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118 <param name="output_format" value="anndata"/>
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119 <param name="output_txt" value="true"/>
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120 <param name="default" value="false"/>
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121 <param name="method" value="louvain"/>
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122 <param name="resolution" value="1.0"/>
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123 <param name="key_added" value="METHOD_RESOLUTION"/>
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124 <param name="random_seed" value="0"/>
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125 <output name="output_h5" file="louvain_1.0" ftype="h5" compare="sim_size"/>
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126 <output name="output_txt" file="louvain_1.0.tsv" ftype="tsv"/>
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127 </test>
0
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128 </tests>
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129
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130 <help><![CDATA[
1
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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131 ======================================================================
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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132 Cluster cells into subgroups (`scanpy.tl.louvain`, `scanpy.tl.leiden`)
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133 ======================================================================
0
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134
1
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135 Cluster cells using the Louvain algorithm (Blondel et al, 2008) in the
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136 implementation of Traag et al, 2017, or the Leiden algorithm (Traag et al,
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137 2019). The Louvain algorithm has been proposed for single-cell analysis by
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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138 Levine et al, 2015.
0
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139
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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140 This requires to run `Scanpy ComputeGraph`, first.
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141
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142 It by default yields `louvain` or `leiden`, generated cluster label.
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143
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144 @HELP@
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145
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146 @VERSION_HISTORY@
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147 ]]></help>
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148 <expand macro="citations">
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149 <citation type="doi">10.1088/1742-5468/2008/10/P10008</citation>
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150 <citation type="doi">10.1016/j.cell.2015.05.047</citation>
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151 <citation type="doi">10.1038/s41598-019-41695-z</citation>
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152 <citation type="doi">10.5281/zenodo.35117</citation>
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153 </expand>
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154 </tool>