Mercurial > repos > iuc > scanpy_normalize

annotate normalize.xml @ 19:146ae5d70b47 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
author iuc
date Thu, 03 Oct 2024 22:45:12 +0000
parents 5dada6f76047
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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1 <tool id="scanpy_normalize" name="Scanpy normalize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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2 <description>and impute</description>
0
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3 <macros>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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4 <import>macros.xml</import>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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5 </macros>
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements">
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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8 <requirement type="package" version="3.0.0">magic-impute</requirement>
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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9 </expand>
0
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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10 <expand macro="version_command"/>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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11 <command detect_errors="exit_code"><![CDATA[
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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12 @CMD@
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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13 ]]></command>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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14 <configfiles>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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15 <configfile name="script_file"><![CDATA[
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16 @CMD_IMPORTS@
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17 @CMD_READ_INPUTS@
0
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18
17
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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19 #if str($method.method) == 'pp.normalize_total':
1
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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20 sc.pp.normalize_total(
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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21 adata,
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22 #if str($method.target_sum) != '':
1
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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23 target_sum=$method.target_sum,
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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24 #end if
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25 exclude_highly_expressed=$method.exclude_highly_expressed.exclude_highly_expressed,
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26 #if str($method.exclude_highly_expressed.exclude_highly_expressed) == 'True':
1
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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27 max_fraction=$method.exclude_highly_expressed.max_fraction,
0
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28 #end if
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5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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29 #if str($method.key_added) != '':
1
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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30 key_added='$method.key_added',
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31 #end if
17
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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32 #if str($method.layer) != '':
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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33 layer='$method.layer',
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34 #end if
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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35 inplace=True)
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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36
17
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37 #else if str($method.method) == 'pp.recipe_zheng17':
0
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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38 sc.pp.recipe_zheng17(
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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39 adata=adata,
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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40 n_top_genes=$method.n_top_genes,
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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41 log=$method.log,
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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42 plot=False,
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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43 copy=False)
1
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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44
17
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45 #else if str($method.method) == 'pp.recipe_weinreb17':
0
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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46 sc.pp.recipe_weinreb17(
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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47 adata=adata,
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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48 log=$method.log,
17
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49 mean_threshold=0.01,
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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50 cv_threshold=2,
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51 n_pcs=50,
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52 svd_solver='randomized',
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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53 random_state=0,
0
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54 copy=False)
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55
17
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56 #else if str($method.method) == 'pp.recipe_seurat':
0
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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57 sc.pp.recipe_seurat(
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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58 adata=adata,
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59 log=$method.log,
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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60 plot=False,
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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61 copy=False)
1
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62
17
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63 #else if str($method.method) == 'external.pp.magic':
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64 print("stats before magic:", "min=", f"{adata.X.min():.5f}", "max=", f"{adata.X.max():.5f}", "mean=", f"{adata.X.mean():.5f}")
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65
13
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66 sc.external.pp.magic(
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67 adata=adata,
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68 name_list='$method.name_list',
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69 knn=$method.knn,
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70 #if str($method.decay) != '':
13
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71 decay=$method.decay,
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72 #end if
17
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73 #if str($method.knn_max) != '':
13
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74 knn_max=$method.knn_max,
7b9fafe32c86 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3974c0ff86bb1d6633281f29dfb4c605a74e1e6e
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75 #end if
17
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76 #if $method.t == -1:
13
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77 t='auto',
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78 #else
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79 t=$method.t,
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80 #end if
17
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81 #if str($method.n_pca) != '':
13
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82 n_pca=$method.n_pca,
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83 #end if
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84 solver='$method.solver',
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85 knn_dist='$method.knn_dist',
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86 #if str($method.random_state) != '':
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87 random_state=$method.random_state,
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88 #else
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89 random_state=None,
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90 #end if
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91 copy=False)
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92
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93 #if str($method.name_list) == 'all_genes':
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94 print("stats after magic:", "min=", f"{adata.X.min():.5f}", "max=", f"{adata.X.max():.5f}", "mean=", f"{adata.X.mean():.5f}")
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95 #end if
0
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96 #end if
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97
17
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98 @CMD_ANNDATA_WRITE_OUTPUTS@
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99 ]]>
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100 </configfile>
0
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101 </configfiles>
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102 <inputs>
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103 <expand macro="inputs_anndata"/>
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104 <conditional name="method">
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105 <param argument="method" type="select" label="Method used for normalization">
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106 <option value="pp.normalize_total">Normalize counts per cell, using 'pp.normalize_total'</option>
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107 <option value="pp.recipe_zheng17">Normalization and filtering as of Zheng et al. (2017), using 'pp.recipe_zheng17'</option>
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108 <option value="pp.recipe_weinreb17">Normalization and filtering as of Weinreb et al (2017), using 'pp.recipe_weinreb17'</option>
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109 <option value="pp.recipe_seurat">Normalization and filtering as of Seurat et al (2015), using 'pp.recipe_seurat'</option>
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110 <option value="external.pp.magic">Denoising using Markov Affinity-based Graph Imputation of Cells (MAGIC) API 'external.pp.magic'</option>
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111 </param>
1
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112 <when value="pp.normalize_total">
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113 <param argument="target_sum" type="float" value="" optional="true" label="Target sum" help="If not provided, after normalization, each observation (cell) has a total count equal to the median of the total counts (cells) before normalization."/>
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114 <conditional name="exclude_highly_expressed">
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115 <param argument="exclude_highly_expressed" type="select" label="Exclude (very) highly expressed genes for the computation of the normalization factor (size factor) for each cell" help=" A gene is considered highly expressed, if it has more than max_fraction of the total counts in at least one cell. The not-excluded genes will sum up to target_sum">
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116 <option value="False" selected="true">No</option>
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117 <option value="True">Yes</option>
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118 </param>
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119 <when value="True">
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120 <param argument="max_fraction" type="float" value="0.05" label="Consider cells as highly expressed that have more counts than this value of the original total counts in at least one cell."/>
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121 </when>
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122 <when value="False"/>
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123 </conditional>
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124 <param argument="key_added" type="text" value="" optional="true" label="Name of the field in 'adata.obs' where the normalization factor is stored">
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125 <expand macro="sanitize_query"/>
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126 </param>
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127 <param argument="layer" type="text" value="" label="Layer to normalize instead of X. If not provided, X is normalized.">
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128 <expand macro="sanitize_query"/>
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129 </param>
0
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130 </when>
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131 <when value="pp.recipe_zheng17">
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132 <param argument="n_top_genes" type="integer" min="0" value="1000" label="Number of genes to keep"/>
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133 <expand macro="param_log" checked="true"/>
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134 </when>
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135 <when value="pp.recipe_weinreb17">
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136 <expand macro="param_log" checked="true"/>
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137 </when>
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138 <when value="pp.recipe_seurat">
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139 <expand macro="param_log" checked="true"/>
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140 </when>
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141 <when value="external.pp.magic">
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142 <param name="name_list" type="select" label="Denoised genes to return" help="Selecting all genes may require a large amount of memory">
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143 <option value="all_genes" selected="true">All genes</option>
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144 <option value="pca_only">PCA only</option>
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145 </param>
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146 <param argument="knn" type="integer" min="1" value="5" label="Number of nearest neighbors on which to build kernel"/>
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147 <param argument="decay" type="integer" optional="true" value="1" label="Set decay rate of kernel tails" help="If not set, alpha decaying kernel is not used"/>
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148 <param argument="knn_max" type="integer" min="1" optional="true" value="" label="Maximum number of nearest neighbors with nonzero connection" help="If not set, will be set to 3 * knn"/>
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149 <param argument="t" type="integer" min="-1" value="3" label="Power to which the diffusion operator is powered. This sets the level of diffusion" help="If ‘-1’, this parameter is selected according to the Procrustes disparity of the diffused data."/>
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150 <param argument="n_pca" type="integer" value="100" optional="true" label="Number of principal components to use for calculating neighborhoods"
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151 help="For extremely large datasets, using n_pca less than 20 allows neighborhoods to be calculated in roughly log(n_samples) time. If not set, no PCA is performed."/>
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152 <param name="solver" type="select" label="Which solver to use" help="Selecting all genes may require a large amount of memory">
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153 <option value="exact" selected="true">"exact", the implementation described in van Dijk et al. (2018) </option>
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154 <option value="approximate">"approximate", is faster that performs imputation in the PCA space and then projects back to the gene space</option>
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155 </param>
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156 <param name="knn_dist" type="select" label="Distance metric to use for the data" help="See scipy.spatial.distance.pdist documentation for more options https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.pdist.html">
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157 <expand macro="distance_metric_options"/>
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158 </param>
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159 <param argument="random_state" type="integer" optional="true" label="Random seed" help="Defaults to the global numpy random number generator."/>
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160 </when>
0
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161 </conditional>
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162 <expand macro="inputs_common_advanced"/>
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163 </inputs>
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164 <outputs>
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165 <expand macro="anndata_outputs"/>
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166 </outputs>
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167 <tests>
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168
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169 <!-- test 1 -->
11
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iuc
parents: 10
diff changeset
170 <test expect_num_outputs="2">
17
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iuc
parents: 14
diff changeset
171 <param name="adata" value="krumsiek11.h5ad"/>
0
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
172 <conditional name="method">
1
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
173 <param name="method" value="pp.normalize_total"/>
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
174 <param name="key_added" value="n_counts"/>
0
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
175 </conditional>
6
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
176 <section name="advanced_common">
17
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parents: 14
diff changeset
177 <param name="show_log" value="true"/>
6
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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parents: 5
diff changeset
178 </section>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
179 <output name="hidden_output">
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
180 <assert_contents>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
181 <has_text_matching expression="sc.pp.normalize_total"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
182 <has_text_matching expression="exclude_highly_expressed=False"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
183 <has_text_matching expression="key_added='n_counts'"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
184 </assert_contents>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
185 </output>
17
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iuc
parents: 14
diff changeset
186 <output name="anndata_out" ftype="h5ad">
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 14
diff changeset
187 <assert_contents>
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 14
diff changeset
188 <has_h5_keys keys="obs/n_counts"/>
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 14
diff changeset
189 </assert_contents>
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 14
diff changeset
190 </output>
0
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
191 </test>
17
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iuc
parents: 14
diff changeset
192
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 14
diff changeset
193 <!-- test 2 -->
11
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iuc
parents: 10
diff changeset
194 <test expect_num_outputs="2">
1
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
195 <param name="adata" value="random-randint.h5ad"/>
0
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
196 <conditional name="method">
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
197 <param name="method" value="pp.recipe_zheng17"/>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
198 </conditional>
6
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
199 <section name="advanced_common">
17
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iuc
parents: 14
diff changeset
200 <param name="show_log" value="true"/>
6
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
201 </section>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
202 <output name="hidden_output">
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
203 <assert_contents>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
204 <has_text_matching expression="sc.pp.recipe_zheng17"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
205 <has_text_matching expression="n_top_genes=1000"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
206 <has_text_matching expression="log=True"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
207 </assert_contents>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
208 </output>
17
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iuc
parents: 14
diff changeset
209 <output name="anndata_out" ftype="h5ad">
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 14
diff changeset
210 <assert_contents>
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 14
diff changeset
211 <has_h5_keys keys="obs/n_counts_all"/>
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 14
diff changeset
212 <has_h5_keys keys="var/n_counts,var/mean,var/std"/>
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 14
diff changeset
213 <has_h5_keys keys="uns/log1p"/>
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 14
diff changeset
214 </assert_contents>
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 14
diff changeset
215 </output>
0
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
216 </test>
17
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 14
diff changeset
217
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 14
diff changeset
218 <!-- test 3 -->
11
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iuc
parents: 10
diff changeset
219 <test expect_num_outputs="2">
17
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iuc
parents: 14
diff changeset
220 <param name="adata" value="paul15_subsample.h5ad"/>
0
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
221 <conditional name="method">
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
222 <param name="method" value="pp.recipe_weinreb17"/>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
223 </conditional>
6
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
224 <section name="advanced_common">
17
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iuc
parents: 14
diff changeset
225 <param name="show_log" value="true"/>
6
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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diff changeset
226 </section>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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diff changeset
227 <output name="hidden_output">
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
228 <assert_contents>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
229 <has_text_matching expression="sc.pp.recipe_weinreb17"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
230 <has_text_matching expression="log=True"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
231 <has_text_matching expression="mean_threshold=0.01"/>
17
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iuc
parents: 14
diff changeset
232 <has_text_matching expression="cv_threshold=2"/>
6
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
233 <has_text_matching expression="n_pcs=50"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
234 <has_text_matching expression="svd_solver='randomized'"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
235 <has_text_matching expression="random_state=0"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
236 </assert_contents>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
237 </output>
17
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 14
diff changeset
238 <output name="anndata_out" ftype="h5ad">
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 14
diff changeset
239 <assert_contents>
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 14
diff changeset
240 <has_h5_keys keys="uns/log1p"/>
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 14
diff changeset
241 </assert_contents>
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 14
diff changeset
242 </output>
0
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
243 </test>
17
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 14
diff changeset
244
5dada6f76047 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 14
diff changeset
245 <!-- test 4 -->
11
c9cb76cf8d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
246 <test expect_num_outputs="2">
17
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iuc
parents: 14
diff changeset
247 <param name="adata" value="pp.recipe_zheng17.random-randint.h5ad"/>
0
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
248 <conditional name="method">
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
249 <param name="method" value="pp.recipe_seurat"/>
17
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iuc
parents: 14
diff changeset
250 </conditional>
6
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
251 <section name="advanced_common">
17
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iuc
parents: 14
diff changeset
252 <param name="show_log" value="true"/>
6
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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parents: 5
diff changeset
253 </section>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
254 <output name="hidden_output">
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
255 <assert_contents>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
256 <has_text_matching expression="sc.pp.recipe_seurat"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
257 <has_text_matching expression="log=True"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
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258 </assert_contents>
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259 </output>
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260 <output name="anndata_out" ftype="h5ad">
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261 <assert_contents>
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262 <has_h5_keys keys="obs/n_genes"/>
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263 <has_h5_keys keys="var/n_cells"/>
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264 <has_h5_keys keys="uns/log1p"/>
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265 </assert_contents>
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266 </output>
0
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267 </test>
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268
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269 <!-- test 5 -->
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270 <test expect_num_outputs="2">
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271 <param name="adata" value="krumsiek11.h5ad"/>
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272 <conditional name="method">
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273 <param name="method" value="external.pp.magic"/>
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274 <param name="t" value="-1"/>
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275 <param name="n_pca" value="5"/>
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276 </conditional>
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277 <section name="advanced_common">
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278 <param name="show_log" value="true"/>
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279 </section>
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280 <output name="hidden_output">
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281 <assert_contents>
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282 <has_text_matching expression="external.pp.magic"/>
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283 <has_text_matching expression="name_list='all_genes'"/>
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284 <has_text_matching expression="t='auto'"/>
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285 <has_text_matching expression="n_pca=5"/>
17
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286 <has_text_matching expression="stats before magic: min= -0.01630 max= 1.01060 mean= 0.28644"/>
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287 <has_text_matching expression="stats after magic: min= -0.00857 max= 1.00546 mean= 0.28645"/>
13
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288 </assert_contents>
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289 </output>
17
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290 <output name="anndata_out" ftype="h5ad">
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291 <assert_contents>
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292 <has_h5_keys keys="obs/cell_type"/>
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293 </assert_contents>
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294 </output>
13
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295 </test>
17
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296
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297 <!-- test 6 -->
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298 <test expect_num_outputs="2">
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299 <param name="adata" value="krumsiek11.h5ad"/>
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300 <conditional name="method">
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301 <param name="method" value="external.pp.magic"/>
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302 <param name="name_list" value="pca_only"/>
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303 <param name="t" value="3"/>
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304 <param name="n_pca" value="5"/>
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305 </conditional>
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306 <section name="advanced_common">
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307 <param name="show_log" value="true"/>
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308 </section>
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309 <output name="hidden_output">
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310 <assert_contents>
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311 <has_text_matching expression="external.pp.magic"/>
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312 <has_text_matching expression="name_list='pca_only'"/>
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313 <has_text_matching expression="t=3"/>
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314 <has_text_matching expression="n_pca=5"/>
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315 </assert_contents>
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316 </output>
17
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317 <output name="anndata_out" ftype="h5ad">
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318 <assert_contents>
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319 <has_h5_keys keys="obsm/X_magic"/>
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320 </assert_contents>
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321 </output>
13
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322 <assert_stdout>
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323 <has_text text="X_magic"/>
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324 </assert_stdout>
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325 </test>
0
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326 </tests>
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327 <help><![CDATA[
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328 Normalize total counts per cell (`pp.normalize_total`)
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329 ======================================================
0
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330
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331 Normalize each cell by total counts over all genes, so that every cell has the same total count after normalization. If choosing target_sum=1e6, this is CPM normalization.
0
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332
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333 Similar functions are used, for example, by Seurat, Cell Ranger or SPRING.
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334
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335 More details on the `scanpy documentation
17
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336 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.normalize_total.html>`__
0
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337
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338
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339 Normalization and filtering as of Zheng et al. (2017), the Cell Ranger R Kit of 10x Genomics (`pp.recipe_zheng17`)
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340 ==================================================================================================================
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341
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342 Expects non-logarithmized data. If using logarithmized data, pass `log=False`.
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343
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344 The recipe runs the following steps:
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345
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346 - only consider genes with more than 1 count
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347 - normalize with total UMI count per cell
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348 - select highly-variable genes
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349 - subset the genes
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350 - renormalize after filtering
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351 - log transform (if needed)
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352 - scale to unit variance and shift to zero mean
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353
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354 More details on the `scanpy documentation
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355 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.recipe_zheng17.html>`__
0
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356
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357
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358 Normalization and filtering as of Weinreb et al (2017) (`pp.recipe_weinreb17`)
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359 ==============================================================================
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360
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361 Expects non-logarithmized data. If using logarithmized data, pass `log=False`.
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362
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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363 More details on the `scanpy documentation
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364 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.recipe_weinreb17.html>`__
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365
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366
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367 Normalization and filtering as of Seurat et al (2015) (`pp.recipe_seurat`)
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368 ==========================================================================
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369
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370 This uses a particular preprocessing.
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371
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372 Expects non-logarithmized data. If using logarithmized data, pass `log=False`.
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373
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374 More details on the `scanpy documentation
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375 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.recipe_seurat.html>`__
0
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376
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377
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378 Markov Affinity-based Graph Imputation of Cells (MAGIC) as of Van Dijk D et al. (2018) (`external.pp.magic`)
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379 ============================================================================================================
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380
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381 MAGIC is an algorithm for denoising and transcript recover of single cells applied to single-cell sequencing data. MAGIC builds a graph from the data and uses diffusion to smooth out noise and recover the data manifold.
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382
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383 The algorithm implemented here has changed primarily in two ways compared to the algorithm described in Van Dijk D et al. (2018).
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384
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385 - Firstly, we use the adaptive kernel described in Moon et al, (2019) for improved stability.
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386 - Secondly, data diffusion is applied in the PCA space, rather than the data space, for speed and memory improvements.
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387
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388 More details on the `scanpy documentation
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389 <https://scanpy.readthedocs.io/en/stable/api/scanpy.external.pp.magic.html>`__
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390
0
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391 ]]></help>
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392 <expand macro="citations"/>
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393 </tool>