Mercurial > repos > iuc > scanpy_filter

annotate filter.xml @ 14:eb36554fd6f9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
author iuc
date Sat, 14 Sep 2024 12:37:46 +0000
parents e299752da98e
children 2a55e0dae43a
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eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
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1 <tool id="scanpy_filter" name="Scanpy filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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2 <description>mark and subsample</description>
0
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3 <macros>
7edb8980267d 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>
7edb8980267d 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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eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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7 <expand macro="requirements">
eb36554fd6f9 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="0.2.3">scrublet</requirement>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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9 <requirement type="package" version="0.1.4">scikit-misc</requirement>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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10 </expand>
0
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11 <expand macro="version_command"/>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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12 <command detect_errors="exit_code"><![CDATA[
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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13 @CMD@
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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14 ]]></command>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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15 <configfiles>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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16 <configfile name="script_file"><![CDATA[
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17 @CMD_IMPORTS@
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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18 @CMD_READ_INPUTS@
0
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7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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20 #if $method.method == 'pp.filter_cells'
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21 sc.pp.filter_cells(
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7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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22 adata,
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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23 #if $method.filter.filter == 'min_counts'
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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24 min_counts=$method.filter.min_counts,
1
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25 #else if $method.filter.filter == 'max_counts'
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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26 max_counts=$method.filter.max_counts,
1
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27 #else if $method.filter.filter == 'min_genes'
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7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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28 min_genes=$method.filter.min_genes,
1
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29 #else if $method.filter.filter == 'max_genes'
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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30 max_genes=$method.filter.max_genes,
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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31 #end if
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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32 copy=False)
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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33
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34 @CMD_ANNDATA_WRITE_OUTPUTS@
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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35
1
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36 #else if $method.method == 'pp.filter_genes'
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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37 sc.pp.filter_genes(
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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38 adata,
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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39 #if $method.filter.filter == 'min_counts'
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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40 min_counts=$method.filter.min_counts,
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41 #else if $method.filter.filter == 'max_counts'
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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42 max_counts=$method.filter.max_counts,
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43 #else if $method.filter.filter == 'min_cells'
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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44 min_cells=$method.filter.min_cells,
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45 #else if $method.filter.filter == 'max_cells'
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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46 max_cells=$method.filter.max_cells,
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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47 #end if
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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48 copy=False)
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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49
14
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50 @CMD_ANNDATA_WRITE_OUTPUTS@
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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51
1
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52 #else if $method.method == 'tl.filter_rank_genes_groups'
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53 sc.tl.filter_rank_genes_groups(
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54 adata,
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55 #if $method.key
1
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56 key='$method.key',
0
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57 #end if
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58 #if $method.groupby
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59 groupby='$method.groupby',
0
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60 #end if
1
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61 use_raw=$method.use_raw,
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62 key_added='$method.key_added',
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63 min_in_group_fraction=$method.min_in_group_fraction,
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64 max_out_group_fraction=$method.max_out_group_fraction,
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65 min_fold_change=$method.min_fold_change,
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66 compare_abs=$method.compare_abs)
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67
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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68 # Temporary fix for Issue reported here: https://github.com/scverse/anndata/issues/726
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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69 # Check and convert elements in 'rank_genes_groups_filtered' to strings
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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70 if 'rank_genes_groups_filtered' in adata.uns:
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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71 for key, value in adata.uns['rank_genes_groups_filtered'].items():
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72 if not isinstance(value, str):
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73 adata.uns['rank_genes_groups_filtered'][key] = str(value)
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74
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75 @CMD_ANNDATA_WRITE_OUTPUTS@
0
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76
1
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77 #else if $method.method == "pp.highly_variable_genes"
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78 sc.pp.highly_variable_genes(
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79 adata=adata,
0
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80 flavor='$method.flavor.flavor',
14
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81 #if $method.flavor.flavor == 'seurat':
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82 min_mean=$method.flavor.min_mean,
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83 max_mean=$method.flavor.max_mean,
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84 min_disp=$method.flavor.min_disp,
1
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85 #if str($method.flavor.max_disp) != ''
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86 max_disp=$method.flavor.max_disp,
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87 #end if
14
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88 #else if $method.flavor.flavor == 'cell_ranger':
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89 n_top_genes=$method.flavor.n_top_genes,
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90 #else if $method.flavor.flavor == 'seurat_v3':
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91 n_top_genes=$method.flavor.n_top_genes,
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92 span=$method.flavor.span,
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93 #else if $method.flavor.flavor == 'seurat_v3_paper':
0
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94 n_top_genes=$method.flavor.n_top_genes,
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95 #end if
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96 n_bins=$method.n_bins,
1
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97 subset=$method.subset,
14
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98 #if $method.layer != ''
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99 layer='$method.layer',
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100 #end if
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101 #if $method.batch_key != ''
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102 layer='$method.batch_key',
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103 #end if
1
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104 inplace=True)
0
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105
14
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106 @CMD_ANNDATA_WRITE_OUTPUTS@
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107
1
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108 #else if $method.method == 'pp.subsample'
0
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109 sc.pp.subsample(
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110 data=adata,
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111 #if $method.type.type == 'fraction'
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112 fraction=$method.type.fraction,
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113 #else if $method.type.type == 'n_obs'
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114 n_obs=$method.type.n_obs,
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115 #end if
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116 random_state=$method.random_state,
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117 copy=False)
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118
14
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119 @CMD_ANNDATA_WRITE_OUTPUTS@
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120
1
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121 #else if $method.method == "pp.downsample_counts"
14
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122 #if str($method.counts_per_cell) != ''
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123 print("Sum of counts for the first cell before:", adata.X[0, :].sum())
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124 print("Sum of counts for the last cell before:", adata.X[adata.X.shape[0]-1, :].sum())
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125 #else if str($method.total_counts) != ''
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126 print("Sum of total counts before:", adata.X.sum())
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127 #end if
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128
1
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129 sc.pp.downsample_counts(
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130 adata=adata,
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131 #if str($method.counts_per_cell) != ''
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132 counts_per_cell=$method.counts_per_cell,
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133 #end if
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134 #if str($method.total_counts) != ''
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135 total_counts=$method.total_counts,
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136 #end if
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137 random_state=$method.random_state,
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138 replace=$method.replace,
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139 copy=False)
12
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140
14
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141 #if str($method.counts_per_cell) != ''
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142 print("Sum of counts for the first cell after:", adata.X[0, :].sum())
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143 print("Sum of counts for the last cell after:", adata.X[adata.X.shape[0]-1, :].sum())
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144 #else if str($method.total_counts) != ''
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145 print("Sum of total counts after:", adata.X.sum())
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146 #end if
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147
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148 @CMD_ANNDATA_WRITE_OUTPUTS@
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149
12
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150 #else if $method.method == "filter_marker"
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151
14
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152 #if $method.layer_selection.use_raw == 'False':
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153 adata.X = adata.layers['$method.layer_selection.layer']
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154 #end if
12
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155
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156 def check_marker(adata, group, gene, thresh_mean, thresh_frac, groupby):
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157 filtered_data = adata[adata.obs[groupby] == group, adata.var_names == gene]
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158 mean_expression = np.mean(filtered_data.X)
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159 frac_cell_mean_expression = len(filtered_data.X[filtered_data.X > mean_expression]) / filtered_data.n_obs
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160 if ( mean_expression > thresh_mean and frac_cell_mean_expression >= thresh_frac ):
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161 return(True)
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162 return(False)
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163
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164 header='infer'
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165
14
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166 #if $method.header == 'not_included':
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167 header=None
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168 #end if
12
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169
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170 marker_list={key: list(value.values()) for key, value in pd.read_csv('$method.markerfile', sep='\t', index_col=0, header=header).to_dict(orient='index').items()}
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171
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172 for key, value in marker_list.items():
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173 marker_list[key] = [x for x in value if check_marker(adata, key, x, $method.thresh_mean, $method.thresh_frac, '$method.groupby')]
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174
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175 # Find the maximum length of lists
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176 max_len = max(len(lst) for lst in marker_list.values())
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177
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178 # Fill smaller lists with empty values
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179 for key, value in marker_list.items():
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180 marker_list[key] = value + [''] * (max_len - len(value))
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181
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182 df = pd.DataFrame(marker_list).T
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183 df.to_csv('marker.tsv', sep='\t', index=True)
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184
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185 #else if $method.method == "pp.scrublet"
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186 sc.pp.scrublet(
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187 adata,
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188 #if $method.batch_key != ''
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189 batch_key='$method.batch_key',
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190 #end if
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191 sim_doublet_ratio=$method.sim_doublet_ratio,
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192 expected_doublet_rate=$method.expected_doublet_rate,
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193 stdev_doublet_rate=$method.stdev_doublet_rate,
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194 synthetic_doublet_umi_subsampling=$method.synthetic_doublet_umi_subsampling,
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195 knn_dist_metric='$method.knn_dist_metric',
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196 normalize_variance=$method.normalize_variance,
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197 log_transform=$method.log_transform,
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198 mean_center=$method.mean_center,
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199 n_prin_comps=$method.n_prin_comps,
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200 use_approx_neighbors=$method.use_approx_neighbors,
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201 get_doublet_neighbor_parents=$method.get_doublet_neighbor_parents,
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202 #if str($method.n_neighbors) != ''
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203 n_neighbors=$method.n_neighbors,
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204 #end if
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205 #if str($method.threshold) != ''
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206 threshold=$method.threshold,
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207 #end if
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208 random_state=$method.random_state)
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209
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210 @CMD_ANNDATA_WRITE_OUTPUTS@
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211 #end if
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212 ]]>
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213 </configfile>
0
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214 </configfiles>
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215 <inputs>
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216 <expand macro="inputs_anndata"/>
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217 <conditional name="method">
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218 <param argument="method" type="select" label="Method used for filtering">
3
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219 <option value="pp.filter_cells">Filter cell outliers based on counts and numbers of genes expressed, using 'pp.filter_cells'</option>
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220 <option value="pp.filter_genes">Filter genes based on number of cells or counts, using 'pp.filter_genes'</option>
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221 <option value="tl.filter_rank_genes_groups">Filters out genes based on fold change and fraction of genes expressing the gene within and outside the groupby categories, using 'tl.filter_rank_genes_groups'</option>
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222 <option value="pp.highly_variable_genes">Annotate (and filter) highly variable genes, using 'pp.highly_variable_genes'</option>
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223 <option value="pp.subsample">Subsample to a fraction of the number of observations, using 'pp.subsample'</option>
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224 <option value="pp.downsample_counts">Downsample counts from count matrix, using 'pp.downsample_counts'</option>
12
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225 <option value="filter_marker">Filter markers from count matrix and marker list</option>
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226 <option value="pp.scrublet">Predict doublets using 'pp.scrublet'</option>
0
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227 </param>
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228 <when value="pp.filter_cells">
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229 <conditional name="filter">
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230 <param argument="filter" type="select" label="Filter">
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231 <option value="min_counts" selected="true">Minimum number of counts</option>
0
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232 <option value="max_counts">Maximum number of counts</option>
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233 <option value="min_genes">Minimum number of genes expressed</option>
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234 <option value="max_genes">Maximum number of genes expressed</option>
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235 </param>
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236 <when value="min_counts">
14
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237 <param argument="min_counts" type="integer" min="0" value="" label="Minimum number of counts required for a cell to pass filtering"/>
0
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238 </when>
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239 <when value="max_counts">
14
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240 <param argument="max_counts" type="integer" min="0" value="" label="Maximum number of counts required for a cell to pass filtering"/>
0
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241 </when>
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242 <when value="min_genes">
14
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243 <param argument="min_genes" type="integer" min="0" value="" label="Minimum number of genes expressed required for a cell to pass filtering"/>
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244 </when>
0
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245 <when value="max_genes">
14
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246 <param argument="max_genes" type="integer" min="0" value="" label="Maximum number of genes expressed required for a cell to pass filtering"/>
0
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247 </when>
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248 </conditional>
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249 </when>
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250 <when value="pp.filter_genes">
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251 <conditional name="filter">
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252 <param argument="filter" type="select" label="Filter">
14
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253 <option value="min_counts" selected="true">Minimum number of counts</option>
0
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254 <option value="max_counts">Maximum number of counts</option>
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255 <option value="min_cells">Minimum number of cells expressed</option>
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256 <option value="max_cells">Maximum number of cells expressed</option>
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257 </param>
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258 <when value="min_counts">
1
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259 <param argument="min_counts" type="integer" min="0" value="" label="Minimum number of counts required for a gene to pass filtering"/>
0
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260 </when>
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261 <when value="max_counts">
1
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262 <param argument="max_counts" type="integer" min="0" value="" label="Maximum number of counts required for a gene to pass filtering"/>
0
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263 </when>
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264 <when value="min_cells">
1
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265 <param argument="min_cells" type="integer" min="0" value="" label="Minimum number of cells expressed required for a gene to pass filtering"/>
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266 </when>
0
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267 <when value="max_cells">
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268 <param argument="max_cells" type="integer" min="0" value="" label="Maximum number of cells expressed required for a gene to pass filtering"/>
0
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269 </when>
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270 </conditional>
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271 </when>
1
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272 <when value="tl.filter_rank_genes_groups">
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273 <param argument="key" type="text" optional="true" label="Key in adata.uns where the rank_genes_groups output is stored">
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274 <expand macro="sanitize_query"/>
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275 </param>
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276 <param argument="groupby" type="text" optional="true" label="The key of the observations grouping to consider">
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277 <expand macro="sanitize_query"/>
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278 </param>
1
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279 <expand macro="param_use_raw"/>
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280 <param argument="key_added" type="text" value="rank_genes_groups_filtered" label="Key that will contain new values">
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281 <expand macro="sanitize_query"/>
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282 </param>
1
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283 <param argument="min_in_group_fraction" type="float" min="0" max="1" value="0.25" label="Minimum fraction of genes expressing the gene within the categories"/>
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284 <param argument="max_out_group_fraction" type="float" min="0" max="1" value="0.5" label="Maximum fraction of genes expressing the gene outside the categories"/>
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285 <param argument="min_fold_change" type="integer" value="1" label="Minimum fold change"/>
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286 <param argument="compare_abs" type="boolean" truevalue="True" falsevalue="False" checked="false" label="If selected, compare absolute values of log fold change with min_fold_change"/>
1
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287 </when>
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288 <when value="pp.highly_variable_genes">
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289 <conditional name='flavor'>
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290 <param argument="flavor" type="select" label="Choose the flavor for identifying highly variable genes" help="Expects logarithmized data, except when flavor='seurat_v3'/'seurat_v3_paper', in which count">
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291 <option value="seurat" selected="true">Seurat</option>
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292 <option value="cell_ranger">Cell Ranger</option>
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293 <option value="seurat_v3">Seurat v3</option>
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294 <option value="seurat_v3_paper">Seurat v3 (paper)</option>
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295 </param>
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296 <when value="seurat">
1
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297 <param argument="min_mean" type="float" value="0.0125" label="Minimal mean cutoff"/>
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298 <param argument="max_mean" type="float" value="3" label="Maximal mean cutoff"/>
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299 <param argument="min_disp" type="float" value="0.5" label="Minimal normalized dispersion cutoff"/>
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300 <param argument="max_disp" type="float" value="" optional="true" label="Maximal normalized dispersion cutoff"/>
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301 </when>
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302 <when value="cell_ranger">
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303 <param argument="n_top_genes" type="integer" value="" label="Number of highly-variable genes to keep"/>
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304 </when>
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305 <when value="seurat_v3">
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306 <param argument="n_top_genes" type="integer" value="" optional="false" label="Number of highly-variable genes to keep"/>
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307 <param argument="span" type="float" value="0.3" label="The fraction of the data (cells) used when estimating the variance in the loess model fit"/>
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308 </when>
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309 <when value="seurat_v3_paper">
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310 <param argument="n_top_genes" type="integer" value="" optional="false" label="Number of highly-variable genes to keep"/>
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311 </when>
0
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312 </conditional>
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313 <param argument="n_bins" type="integer" value="20" label="Number of bins for binning the mean gene expression" help="Normalization is done with respect to each bin. If just a single gene falls into a bin, the normalized dispersion is artificially set to 1"/>
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314 <param argument="subset" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Inplace subset to highly-variable genes?" help="Otherwise it merely indicates highly variable genes."/>
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315 <expand macro="param_layer"/>
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316 <param argument="batch_key" type="text" value="" label="Specify the batch key" help="If specified, highly-variable genes are selected within each batch separately and merged.">
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317 <expand macro="sanitize_query"/>
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318 </param>
0
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319 </when>
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320 <when value="pp.subsample">
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321 <conditional name="type">
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322 <param name="type" type="select" label="Type of subsampling">
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323 <option value="fraction" selected="true">By fraction</option>
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324 <option value="n_obs">By number of observation</option>
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325 </param>
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326 <when value="fraction">
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327 <param argument="fraction" type="float" min="0" value="" label="Subsample to this 'fraction' of the number of observations"/>
0
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328 </when>
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329 <when value="n_obs">
1
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330 <param argument="n_obs" type="integer" min="0" value="" label="Subsample to this number of observations"/>
0
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331 </when>
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332 </conditional>
1
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333 <param argument="random_state" type="integer" value="0" label="Random seed to change subsampling"/>
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334 </when>
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335 <when value="pp.downsample_counts">
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336 <param argument="counts_per_cell" type="integer" min="0" optional="true" label="Target total counts per cell" help="If a cell has more than ‘counts_per_cell’, it will be downsampled to this number. Resulting counts can be specified on a per cell basis by passing an array."/>
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337 <param argument="total_counts" type="integer" min="0" optional="true" label="Target total counts" help="If the count matrix has more than total_counts it will be downsampled to have this number."/>
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338 <param argument="random_state" type="integer" value="0" label="Random seed to change subsampling"/>
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339 <param argument="replace" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Sample the counts with replacement?"/>
0
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340 </when>
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341 <when value="filter_marker">
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342 <param argument="markerfile" type="data" format="tabular" label="List of markers" help="This should be a tsv where row = group (e.g. celltypes) and columns = markers."></param>
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343 <param name="header" type="boolean" truevalue="included" falsevalue="not_included" checked="true" label="Header is included in the list of markers?"/>
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344 <param argument="thresh_mean" type="float" min="0.0" value="1.0" label="Minimal average count of all cells of a group (e.g., celltype) for a particular marker" help="Increasing the threshold will result in a smaller marker set."/>
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345 <param argument="thresh_frac" type="float" min="0.0" max="1.0" value="0.1" label="Minimal fractions of cells that has a higher count than the average count of all cells of the group for the marker" help="Increasing this threshold might remove marker outliers."/>
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346 <conditional name="layer_selection">
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347 <param name="use_raw" type="select" label="Use .X of adata to perform the filtering">
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348 <option value="True" selected="true">Yes</option>
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349 <option value="False">No</option>
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350 </param>
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351 <when value="False">
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352 <param argument="layer" type="text" value="" label="Key from adata.layers whose value will be used to filter" help="If layers specified then use adata.layers[layer]."/>
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353 </when>
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354 <when value="True"/>
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355 </conditional>
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356 <param argument="groupby" type="text" value="" label="The key of the observation grouping to consider (e.g., celltype)">
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357 <expand macro="sanitize_query"/>
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358 </param>
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359 </when>
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360 <when value="pp.scrublet">
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361 <param argument="batch_key" type="text" value="" optional="true" label="Batch key for the concatenate">
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362 <expand macro="sanitize_query" />
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363 </param>
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364 <param argument="sim_doublet_ratio" type="float" value="2.0" label="Number of doublets to simulate relative to the number of observed transcriptomes"/>
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365 <param argument="expected_doublet_rate" type="float" value="0.05" label="The estimated doublet rate for the experiment"/>
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366 <param argument="stdev_doublet_rate" type="float" value="0.02" label="Uncertainty in the expected doublet rate"/>
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367 <param argument="synthetic_doublet_umi_subsampling" type="float" value="1.0" label="Rate for sampling UMIs when creating synthetic doublets" help="f 1.0, each doublet is created by simply adding the UMI counts from two randomly sampled observed transcriptomes. For values less than 1, the UMI counts are added and then randomly sampled at the specified rate."/>
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368 <param name="knn_dist_metric" type="select" label="Distance metric used when finding nearest neighbors">
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369 <expand macro="distance_metric_options"/>
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370 </param>
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371 <param argument="normalize_variance" type="boolean" truevalue="True" falsevalue="False" checked="true" label="normalize the data such that each gene has a variance of 1"/>
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372 <param argument="log_transform" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Whether to use log1p() to log-transform the data prior to PCA"/>
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373 <param argument="mean_center" type="boolean" truevalue="True" falsevalue="False" checked="true" label="If True, center the data such that each gene has a mean of 0"/>
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374 <param argument="n_prin_comps" type="integer" value="30" label="Number of principal components used to embed the transcriptomes prior to k-nearest-neighbor graph construction"/>
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375 <param argument="use_approx_neighbors" type="boolean" truevalue="True" falsevalue="None" checked="false" label="Use approximate nearest neighbor method (annoy) for the KNN classifier"/>
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376 <param argument="get_doublet_neighbor_parents" type="boolean" truevalue="True" falsevalue="False" checked="false" label="If True, return (in .uns) the parent transcriptomes that generated the doublet neighbors of each observed transcriptome" help="This information can be used to infer the cell states that generated a given doublet state."/>
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377 <param argument="n_neighbors" type="integer" value="" optional="true" label="Number of neighbors used to construct the KNN graph of observed transcriptomes and simulated doublets"/>
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378 <param argument="threshold" type="float" value="" optional="true" label="Doublet score threshold for calling a transcriptome a doublet" help="If None, this is set automatically"/>
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379 <param name="random_state" type="integer" value="0" label="Initial state for doublet simulation and nearest neighbors"/>
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380 </when>
0
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381 </conditional>
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382 <expand macro="inputs_common_advanced"/>
0
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383 </inputs>
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384 <outputs>
14
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385 <expand macro="anndata_outputs">
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386 <filter>method['method'] != 'filter_marker'</filter>
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387 </expand>
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388 <data name="marker_out" format="tabular" from_work_dir="marker.tsv" label="${tool.name} on ${on_string}: Markers">
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389 <filter>method['method'] == 'filter_marker'</filter>
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390 </data>
0
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391 </outputs>
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392 <tests>
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393 <!-- test 1 -->
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394 <test expect_num_outputs="2">
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395 <param name="adata" value="krumsiek11.h5ad"/>
0
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396 <conditional name="method">
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397 <param name="method" value="pp.filter_cells"/>
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398 <conditional name="filter">
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399 <param name="filter" value="min_counts"/>
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400 <param name="min_counts" value="3"/>
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401 </conditional>
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402 </conditional>
14
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403 <section name="advanced_common">
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404 <param name="show_log" value="true"/>
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405 </section>
0
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406 <assert_stdout>
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407 <has_text_matching expression="336 × 11"/>
0
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408 </assert_stdout>
6
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409 <output name="hidden_output">
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410 <assert_contents>
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411 <has_text_matching expression="sc.pp.filter_cells"/>
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412 <has_text_matching expression="min_counts=3"/>
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413 </assert_contents>
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414 </output>
14
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415 <output name="anndata_out" ftype="h5ad">
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416 <assert_contents>
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417 <has_h5_keys keys="obs/cell_type"/>
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418 </assert_contents>
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419 </output>
0
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420 </test>
14
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421
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422 <!-- test 2 -->
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423 <test expect_num_outputs="2">
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424 <param name="adata" value="krumsiek11.h5ad"/>
0
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425 <conditional name="method">
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426 <param name="method" value="pp.filter_cells"/>
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427 <conditional name="filter">
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428 <param name="filter" value="max_genes"/>
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429 <param name="max_genes" value="10"/>
0
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diff changeset
430 </conditional>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
431 </conditional>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
432 <section name="advanced_common">
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
433 <param name="show_log" value="true"/>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
434 </section>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
435 <assert_stdout>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
436 <has_text_matching expression="354 × 11"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
437 </assert_stdout>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
438 <output name="hidden_output">
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
439 <assert_contents>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
440 <has_text_matching expression="sc.pp.filter_cells"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
441 <has_text_matching expression="adata"/>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
442 <has_text_matching expression="max_genes=10"/>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
443 </assert_contents>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
444 </output>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
445 <output name="anndata_out" ftype="h5ad">
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
446 <assert_contents>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
447 <has_h5_keys keys="obs/cell_type"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
448 </assert_contents>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
449 </output>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
450 </test>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
451
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
452 <!-- test 3 -->
12
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
453 <test expect_num_outputs="2">
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
454 <param name="adata" value="krumsiek11.h5ad"/>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
455 <conditional name="method">
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
456 <param name="method" value="pp.filter_genes"/>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
457 <conditional name="filter">
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
458 <param name="filter" value="min_counts"/>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
459 <param name="min_counts" value="100"/>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
460 </conditional>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
461 </conditional>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
462 <section name="advanced_common">
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
463 <param name="show_log" value="true"/>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
464 </section>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
465 <assert_stdout>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
466 <has_text_matching expression="640 × 8"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
467 </assert_stdout>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
468 <output name="hidden_output">
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
469 <assert_contents>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
470 <has_text_matching expression="sc.pp.filter_genes"/>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
471 <has_text_matching expression="min_counts=100"/>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
472 </assert_contents>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
473 </output>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
474 <output name="anndata_out" ftype="h5ad">
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
475 <assert_contents>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
476 <has_h5_keys keys="obs/cell_type"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
477 </assert_contents>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
478 </output>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
479 </test>
12
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
480
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
481 <!-- test 4 -->
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
482 <!-- Fails to write to anndata after tl.filter_rank_genes_groups
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
483 Issue has been reported here: https://github.com/scverse/anndata/issues/726
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
484 The current fix is: del adata.uns['rank_genes_groups_filtered'] -->
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
485 <!-- The issue is fixed in the script here -->
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
486 <test expect_num_outputs="2">
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
487 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
12
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
488 <conditional name="method">
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
489 <param name="method" value="tl.filter_rank_genes_groups"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
490 <param name="key" value="rank_genes_groups"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
491 <param name="min_fold_change" value="3"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
492 </conditional>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
493 <section name="advanced_common">
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
494 <param name="show_log" value="true"/>
12
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
495 </section>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
496 <output name="hidden_output">
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
497 <assert_contents>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
498 <has_text_matching expression="tl.filter_rank_genes_groups"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
499 <has_text_matching expression="key='rank_genes_groups'"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
500 <has_text_matching expression="use_raw=False"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
501 <has_text_matching expression="key_added='rank_genes_groups_filtered'"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
502 <has_text_matching expression="min_in_group_fraction=0.25"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
503 <has_text_matching expression="max_out_group_fraction=0.5"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
504 <has_text_matching expression="min_fold_change=3"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
505 </assert_contents>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
506 </output>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
507 <output name="anndata_out" ftype="h5ad">
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
508 <assert_contents>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
509 <has_h5_keys keys="uns/rank_genes_groups_filtered"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
510 </assert_contents>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
511 </output>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
512 </test>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
513
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
514 <!-- test 5 -->
12
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
515 <test expect_num_outputs="2">
1
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
516 <param name="adata" value="blobs.h5ad"/>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
517 <conditional name="method">
1
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
518 <param name="method" value="pp.highly_variable_genes"/>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
519 </conditional>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
520 <section name="advanced_common">
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
521 <param name="show_log" value="true"/>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
522 </section>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
523 <output name="hidden_output">
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
524 <assert_contents>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
525 <has_text_matching expression="sc.pp.highly_variable_genes"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
526 <has_text_matching expression="flavor='seurat'"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
527 <has_text_matching expression="min_mean=0.0125"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
528 <has_text_matching expression="max_mean=3"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
529 <has_text_matching expression="min_disp=0.5"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
530 <has_text_matching expression="n_bins=20"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
531 <has_text_matching expression="subset=False"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
532 </assert_contents>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
533 </output>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
534 <output name="anndata_out" ftype="h5ad">
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
535 <assert_contents>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
536 <has_h5_keys keys="var/highly_variable,var/means,var/dispersions,var/dispersions_norm"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
537 <has_h5_keys keys="uns/hvg"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
538 </assert_contents>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
539 </output>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
540 </test>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
541
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
542 <!-- test 6 -->
12
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
543 <test expect_num_outputs="2">
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
544 <param name="adata" value="krumsiek11.h5ad"/>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
545 <conditional name="method">
1
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
546 <param name="method" value="pp.highly_variable_genes"/>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
547 <conditional name="flavor">
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
548 <param name="flavor" value="cell_ranger"/>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
549 <param name="n_top_genes" value="2"/>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
550 </conditional>
3
1a4b233265e3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
551 <param name="subset" value="true"/>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
552 </conditional>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
553 <section name="advanced_common">
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
554 <param name="show_log" value="true"/>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
555 </section>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
556 <output name="hidden_output">
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
557 <assert_contents>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
558 <has_text_matching expression="sc.pp.highly_variable_genes"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
559 <has_text_matching expression="flavor='cell_ranger'"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
560 <has_text_matching expression="n_top_genes=2"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
561 <has_text_matching expression="n_bins=20"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
562 <has_text_matching expression="subset=True"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
563 </assert_contents>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
564 </output>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
565 <output name="anndata_out" ftype="h5ad">
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
566 <assert_contents>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
567 <has_h5_keys keys="var/highly_variable,var/means,var/dispersions,var/dispersions_norm"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
568 <has_h5_keys keys="uns/hvg"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
569 </assert_contents>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
570 </output>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
571 </test>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
572
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
573 <!-- test 7 -->
12
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
574 <test expect_num_outputs="2">
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
575 <param name="adata" value="krumsiek11.h5ad"/>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
576 <conditional name="method">
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
577 <param name="method" value="pp.subsample"/>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
578 <conditional name="type">
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
579 <param name="type" value="fraction"/>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
580 <param name="fraction" value="0.5"/>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
581 </conditional>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
582 </conditional>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
583 <section name="advanced_common">
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
584 <param name="show_log" value="true"/>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
585 </section>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
586 <assert_stdout>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
587 <has_text_matching expression="320 × 11"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
588 </assert_stdout>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
589 <output name="hidden_output">
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
590 <assert_contents>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
591 <has_text_matching expression="sc.pp.subsample"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
592 <has_text_matching expression="fraction=0.5"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
593 <has_text_matching expression="random_state=0"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
594 </assert_contents>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
595 </output>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
596 <output name="anndata_out" ftype="h5ad">
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
597 <assert_contents>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
598 <has_h5_keys keys="obs/cell_type"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
599 </assert_contents>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
600 </output>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
601 </test>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
602
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
603 <!-- test 8 -->
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
604 <test expect_num_outputs="2">
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
605 <param name="adata" value="krumsiek11.h5ad"/>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
606 <conditional name="method">
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
607 <param name="method" value="pp.subsample"/>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
608 <conditional name="type">
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
609 <param name="type" value="n_obs"/>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
610 <param name="n_obs" value="10"/>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
611 </conditional>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
612 </conditional>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
613 <section name="advanced_common">
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
614 <param name="show_log" value="true"/>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
615 </section>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
616 <assert_stdout>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
617 <has_text_matching expression="10 × 11"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
618 </assert_stdout>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
619 <output name="hidden_output">
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
620 <assert_contents>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
621 <has_text_matching expression="sc.pp.subsample"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
622 <has_text_matching expression="n_obs=10"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
623 <has_text_matching expression="random_state=0"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
624 </assert_contents>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
625 </output>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
626 <output name="anndata_out" ftype="h5ad">
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
627 <assert_contents>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
628 <has_h5_keys keys="obs/cell_type"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
629 </assert_contents>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
630 </output>
1
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
631 </test>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
632
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
633 <!-- test 9 -->
12
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
634 <test expect_num_outputs="2">
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
635 <param name="adata" value="random-randint.h5ad"/>
1
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
636 <conditional name="method">
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
637 <param name="method" value="pp.downsample_counts"/>
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
638 <param name="total_counts" value="20000"/>
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
639 </conditional>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
640 <section name="advanced_common">
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
641 <param name="show_log" value="true"/>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
642 </section>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
643 <output name="hidden_output">
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
644 <assert_contents>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
645 <has_text_matching expression="sc.pp.downsample_counts"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
646 <has_text_matching expression="total_counts=20000"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
647 <has_text_matching expression="random_state=0"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
648 <has_text_matching expression="replace=False"/>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
649 <has_text_matching expression="Sum of total counts before: 49983776.0"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
650 <has_text_matching expression="Sum of total counts after: 20000"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
651 </assert_contents>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
652 </output>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
653 <output name="anndata_out" ftype="h5ad">
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
654 <assert_contents>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
655 <has_h5_keys keys="var/index"/>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
656 </assert_contents>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
657 </output>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
658 </test>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
659
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
660 <!-- test 10 -->
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
661 <test expect_num_outputs="2">
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
662 <param name="adata" value="random-randint.h5ad"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
663 <conditional name="method">
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
664 <param name="method" value="pp.downsample_counts"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
665 <param name="counts_per_cell" value="20000"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
666 </conditional>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
667 <section name="advanced_common">
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
668 <param name="show_log" value="true"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
669 </section>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
670 <output name="hidden_output">
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
671 <assert_contents>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
672 <has_text_matching expression="sc.pp.downsample_counts"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
673 <has_text_matching expression="counts_per_cell=20000"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
674 <has_text_matching expression="random_state=0"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
675 <has_text_matching expression="replace=False"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
676 <has_text_matching expression="Sum of counts for the first cell before: 489934.0"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
677 <has_text_matching expression="Sum of counts for the last cell before: 503669.0"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
678 <has_text_matching expression="Sum of counts for the first cell after: 20000.0"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
679 <has_text_matching expression="Sum of counts for the last cell after: 20000.0"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
680 </assert_contents>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
681 </output>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
682 <output name="anndata_out" ftype="h5ad">
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
683 <assert_contents>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
684 <has_h5_keys keys="var/index"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
685 </assert_contents>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
686 </output>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
687 </test>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
688
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
689 <!-- test 10 -->
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
690 <test expect_num_outputs="2">
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
691 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad"/>
12
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
692 <conditional name="method">
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
693 <param name="method" value="filter_marker"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
694 <param name="markerfile" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.tsv"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
695 <param name="thresh_frac" value="0.2"/>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
696 <conditional name="layer_selection">
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
697 <param name="use_raw" value="True"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
698 </conditional>
12
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
699 <param name="groupby" value="bulk_labels"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
700 </conditional>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
701 <section name="advanced_common">
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
702 <param name="show_log" value="true"/>
12
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
703 </section>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
704 <output name="hidden_output">
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
705 <assert_contents>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
706 <has_text_matching expression="adata, key, x, 1.0, 0.2, 'bulk_labels'"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
707 </assert_contents>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
708 </output>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
709 <output name="marker_out" ftype="tabular">
12
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
710 <assert_contents>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
711 <has_text text="CD14+ Monocyte"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
712 <has_text text="C9orf142"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
713 <has_text text="EGR1"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
714 <has_text text="GZMB"/>
12
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
715 </assert_contents>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
716 </output>
14
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
717 </test>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
718
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
719 <!-- test 11 -->
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
720 <test expect_num_outputs="2">
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
721 <param name="adata" value="krumsiek11.h5ad"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
722 <conditional name="method">
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
723 <param name="method" value="pp.scrublet"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
724 <param name="n_prin_comps" value="5"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
725 </conditional>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
726 <section name="advanced_common">
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
727 <param name="show_log" value="true"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
728 </section>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
729 <output name="hidden_output">
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
730 <assert_contents>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
731 <has_text_matching expression="sc.pp.scrublet"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
732 <has_text_matching expression="sim_doublet_ratio=2.0"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
733 <has_text_matching expression="expected_doublet_rate=0.05"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
734 <has_text_matching expression="n_prin_comps=5"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
735 </assert_contents>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
736 </output>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
737 <output name="anndata_out" ftype="h5ad">
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
738 <assert_contents>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
739 <has_h5_keys keys="obs/doublet_score,obs/predicted_doublet"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
740 <has_h5_keys keys="uns/scrublet"/>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
741 </assert_contents>
eb36554fd6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 13
diff changeset
742 </output>
12
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
743 </test>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
744 </tests>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
745 <help><![CDATA[
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
746
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
747 Filter cells outliers based on counts and numbers of genes expressed (`pp.filter_cells`)
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
748 ========================================================================================
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
749
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
750 For instance, only keep cells with at least `min_counts` counts or
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
751 `min_genes` genes expressed. This is to filter measurement outliers, i.e.,
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
752 "unreliable" observations.
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
753
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
754 Only provide one of the optional parameters `min_counts`, `min_genes`,
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
755 `max_counts`, `max_genes` per call.
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
756
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
757 More details on the `scanpy documentation
12
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
758 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.filter_cells.html>`__
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
759
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
760
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
761 Filter genes based on number of cells or counts (`pp.filter_genes`)
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
762 ===================================================================
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
763
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
764 Keep genes that have at least `min_counts` counts or are expressed in at
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
765 least `min_cells` cells or have at most `max_counts` counts or are expressed
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
766 in at most `max_cells` cells.
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
767
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
768 Only provide one of the optional parameters `min_counts`, `min_cells`,
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
769 `max_counts`, `max_cells` per call.
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
770
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
771 More details on the `scanpy documentation
12
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
772 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.filter_genes.html>`__
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
773
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
774
1
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
775 Filters out genes based on fold change and fraction of genes expressing the gene within and outside the groupby categories (`tl.filter_rank_genes_groups`)
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
776 ==========================================================================================================================================================
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
777
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
778 More details on the `scanpy documentation
12
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
779 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.filter_rank_genes_groups.html>`__
1
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
780
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
781
1
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
782 Annotate highly variable genes (`pp.highly_variable_genes`)
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
783 ===========================================================
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
784
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
785 It expects logarithmized data.
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
786
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
787 Depending on flavor, this reproduces the R-implementations of Seurat or Cell Ranger. The normalized dispersion is obtained by scaling with the mean and standard deviation of the dispersions for genes falling into a given bin for mean expression of genes. This means that for each bin of mean expression, highly variable genes are selected.
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
788
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
789
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
790 Subsample to a fraction of the number of observations (`pp.subsample`)
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
791 ======================================================================
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
792
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
793 More details on the `scanpy documentation
12
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
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794 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.subsample.html>`__
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795
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796 Downsample counts (`pp.downsample_counts`)
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797 ==========================================
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798
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799 Downsample counts so that each cell has no more than `target_counts`. Cells with fewer counts than `target_counts` are unaffected by this. This
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800 has been implemented by M. D. Luecken.
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801
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802 More details on the `scanpy documentation
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803 <https://scanpy.readthedocs.io/en/stable/generated/scanpy.pp.downsample_counts.html>`__
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804
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805 Filter marker genes (`filter_marker`)
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806 =====================================
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807
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808 This option is specific for celltype marker gene detection. You can generate a celltype marker gene file (tsv) with **COSG** provided at Galaxy.
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809
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810 The marker gene file should have as rows celltypes and columns as marker genes. Each celltype can have varying number of marker genes.
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811
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812 A marker gene is returned (retained in the list) if the mean expression of the marker gene is bigger than the threshold of mean expression (thresh_mean) and if the fraction of cells with the marker gene expression is equal or higher than the cell fraction threshold (thresh_frac).
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813
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814 More details on the `scanpy documentation
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815 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.downsample_counts.html>`__
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816
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817
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818 Predict cell doublets using a nearest-neighbor classifier of observed transcriptomes and simulated doublets. (`pp.scrublet`)
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819 ============================================================================================================================
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820
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821 Works best if the input is a raw (unnormalized) counts matrix from a single sample or a collection of similar samples from the same experiment. This function is a wrapper around functions that pre-process using Scanpy and directly call functions of Scrublet().
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822
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823 More details on the `scanpy documentation
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824 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.scrublet.html>`__
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825
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826 ]]></help>
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827 <expand macro="citations"/>
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828 </tool>