Mercurial > repos > iuc > scanpy_filter

annotate filter.xml @ 20:64388be6d510 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9
author iuc
date Fri, 18 Oct 2024 10:35:58 +0000
parents 713a0c65b1fe
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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1 <tool id="scanpy_filter" name="Scanpy filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
713a0c65b1fe 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>
6ea5a05a260a 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>
6ea5a05a260a 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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713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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7 <expand macro="requirements">
713a0c65b1fe 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>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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9 <requirement type="package" version="0.1.4">scikit-misc</requirement>
713a0c65b1fe 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"/>
6ea5a05a260a 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[
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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13 @CMD@
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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14 ]]></command>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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15 <configfiles>
6ea5a05a260a 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[
17
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17 @CMD_IMPORTS@
713a0c65b1fe 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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6ea5a05a260a 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'
1
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21 sc.pp.filter_cells(
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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22 adata,
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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23 #if $method.filter.filter == 'min_counts'
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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24 min_counts=$method.filter.min_counts,
1
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25 #else if $method.filter.filter == 'max_counts'
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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26 max_counts=$method.filter.max_counts,
1
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27 #else if $method.filter.filter == 'min_genes'
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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28 min_genes=$method.filter.min_genes,
1
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iuc
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29 #else if $method.filter.filter == 'max_genes'
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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30 max_genes=$method.filter.max_genes,
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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31 #end if
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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32 copy=False)
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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33
17
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34 @CMD_ANNDATA_WRITE_OUTPUTS@
713a0c65b1fe 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'
6a76b60e05f5 "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
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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38 adata,
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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39 #if $method.filter.filter == 'min_counts'
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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40 min_counts=$method.filter.min_counts,
1
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41 #else if $method.filter.filter == 'max_counts'
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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42 max_counts=$method.filter.max_counts,
1
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43 #else if $method.filter.filter == 'min_cells'
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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44 min_cells=$method.filter.min_cells,
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45 #else if $method.filter.filter == 'max_cells'
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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46 max_cells=$method.filter.max_cells,
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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47 #end if
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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48 copy=False)
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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49
17
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50 @CMD_ANNDATA_WRITE_OUTPUTS@
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51
1
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52 #else if $method.method == 'tl.filter_rank_genes_groups'
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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53 sc.tl.filter_rank_genes_groups(
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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54 adata,
12
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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
12
a03ff8633507 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0
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58 #if $method.groupby
1
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59 groupby='$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=$method.min_in_group_fraction,
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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64 max_out_group_fraction=$method.max_out_group_fraction,
17
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65 min_fold_change=$method.min_fold_change,
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66 compare_abs=$method.compare_abs)
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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67
713a0c65b1fe 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
713a0c65b1fe 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
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70 if 'rank_genes_groups_filtered' in adata.uns:
713a0c65b1fe 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
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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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',
17
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81 #if $method.flavor.flavor == 'seurat':
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82 min_mean=$method.flavor.min_mean,
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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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($method.flavor.max_disp) != ''
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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86 max_disp=$method.flavor.max_disp,
0
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87 #end if
17
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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,
17
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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
17
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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
17
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119 @CMD_ANNDATA_WRITE_OUTPUTS@
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120
1
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121 #else if $method.method == "pp.downsample_counts"
17
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122 #if str($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=$method.replace,
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139 copy=False)
15
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140
17
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141 #if str($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
15
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150 #else if $method.method == "filter_marker"
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151
17
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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
15
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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
17
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166 #if $method.header == 'not_included':
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167 header=None
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168 #end if
15
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169
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170 marker_list={key: list(value.values()) for key, value in pd.read_csv('$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
17
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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">
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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>
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225 <option value="filter_marker">Filter markers from count matrix and marker list</option>
17
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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">
17
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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">
17
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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">
17
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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">
17
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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">
17
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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">
17
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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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parents: 0
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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"/>
17
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266 </when>
0
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267 <when value="max_cells">
1
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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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parents: 0
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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">
17
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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">
17
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277 <expand macro="sanitize_query"/>
7
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278 </param>
1
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parents: 0
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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">
17
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281 <expand macro="sanitize_query"/>
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282 </param>
1
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parents: 0
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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"/>
17
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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">
0
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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>
0
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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"/>
0
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301 </when>
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302 <when value="cell_ranger">
1
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303 <param argument="n_top_genes" type="integer" value="" label="Number of highly-variable genes to keep"/>
0
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304 </when>
17
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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"/>
3
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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."/>
17
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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>
0
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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">
17
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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>
17
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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>
15
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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>
17
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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>
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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>
17
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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>
17
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diff changeset
421
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422 <!-- test 2 -->
11
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423 <test expect_num_outputs="2">
17
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424 <param name="adata" value="krumsiek11.h5ad"/>
0
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diff changeset
425 <conditional name="method">
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
426 <param name="method" value="pp.filter_cells"/>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
427 <conditional name="filter">
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
428 <param name="filter" value="max_genes"/>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
429 <param name="max_genes" value="10"/>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
430 </conditional>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
431 </conditional>
6
a97abb8cd15b "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">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
433 <param name="show_log" value="true"/>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
434 </section>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
435 <assert_stdout>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
436 <has_text_matching expression="354 × 11"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
437 </assert_stdout>
6
a97abb8cd15b "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">
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
439 <assert_contents>
a97abb8cd15b "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"/>
a97abb8cd15b "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"/>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
442 <has_text_matching expression="max_genes=10"/>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
443 </assert_contents>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
444 </output>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
445 <output name="anndata_out" ftype="h5ad">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
446 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
447 <has_h5_keys keys="obs/cell_type"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
448 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
449 </output>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
450 </test>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
451
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
452 <!-- test 3 -->
11
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
453 <test expect_num_outputs="2">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
454 <param name="adata" value="krumsiek11.h5ad"/>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
455 <conditional name="method">
6ea5a05a260a 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"/>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
457 <conditional name="filter">
6ea5a05a260a 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"/>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
459 <param name="min_counts" value="100"/>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
460 </conditional>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
461 </conditional>
6
a97abb8cd15b "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">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
463 <param name="show_log" value="true"/>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
464 </section>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
465 <assert_stdout>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
466 <has_text_matching expression="640 × 8"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
467 </assert_stdout>
6
a97abb8cd15b "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">
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
469 <assert_contents>
a97abb8cd15b "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"/>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
471 <has_text_matching expression="min_counts=100"/>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
472 </assert_contents>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
473 </output>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
474 <output name="anndata_out" ftype="h5ad">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
475 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
476 <has_h5_keys keys="obs/cell_type"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
477 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
478 </output>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
479 </test>
11
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
480
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
481 <!-- test 4 -->
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
482 <!-- Fails to write to anndata after tl.filter_rank_genes_groups
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
483 Issue has been reported here: https://github.com/scverse/anndata/issues/726
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
484 The current fix is: del adata.uns['rank_genes_groups_filtered'] -->
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
485 <!-- The issue is fixed in the script here -->
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
486 <test expect_num_outputs="2">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
487 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
11
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
488 <conditional name="method">
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
489 <param name="method" value="tl.filter_rank_genes_groups"/>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
490 <param name="key" value="rank_genes_groups"/>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
491 <param name="min_fold_change" value="3"/>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
492 </conditional>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
493 <section name="advanced_common">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
494 <param name="show_log" value="true"/>
11
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
495 </section>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
496 <output name="hidden_output">
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
497 <assert_contents>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
498 <has_text_matching expression="tl.filter_rank_genes_groups"/>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
499 <has_text_matching expression="key='rank_genes_groups'"/>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
500 <has_text_matching expression="use_raw=False"/>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
501 <has_text_matching expression="key_added='rank_genes_groups_filtered'"/>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
502 <has_text_matching expression="min_in_group_fraction=0.25"/>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
503 <has_text_matching expression="max_out_group_fraction=0.5"/>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
504 <has_text_matching expression="min_fold_change=3"/>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
505 </assert_contents>
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
506 </output>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
507 <output name="anndata_out" ftype="h5ad">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
508 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
509 <has_h5_keys keys="uns/rank_genes_groups_filtered"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
510 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
511 </output>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
512 </test>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
513
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
514 <!-- test 5 -->
11
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
515 <test expect_num_outputs="2">
1
6a76b60e05f5 "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
6ea5a05a260a 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
6a76b60e05f5 "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
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
519 </conditional>
6
a97abb8cd15b "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">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
521 <param name="show_log" value="true"/>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
522 </section>
a97abb8cd15b "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">
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
524 <assert_contents>
a97abb8cd15b "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"/>
a97abb8cd15b "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'"/>
a97abb8cd15b "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"/>
a97abb8cd15b "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"/>
a97abb8cd15b "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"/>
a97abb8cd15b "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"/>
a97abb8cd15b "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"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
532 </assert_contents>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
533 </output>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
534 <output name="anndata_out" ftype="h5ad">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
535 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
536 <has_h5_keys keys="var/highly_variable,var/means,var/dispersions,var/dispersions_norm"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
537 <has_h5_keys keys="uns/hvg"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
538 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
539 </output>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
540 </test>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
541
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
542 <!-- test 6 -->
11
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
543 <test expect_num_outputs="2">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
544 <param name="adata" value="krumsiek11.h5ad"/>
0
6ea5a05a260a 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
6a76b60e05f5 "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
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
547 <conditional name="flavor">
6ea5a05a260a 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"/>
6ea5a05a260a 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"/>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
550 </conditional>
3
0a6de5e65992 "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
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
552 </conditional>
6
a97abb8cd15b "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">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
554 <param name="show_log" value="true"/>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
555 </section>
a97abb8cd15b "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">
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
557 <assert_contents>
a97abb8cd15b "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"/>
a97abb8cd15b "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'"/>
a97abb8cd15b "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"/>
a97abb8cd15b "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"/>
a97abb8cd15b "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"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
563 </assert_contents>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
564 </output>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
565 <output name="anndata_out" ftype="h5ad">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
566 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
567 <has_h5_keys keys="var/highly_variable,var/means,var/dispersions,var/dispersions_norm"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
568 <has_h5_keys keys="uns/hvg"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
569 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
570 </output>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
571 </test>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
572
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
573 <!-- test 7 -->
11
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
574 <test expect_num_outputs="2">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
575 <param name="adata" value="krumsiek11.h5ad"/>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
576 <conditional name="method">
6ea5a05a260a 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"/>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
578 <conditional name="type">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
579 <param name="type" value="fraction"/>
0
6ea5a05a260a 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"/>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
581 </conditional>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
582 </conditional>
6
a97abb8cd15b "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">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
584 <param name="show_log" value="true"/>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
585 </section>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
586 <assert_stdout>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
587 <has_text_matching expression="320 × 11"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
588 </assert_stdout>
6
a97abb8cd15b "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">
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
590 <assert_contents>
a97abb8cd15b "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"/>
a97abb8cd15b "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"/>
a97abb8cd15b "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"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
594 </assert_contents>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
595 </output>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
596 <output name="anndata_out" ftype="h5ad">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
597 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
598 <has_h5_keys keys="obs/cell_type"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
599 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
600 </output>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
601 </test>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
602
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
603 <!-- test 8 -->
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
604 <test expect_num_outputs="2">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
605 <param name="adata" value="krumsiek11.h5ad"/>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
606 <conditional name="method">
6ea5a05a260a 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"/>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
608 <conditional name="type">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
609 <param name="type" value="n_obs"/>
0
6ea5a05a260a 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"/>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
611 </conditional>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
612 </conditional>
6
a97abb8cd15b "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">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
614 <param name="show_log" value="true"/>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
615 </section>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
616 <assert_stdout>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
617 <has_text_matching expression="10 × 11"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
618 </assert_stdout>
6
a97abb8cd15b "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">
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
620 <assert_contents>
a97abb8cd15b "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"/>
a97abb8cd15b "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"/>
a97abb8cd15b "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"/>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
624 </assert_contents>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
625 </output>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
626 <output name="anndata_out" ftype="h5ad">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
627 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
628 <has_h5_keys keys="obs/cell_type"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
629 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
630 </output>
1
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
631 </test>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
632
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
633 <!-- test 9 -->
11
2d02d9702d3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
634 <test expect_num_outputs="2">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
635 <param name="adata" value="random-randint.h5ad"/>
1
6a76b60e05f5 "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">
6a76b60e05f5 "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"/>
6a76b60e05f5 "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"/>
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
639 </conditional>
6
a97abb8cd15b "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">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
641 <param name="show_log" value="true"/>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
642 </section>
a97abb8cd15b "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">
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
644 <assert_contents>
a97abb8cd15b "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"/>
a97abb8cd15b "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"/>
a97abb8cd15b "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"/>
a97abb8cd15b "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"/>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
649 <has_text_matching expression="Sum of total counts before: 49983776.0"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
650 <has_text_matching expression="Sum of total counts after: 20000"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
651 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
652 </output>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
653 <output name="anndata_out" ftype="h5ad">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
654 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
655 <has_h5_keys keys="var/index"/>
6
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
656 </assert_contents>
a97abb8cd15b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
657 </output>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
658 </test>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
659
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
660 <!-- test 10 -->
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
661 <test expect_num_outputs="2">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
662 <param name="adata" value="random-randint.h5ad"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
663 <conditional name="method">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
664 <param name="method" value="pp.downsample_counts"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
665 <param name="counts_per_cell" value="20000"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
666 </conditional>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
667 <section name="advanced_common">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
668 <param name="show_log" value="true"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
669 </section>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
670 <output name="hidden_output">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
671 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
672 <has_text_matching expression="sc.pp.downsample_counts"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
673 <has_text_matching expression="counts_per_cell=20000"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
674 <has_text_matching expression="random_state=0"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
675 <has_text_matching expression="replace=False"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
676 <has_text_matching expression="Sum of counts for the first cell before: 489934.0"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
677 <has_text_matching expression="Sum of counts for the last cell before: 503669.0"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
678 <has_text_matching expression="Sum of counts for the first cell after: 20000.0"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
679 <has_text_matching expression="Sum of counts for the last cell after: 20000.0"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
680 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
681 </output>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
682 <output name="anndata_out" ftype="h5ad">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
683 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
684 <has_h5_keys keys="var/index"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
685 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
686 </output>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
687 </test>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
688
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
689 <!-- test 10 -->
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
690 <test expect_num_outputs="2">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
691 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad"/>
15
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
692 <conditional name="method">
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
693 <param name="method" value="filter_marker"/>
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
694 <param name="markerfile" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.tsv"/>
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
695 <param name="thresh_frac" value="0.2"/>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
696 <conditional name="layer_selection">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
697 <param name="use_raw" value="True"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
698 </conditional>
15
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
699 <param name="groupby" value="bulk_labels"/>
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
700 </conditional>
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
701 <section name="advanced_common">
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
702 <param name="show_log" value="true"/>
15
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
703 </section>
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
704 <output name="hidden_output">
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
705 <assert_contents>
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
706 <has_text_matching expression="adata, key, x, 1.0, 0.2, 'bulk_labels'"/>
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
707 </assert_contents>
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
708 </output>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
709 <output name="marker_out" ftype="tabular">
15
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
710 <assert_contents>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
711 <has_text text="CD14+ Monocyte"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
712 <has_text text="C9orf142"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
713 <has_text text="EGR1"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
714 <has_text text="GZMB"/>
15
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
715 </assert_contents>
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
716 </output>
17
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
717 </test>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
718
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
719 <!-- test 11 -->
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
720 <test expect_num_outputs="2">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
721 <param name="adata" value="krumsiek11.h5ad"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
722 <conditional name="method">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
723 <param name="method" value="pp.scrublet"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
724 <param name="n_prin_comps" value="5"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
725 </conditional>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
726 <section name="advanced_common">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
727 <param name="show_log" value="true"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
728 </section>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
729 <output name="hidden_output">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
730 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
731 <has_text_matching expression="sc.pp.scrublet"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
732 <has_text_matching expression="sim_doublet_ratio=2.0"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
733 <has_text_matching expression="expected_doublet_rate=0.05"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
734 <has_text_matching expression="n_prin_comps=5"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
735 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
736 </output>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
737 <output name="anndata_out" ftype="h5ad">
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
738 <assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
739 <has_h5_keys keys="obs/doublet_score,obs/predicted_doublet"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
740 <has_h5_keys keys="uns/scrublet"/>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
741 </assert_contents>
713a0c65b1fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 16
diff changeset
742 </output>
15
aa0059118fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 14
diff changeset
743 </test>
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
744 </tests>
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
745 <help><![CDATA[
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
746
6ea5a05a260a 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`)
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
748 ========================================================================================
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
749
6ea5a05a260a 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
6ea5a05a260a 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.,
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
752 "unreliable" observations.
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
753
6ea5a05a260a 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`,
6ea5a05a260a 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.
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
756
6ea5a05a260a 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
14
d636ce5cde16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
758 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.filter_cells.html>`__
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
759
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
760
6ea5a05a260a 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`)
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
762 ===================================================================
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
763
6ea5a05a260a 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
6ea5a05a260a 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
6ea5a05a260a 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.
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
767
6ea5a05a260a 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`,
6ea5a05a260a 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.
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
770
6ea5a05a260a 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
14
d636ce5cde16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
772 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.filter_genes.html>`__
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
773
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
774
1
6a76b60e05f5 "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`)
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
776 ==========================================================================================================================================================
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
777
6ea5a05a260a 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
14
d636ce5cde16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
iuc
parents: 12
diff changeset
779 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.filter_rank_genes_groups.html>`__
1
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
780
0
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
781
1
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
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782 Annotate highly variable genes (`pp.highly_variable_genes`)
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783 ===========================================================
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784
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785 It expects logarithmized data.
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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786
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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.
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788
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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789
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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790 Subsample to a fraction of the number of observations (`pp.subsample`)
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791 ======================================================================
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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792
6ea5a05a260a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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793 More details on the `scanpy documentation
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794 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.subsample.html>`__
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795
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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796 Downsample counts (`pp.downsample_counts`)
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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797 ==========================================
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798
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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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
6a76b60e05f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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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>