Mercurial > repos > ebi-gxa > scanpy_run_umap

annotate scanpy-run-umap.xml @ 1:0ac2f9f2313b 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 08:16:59 -0400
parents 88c1516e25e0
children 6eb7a2e37adf
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88c1516e25e0 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"?>
88c1516e25e0 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_run_umap" name="Scanpy RunUMAP" version="@TOOL_VERSION@+galaxy1">
88c1516e25e0 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>visualise cell clusters using UMAP</description>
88c1516e25e0 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>
1
0ac2f9f2313b "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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88c1516e25e0 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>
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7 <expand macro="requirements"/>
88c1516e25e0 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[
88c1516e25e0 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 '${input_obj_file}' input.h5 &&
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0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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10 PYTHONIOENCODING=utf-8 scanpy-run-umap
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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11 --use-graph '${use_graph}'
0ac2f9f2313b "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 --key-added '${key_added}'
0ac2f9f2313b "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 #if $embeddings
0ac2f9f2313b "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 --export-embedding embeddings.csv
0ac2f9f2313b "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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15 #end if
0ac2f9f2313b "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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16 #if $settings.default == "false"
0ac2f9f2313b "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 --n-components ${settings.n_components}
0ac2f9f2313b "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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18 --min-dist ${settings.min_dist}
0ac2f9f2313b "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 --spread ${settings.spread}
0ac2f9f2313b "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 --alpha ${settings.alpha}
0ac2f9f2313b "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 --gamma ${settings.gamma}
0ac2f9f2313b "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 --negative-sample-rate ${settings.negative_sample_rate}
0ac2f9f2313b "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 --random-state ${settings.random_seed}
0ac2f9f2313b "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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24 #if $settings.init_pos
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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25 --init-pos '${settings.init_pos}'
0
88c1516e25e0 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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26 #end if
1
0ac2f9f2313b "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 #if $settings.maxiter
0ac2f9f2313b "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 --maxiter ${settings.maxiter}
0ac2f9f2313b "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 #end if
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30 #end if
0ac2f9f2313b "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 @INPUT_OPTS@
0ac2f9f2313b "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 @OUTPUT_OPTS@
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33
88c1516e25e0 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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34 ]]></command>
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35
88c1516e25e0 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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36 <inputs>
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37 <expand macro="input_object_params"/>
88c1516e25e0 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 <expand macro="output_object_params"/>
88c1516e25e0 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 <param name="embeddings" type="boolean" checked="true" label="Output embeddings in csv format"/>
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40 <param name="use_graph" argument="--use-graph" value="neighbors" type="text"
0ac2f9f2313b "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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41 label="Name of the slot that holds the KNN graph"/>
0ac2f9f2313b "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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42 <param name="key_added" argument="--key-added" type="text" optional="true"
0ac2f9f2313b "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 label="Additional suffix to the name of the slot to save the embedding"/>
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44
0
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45 <conditional name="settings">
88c1516e25e0 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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46 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
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47 <when value="true"/>
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48 <when value="false">
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49 <param name="n_components" argument="--n-components" type="integer" value="2" label="The number of dimensions of the embedding"/>
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50 <param name="min_dist" argument="--min-dist" type="float" value="0.5" label="The effective minimum distance between embedded points"/>
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51 <param name="spread" argument="--spread" type="float" value="1.0" label="The effective spread of embedded points"/>
88c1516e25e0 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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52 <param name="alpha" argument="--alpha" type="float" value="1.0" label="Initial learning rate"/>
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53 <param name="gamma" argument="--gamma" type="float" value="1.0" label="Weighting applied to negative samples"/>
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54 <param name="negative_sample_rate" argument="--negative-sample-rate" type="integer" value="5" label="The ratio of negative to positive edge in optimisation"/>
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55 <param name="init_pos" argument="--init-pos" type="text" label="Method to initialise embedding, any key for adata.obsm or choose from the preset methods">
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56 <option value="spectral" selected="true">spectral</option>
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57 <option value="paga">paga</option>
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58 <option value="random">random</option>
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59 </param>
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60 <param name="maxiter" argument="--maxiter" type="integer" optional="true" label="Number of iterations of optimisation"/>
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61 <param name="random_seed" argument="--random-state" type="integer" value="0" label="Seed for numpy random number generator"/>
0
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62 </when>
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63 </conditional>
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64 </inputs>
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65
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66 <outputs>
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67 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: UMAP object"/>
88c1516e25e0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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68 <data name="output_embed" format="csv" from_work_dir="embeddings.csv" label="${tool.name} on ${on_string}: UMAP embeddings">
88c1516e25e0 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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69 <filter>embeddings</filter>
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70 </data>
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71 </outputs>
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72
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73 <tests>
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74 <test>
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75 <param name="input_obj_file" value="find_cluster.h5"/>
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76 <param name="input_format" value="anndata"/>
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77 <param name="output_format" value="anndata"/>
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78 <param name="default" value="false"/>
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79 <param name="embeddings" value="true"/>
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80 <param name="random_seed" value="0"/>
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81 <output name="output_h5" file="run_umap.h5" ftype="h5" compare="sim_size"/>
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82 <output name="output_embed" file="run_umap.embeddings.csv" ftype="csv" compare="sim_size">
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83 <assert_contents>
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84 <has_n_columns n="2" sep=","/>
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85 </assert_contents>
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86 </output>
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87 </test>
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88 </tests>
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89
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90 <help><![CDATA[
1
0ac2f9f2313b "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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91 ==========================================================
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92 Embed the neighborhood graph using UMAP (`scanpy.tl.umap`)
0ac2f9f2313b "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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93 ==========================================================
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94
0ac2f9f2313b "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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95 For making UMAP plots, please use `Scanpy PlotEmbed` with the output of this tool and enter "umap" as the
0ac2f9f2313b "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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96 name of the embedding to plot.
0
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97
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98 UMAP (Uniform Manifold Approximation and Projection) is a manifold learning
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99 technique suitable for visualizing high-dimensional data. Besides tending to
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100 be faster than tSNE, it optimizes the embedding such that it best reflects
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101 the topology of the data, which we represent throughout Scanpy using a
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102 neighborhood graph. tSNE, by contrast, optimizes the distribution of
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103 nearest-neighbor distances in the embedding such that these best match the
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104 distribution of distances in the high-dimensional space. We use the
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105 implementation of `umap-learn <https://github.com/lmcinnes/umap>`__
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106 (McInnes et al, 2018). For a few comparisons of UMAP with tSNE, see this `preprint
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107 <https://doi.org/10.1101/298430>`__.
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108
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109 It yields `X_umap`, UMAP coordinates of data.
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110
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111 @HELP@
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112
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113 @VERSION_HISTORY@
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114 ]]></help>
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115 <expand macro="citations"/>
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116 </tool>