Mercurial > repos > iuc > scanpy_filter

annotate filter.xml @ 13:e299752da98e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
author iuc
date Tue, 20 Aug 2024 09:48:25 +0000
parents d600e0947468
children eb36554fd6f9
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d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
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1 <tool id="scanpy_filter" name="Filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@">
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2 <description>with scanpy</description>
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3 <macros>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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4 <import>macros.xml</import>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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5 </macros>
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d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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8 <expand macro="version_command"/>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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9 <command detect_errors="exit_code"><![CDATA[
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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10 @CMD@
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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11 ]]></command>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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12 <configfiles>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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13 <configfile name="script_file"><![CDATA[
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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14 @CMD_imports@
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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15 @CMD_read_inputs@
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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17 #if $method.method == 'pp.filter_cells'
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18 sc.pp.filter_cells(
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19 adata,
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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20 #if $method.filter.filter == 'min_counts'
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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21 min_counts=$method.filter.min_counts,
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22 #else if $method.filter.filter == 'max_counts'
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7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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23 max_counts=$method.filter.max_counts,
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24 #else if $method.filter.filter == 'min_genes'
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7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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25 min_genes=$method.filter.min_genes,
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26 #else if $method.filter.filter == 'max_genes'
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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27 max_genes=$method.filter.max_genes,
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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28 #end if
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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29 copy=False)
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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30
1
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31 #else if $method.method == 'pp.filter_genes'
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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32 sc.pp.filter_genes(
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7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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33 adata,
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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34 #if $method.filter.filter == 'min_counts'
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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35 min_counts=$method.filter.min_counts,
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36 #else if $method.filter.filter == 'max_counts'
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7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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37 max_counts=$method.filter.max_counts,
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38 #else if $method.filter.filter == 'min_cells'
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7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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39 min_cells=$method.filter.min_cells,
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40 #else if $method.filter.filter == 'max_cells'
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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41 max_cells=$method.filter.max_cells,
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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42 #end if
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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43 copy=False)
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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44
1
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45 #else if $method.method == 'tl.filter_rank_genes_groups'
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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46 sc.tl.filter_rank_genes_groups(
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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47 adata,
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48 #if $method.key
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49 key='$method.key',
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50 #end if
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51 #if $method.groupby
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52 groupby='$method.groupby',
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53 #end if
1
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54 use_raw=$method.use_raw,
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55 key_added='$method.key_added',
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56 min_in_group_fraction=$method.min_in_group_fraction,
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57 max_out_group_fraction=$method.max_out_group_fraction,
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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58 min_fold_change=$method.min_fold_change)
0
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59
1
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60 #else if $method.method == "pp.highly_variable_genes"
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61 sc.pp.highly_variable_genes(
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62 adata=adata,
0
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63 flavor='$method.flavor.flavor',
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64 #if $method.flavor.flavor == 'seurat'
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65 min_mean=$method.flavor.min_mean,
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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66 max_mean=$method.flavor.max_mean,
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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67 min_disp=$method.flavor.min_disp,
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68 #if str($method.flavor.max_disp) != ''
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69 max_disp=$method.flavor.max_disp,
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70 #end if
1
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71 #else if $method.flavor.flavor == 'cell_ranger'
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72 n_top_genes=$method.flavor.n_top_genes,
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73 #end if
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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74 n_bins=$method.n_bins,
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75 subset=$method.subset,
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76 inplace=True)
0
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77
1
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78 #else if $method.method == 'pp.subsample'
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79 sc.pp.subsample(
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80 data=adata,
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81 #if $method.type.type == 'fraction'
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82 fraction=$method.type.fraction,
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83 #else if $method.type.type == 'n_obs'
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84 n_obs=$method.type.n_obs,
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85 #end if
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86 random_state=$method.random_state,
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87 copy=False)
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88
1
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89 #else if $method.method == "pp.downsample_counts"
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90 sc.pp.downsample_counts(
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91 adata=adata,
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92 #if str($method.counts_per_cell) != ''
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93 counts_per_cell=$method.counts_per_cell,
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94 #end if
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95 #if str($method.total_counts) != ''
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96 total_counts=$method.total_counts,
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97 #end if
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98 random_state=$method.random_state,
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99 replace=$method.replace,
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100 copy=False)
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101
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102 #else if $method.method == "filter_marker"
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103
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104 #if $method.layer_selection.use_raw == 'False':
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105 adata.X = adata.layers['$method.layer_selection.layer']
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106 #end if
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107
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108 def check_marker(adata, group, gene, thresh_mean, thresh_frac, groupby):
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109 filtered_data = adata[adata.obs[groupby] == group, adata.var_names == gene]
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110 mean_expression = np.mean(filtered_data.X)
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111 frac_cell_mean_expression = len(filtered_data.X[filtered_data.X > mean_expression]) / filtered_data.n_obs
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112 if ( mean_expression > thresh_mean and frac_cell_mean_expression >= thresh_frac ):
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113 return(True)
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114 return(False)
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115
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116 header='infer'
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117
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118 #if $method.header == 'not_included':
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119 header=None
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120 #end if
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121
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122 marker_list={key: list(value.values()) for key, value in pd.read_csv('$method.markerfile', sep='\t', index_col=0, header=header).to_dict(orient='index').items()}
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123
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124 for key, value in marker_list.items():
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125 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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126
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127 # Find the maximum length of lists
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128 max_len = max(len(lst) for lst in marker_list.values())
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129
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130 # Fill smaller lists with empty values
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131 for key, value in marker_list.items():
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132 marker_list[key] = value + [''] * (max_len - len(value))
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133
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134 df = pd.DataFrame(marker_list).T
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135 df.to_csv('marker.tsv', sep='\t', index=True)
0
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136 #end if
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137
1
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138 @CMD_anndata_write_outputs@
0
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139 ]]></configfile>
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140 </configfiles>
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141 <inputs>
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142 <expand macro="inputs_anndata"/>
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143 <conditional name="method">
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144 <param argument="method" type="select" label="Method used for filtering">
3
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145 <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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146 <option value="pp.filter_genes">Filter genes based on number of cells or counts, using 'pp.filter_genes'</option>
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147 <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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148 <option value="pp.highly_variable_genes">Annotate (and filter) highly variable genes, using 'pp.highly_variable_genes'</option>
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149 <option value="pp.subsample">Subsample to a fraction of the number of observations, using 'pp.subsample'</option>
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150 <option value="pp.downsample_counts">Downsample counts from count matrix, using 'pp.downsample_counts'</option>
12
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151 <option value="filter_marker">Filter markers from count matrix and marker list</option>
0
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152 </param>
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153 <when value="pp.filter_cells">
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154 <conditional name="filter">
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155 <param argument="filter" type="select" label="Filter">
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156 <option value="min_counts">Minimum number of counts</option>
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157 <option value="max_counts">Maximum number of counts</option>
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158 <option value="min_genes">Minimum number of genes expressed</option>
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159 <option value="max_genes">Maximum number of genes expressed</option>
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160 </param>
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161 <when value="min_counts">
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162 <param argument="min_counts" type="integer" min="0" value="" label="Minimum number of counts required for a cell to pass filtering" help=""/>
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163 </when>
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164 <when value="max_counts">
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165 <param argument="max_counts" type="integer" min="0" value="" label="Maximum number of counts required for a cell to pass filtering" help=""/>
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166 </when>
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167 <when value="min_genes">
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168 <param argument="min_genes" type="integer" min="0" value="" label="Minimum number of genes expressed required for a cell to pass filtering" help=""/>
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169 </when>
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170 <when value="max_genes">
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171 <param argument="max_genes" type="integer" min="0" value="" label="Maximum number of genes expressed required for a cell to pass filtering" help=""/>
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172 </when>
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173 </conditional>
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174 </when>
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175 <when value="pp.filter_genes">
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176 <conditional name="filter">
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177 <param argument="filter" type="select" label="Filter">
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178 <option value="min_counts">Minimum number of counts</option>
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179 <option value="max_counts">Maximum number of counts</option>
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180 <option value="min_cells">Minimum number of cells expressed</option>
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181 <option value="max_cells">Maximum number of cells expressed</option>
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182 </param>
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183 <when value="min_counts">
1
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184 <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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185 </when>
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186 <when value="max_counts">
1
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187 <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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188 </when>
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189 <when value="min_cells">
1
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190 <param argument="min_cells" type="integer" min="0" value="" label="Minimum number of cells expressed required for a gene to pass filtering"/>
0
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191 </when>
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192 <when value="max_cells">
1
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parents: 0
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193 <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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194 </when>
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195 </conditional>
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196 </when>
1
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197 <when value="tl.filter_rank_genes_groups">
7
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198 <param argument="key" type="text" optional="true" label="Key in adata.uns where the rank_genes_groups output is stored">
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199 <expand macro="sanitize_query" />
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200 </param>
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201 <param argument="groupby" type="text" optional="true" label="The key of the observations grouping to consider">
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202 <expand macro="sanitize_query" />
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203 </param>
1
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parents: 0
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204 <expand macro="param_use_raw"/>
7
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205 <param argument="key_added" type="text" value="rank_genes_groups_filtered" label="Key that will contain new values">
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206 <expand macro="sanitize_query" />
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207 </param>
1
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parents: 0
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208 <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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209 <param argument="max_out_group_fraction" type="float" min="0" max="1" value="0.5" label="Maximum fraction of genes expressing the gene outside the categories"/>
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210 <param argument="min_fold_change" type="integer" value="2" label="Minimum fold change"/>
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211 </when>
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212 <when value="pp.highly_variable_genes">
0
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213 <conditional name='flavor'>
1
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214 <param argument="flavor" type="select" label="Flavor for computing normalized dispersion">
3
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215 <option value="seurat">Seurat</option>
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216 <option value="cell_ranger">Cell Ranger</option>
0
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217 </param>
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218 <when value="seurat">
1
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219 <param argument="min_mean" type="float" value="0.0125" label="Minimal mean cutoff"/>
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220 <param argument="max_mean" type="float" value="3" label="Maximal mean cutoff"/>
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221 <param argument="min_disp" type="float" value="0.5" label="Minimal normalized dispersion cutoff"/>
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222 <param argument="max_disp" type="float" value="" optional="true" label="Maximal normalized dispersion cutoff"/>
0
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223 </when>
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224 <when value="cell_ranger">
1
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225 <param argument="n_top_genes" type="integer" value="" label="Number of highly-variable genes to keep"/>
0
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226 </when>
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227 </conditional>
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228 <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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229 <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."/>
0
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230 </when>
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231 <when value="pp.subsample">
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232 <conditional name="type">
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233 <param name="type" type="select" label="Type of subsampling">
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234 <option value="fraction">By fraction</option>
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235 <option value="n_obs">By number of observation</option>
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236 </param>
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237 <when value="fraction">
3
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238 <param argument="fraction" type="float" value="" label="Subsample to this 'fraction' of the number of observations"/>
0
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239 </when>
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240 <when value="n_obs">
1
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241 <param argument="n_obs" type="integer" min="0" value="" label="Subsample to this number of observations"/>
0
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242 </when>
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243 </conditional>
1
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244 <param argument="random_state" type="integer" value="0" label="Random seed to change subsampling"/>
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245 </when>
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246 <when value="pp.downsample_counts">
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247 <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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248 <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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249 <param argument="random_state" type="integer" value="0" label="Random seed to change subsampling"/>
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250 <param argument="replace" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Sample the counts with replacement?"/>
0
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251 </when>
12
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252 <when value="filter_marker">
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253 <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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254 <param name="header" type="select" label="Header in the list of markers?">
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255 <option value="included">Header incldued</option>
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256 <option value="not_included">Header not included</option>
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257 </param>
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258 <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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259 <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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260 <conditional name="layer_selection">
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261 <param name="use_raw" type="select" label="Use .X of adata to perform the filtering" help="">
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262 <option value="True">Yes</option>
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263 <option value="False">No</option>
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264 </param>
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265 <when value="False">
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266 <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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267 </when>
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268 <when value="True"/>
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269 </conditional>
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270 <param argument="groupby" type="text" value="" label="The key of the observation grouping to consider (e.g., celltype)" help="">
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271 <expand macro="sanitize_query" />
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272 </param>
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273 </when>
0
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274 </conditional>
6
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275 <expand macro="inputs_common_advanced"/>
0
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276 </inputs>
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277 <outputs>
1
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iuc
parents: 0
diff changeset
278 <expand macro="anndata_outputs"/>
12
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279 <data name="marker_out" format="tabular" from_work_dir="marker.tsv" label="${tool.name} on ${on_string}: Markers">
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280 <filter>method['method'] == 'filter_marker'</filter>
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281 </data>
0
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282 </outputs>
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283 <tests>
12
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284 <test expect_num_outputs="2">
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285 <!-- test 1 -->
1
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parents: 0
diff changeset
286 <param name="adata" value="krumsiek11.h5ad" />
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
287 <conditional name="method">
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288 <param name="method" value="pp.filter_cells"/>
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diff changeset
289 <conditional name="filter">
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290 <param name="filter" value="min_counts"/>
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291 <param name="min_counts" value="3"/>
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292 </conditional>
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293 </conditional>
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294 <assert_stdout>
6
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295 <has_text_matching expression="336 × 11"/>
0
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296 </assert_stdout>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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diff changeset
297 <section name="advanced_common">
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298 <param name="show_log" value="true" />
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299 </section>
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diff changeset
300 <output name="hidden_output">
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301 <assert_contents>
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diff changeset
302 <has_text_matching expression="sc.pp.filter_cells"/>
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303 <has_text_matching expression="min_counts=3"/>
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304 </assert_contents>
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diff changeset
305 </output>
1
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parents: 0
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306 <output name="anndata_out" file="pp.filter_cells.krumsiek11-min_counts.h5ad" ftype="h5ad" compare="sim_size"/>
0
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307 </test>
12
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diff changeset
308 <test expect_num_outputs="2">
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309 <!-- test 2 -->
1
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iuc
parents: 0
diff changeset
310 <param name="adata" value="krumsiek11.h5ad" />
0
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iuc
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diff changeset
311 <conditional name="method">
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iuc
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diff changeset
312 <param name="method" value="pp.filter_cells"/>
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iuc
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diff changeset
313 <conditional name="filter">
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314 <param name="filter" value="max_genes"/>
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315 <param name="max_genes" value="100"/>
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316 </conditional>
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317 </conditional>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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diff changeset
318 <section name="advanced_common">
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319 <param name="show_log" value="true" />
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320 </section>
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diff changeset
321 <output name="hidden_output">
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iuc
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322 <assert_contents>
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iuc
parents: 5
diff changeset
323 <has_text_matching expression="sc.pp.filter_cells"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
324 <has_text_matching expression="adata"/>
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iuc
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325 <has_text_matching expression="max_genes=100"/>
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326 </assert_contents>
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diff changeset
327 </output>
1
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iuc
parents: 0
diff changeset
328 <output name="anndata_out" file="pp.filter_cells.krumsiek11-max_genes.h5ad" ftype="h5ad" compare="sim_size"/>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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329 </test>
12
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diff changeset
330 <test expect_num_outputs="2">
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331 <!-- test 3 -->
1
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iuc
parents: 0
diff changeset
332 <param name="adata" value="krumsiek11.h5ad" />
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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diff changeset
333 <conditional name="method">
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iuc
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diff changeset
334 <param name="method" value="pp.filter_genes"/>
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iuc
parents:
diff changeset
335 <conditional name="filter">
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iuc
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336 <param name="filter" value="min_counts"/>
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iuc
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337 <param name="min_counts" value="3"/>
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338 </conditional>
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339 </conditional>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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diff changeset
340 <section name="advanced_common">
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parents: 5
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341 <param name="show_log" value="true" />
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diff changeset
342 </section>
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parents: 5
diff changeset
343 <output name="hidden_output">
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parents: 5
diff changeset
344 <assert_contents>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
345 <has_text_matching expression="sc.pp.filter_genes"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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parents: 5
diff changeset
346 <has_text_matching expression="min_counts=3"/>
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iuc
parents: 5
diff changeset
347 </assert_contents>
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diff changeset
348 </output>
1
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iuc
parents: 0
diff changeset
349 <output name="anndata_out" file="pp.filter_genes.krumsiek11-min_counts.h5ad" ftype="h5ad" compare="sim_size"/>
0
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iuc
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350 </test>
12
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diff changeset
351
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352 <!-- test 4 -->
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353 <!-- Fails to write to anndata after tl.filter_rank_genes_groups
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354 Issue has been reported here: https://github.com/scverse/anndata/issues/726
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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355 The current fix is: del adata.uns['rank_genes_groups_filtered'] -->
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356 <!--<test expect_num_outputs="2">
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357 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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358 <conditional name="method">
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359 <param name="method" value="tl.filter_rank_genes_groups"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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360 <param name="key" value="rank_genes_groups"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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361 <param name="use_raw" value="False"/>
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362 <param name="key_added" value="rank_genes_groups_filtered"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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363 <param name="min_in_group_fraction" value="0.25"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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364 <param name="max_out_group_fraction" value="0.5"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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365 <param name="min_fold_change" value="3"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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366 </conditional>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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367 <section name="advanced_common">
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368 <param name="show_log" value="true" />
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369 </section>
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370 <output name="hidden_output">
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371 <assert_contents>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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372 <has_text_matching expression="tl.filter_rank_genes_groups"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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373 <has_text_matching expression="key='rank_genes_groups'"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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374 <has_text_matching expression="use_raw=False"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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375 <has_text_matching expression="log=False"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
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376 <has_text_matching expression="key_added='rank_genes_groups_filtered'"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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377 <has_text_matching expression="min_in_group_fraction=0.25"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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diff changeset
378 <has_text_matching expression="max_out_group_fraction=0.5"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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379 <has_text_matching expression="min_fold_change=3"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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380 </assert_contents>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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381 </output>
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382 <output name="anndata_out" file="pp.filter_rank_genes_groups.h5ad" ftype="h5ad" compare="sim_size"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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383 </test>-->
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384 <test expect_num_outputs="2">
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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385 <!-- test 5 -->
1
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iuc
parents: 0
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386 <param name="adata" value="blobs.h5ad"/>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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387 <conditional name="method">
1
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
388 <param name="method" value="pp.highly_variable_genes"/>
0
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diff changeset
389 <conditional name="flavor">
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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390 <param name="flavor" value="seurat"/>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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391 <param name="min_mean" value="0.0125"/>
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diff changeset
392 <param name="max_mean" value="3"/>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
393 <param name="min_disp" value="0.5"/>
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394 </conditional>
1
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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395 <param name="n_bins" value="20"/>
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
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396 <param name="subset" value="false"/>
0
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397 </conditional>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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398 <section name="advanced_common">
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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399 <param name="show_log" value="true" />
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400 </section>
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401 <output name="hidden_output">
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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402 <assert_contents>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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403 <has_text_matching expression="sc.pp.highly_variable_genes"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
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404 <has_text_matching expression="flavor='seurat'"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
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405 <has_text_matching expression="min_mean=0.0125"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
406 <has_text_matching expression="max_mean=3"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
407 <has_text_matching expression="min_disp=0.5"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
408 <has_text_matching expression="n_bins=20"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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parents: 5
diff changeset
409 <has_text_matching expression="subset=False"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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410 </assert_contents>
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411 </output>
8
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412 <output name="anndata_out" file="pp.highly_variable_genes.seurat.blobs.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.2"/>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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413 </test>
12
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414 <test expect_num_outputs="2">
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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415 <!-- test 6 -->
1
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
416 <param name="adata" value="krumsiek11.h5ad" />
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
417 <conditional name="method">
1
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
418 <param name="method" value="pp.highly_variable_genes"/>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
419 <conditional name="flavor">
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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420 <param name="flavor" value="cell_ranger"/>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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421 <param name="n_top_genes" value="2"/>
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422 </conditional>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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423 <param name="n_bins" value="20"/>
3
1a4b233265e3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 2
diff changeset
424 <param name="subset" value="true"/>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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425 </conditional>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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parents: 5
diff changeset
426 <section name="advanced_common">
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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parents: 5
diff changeset
427 <param name="show_log" value="true" />
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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diff changeset
428 </section>
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parents: 5
diff changeset
429 <output name="hidden_output">
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iuc
parents: 5
diff changeset
430 <assert_contents>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
431 <has_text_matching expression="sc.pp.highly_variable_genes"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
432 <has_text_matching expression="flavor='cell_ranger'"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
433 <has_text_matching expression="n_top_genes=2"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
434 <has_text_matching expression="n_bins=20"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
435 <has_text_matching expression="subset=True"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
436 </assert_contents>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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diff changeset
437 </output>
8
26d97f4a601c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec"
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parents: 7
diff changeset
438 <output name="anndata_out" file="pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.9"/>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
439 </test>
12
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
440 <test expect_num_outputs="2">
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
441 <!-- test 7 -->
1
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
442 <param name="adata" value="krumsiek11.h5ad" />
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
443 <conditional name="method">
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
444 <param name="method" value="pp.subsample"/>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
445 <conditional name="type">
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
446 <param name="type" value="fraction" />
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
447 <param name="fraction" value="0.5"/>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
448 </conditional>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
449 <param name="random_state" value="0"/>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
450 </conditional>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
451 <section name="advanced_common">
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
452 <param name="show_log" value="true" />
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
453 </section>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
454 <output name="hidden_output">
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
455 <assert_contents>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
456 <has_text_matching expression="sc.pp.subsample"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
457 <has_text_matching expression="fraction=0.5"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
458 <has_text_matching expression="random_state=0"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
459 </assert_contents>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
460 </output>
1
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
461 <output name="anndata_out" file="pp.subsample.krumsiek11_fraction.h5ad" ftype="h5ad" compare="sim_size"/>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
462 </test>
12
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
463 <test expect_num_outputs="2">
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
464 <!-- test 8 -->
1
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
465 <param name="adata" value="krumsiek11.h5ad" />
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
466 <conditional name="method">
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
467 <param name="method" value="pp.subsample"/>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
468 <conditional name="type">
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
469 <param name="type" value="n_obs" />
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
470 <param name="n_obs" value="10"/>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
471 </conditional>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
472 <param name="random_state" value="0"/>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
473 </conditional>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
474 <section name="advanced_common">
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
475 <param name="show_log" value="true" />
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
476 </section>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
477 <output name="hidden_output">
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
478 <assert_contents>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
479 <has_text_matching expression="sc.pp.subsample"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
480 <has_text_matching expression="n_obs=10"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
481 <has_text_matching expression="random_state=0"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
482 </assert_contents>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
483 </output>
1
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
484 <output name="anndata_out" file="pp.subsample.krumsiek11_n_obs.h5ad" ftype="h5ad" compare="sim_size"/>
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
485 </test>
12
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
486 <test expect_num_outputs="2">
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
487 <!-- test 9 -->
1
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
488 <param name="adata" value="random-randint.h5ad" />
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
489 <conditional name="method">
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
490 <param name="method" value="pp.downsample_counts"/>
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
491 <param name="total_counts" value="20000"/>
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
492 <param name="random_state" value="0"/>
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
493 <param name="replace" value="false"/>
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
494 </conditional>
6
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
495 <section name="advanced_common">
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
496 <param name="show_log" value="true" />
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
497 </section>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
498 <output name="hidden_output">
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
499 <assert_contents>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
500 <has_text_matching expression="sc.pp.downsample_counts"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
501 <has_text_matching expression="total_counts=20000"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
502 <has_text_matching expression="random_state=0"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
503 <has_text_matching expression="replace=False"/>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
504 </assert_contents>
9a9944c53825 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
505 </output>
8
26d97f4a601c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec"
iuc
parents: 7
diff changeset
506 <output name="anndata_out" file="pp.downsample_counts.random-randint.h5ad" ftype="h5ad" compare="sim_size" delta="10000000" delta_frac="0.5"/>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
507 </test>
12
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
508 <test expect_num_outputs="3">
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
509 <!-- test 10 -->
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
510 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" />
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
511 <conditional name="method">
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
512 <param name="method" value="filter_marker"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
513 <param name="markerfile" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.tsv"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
514 <param name="thresh_mean" value="1.0"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
515 <param name="thresh_frac" value="0.2"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
516 <param name="layer_selection" value="True"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
517 <param name="groupby" value="bulk_labels"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
518 </conditional>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
519 <section name="advanced_common">
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
520 <param name="show_log" value="true" />
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
521 </section>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
522 <output name="hidden_output">
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
523 <assert_contents>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
524 <has_text_matching expression="adata, key, x, 1.0, 0.2, 'bulk_labels'"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
525 </assert_contents>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
526 </output>
13
e299752da98e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
iuc
parents: 12
diff changeset
527 <output name="anndata_out" file="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1_out.h5ad" ftype="h5ad">
12
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
528 <assert_contents>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
529 <has_h5_keys keys="obs, var, uns" />
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
530 </assert_contents>
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531 </output>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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532 <output name="marker_out" file="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.tsv" ftype="tabular" compare="sim_size"/>
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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533 </test>
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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534 </tests>
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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535 <help><![CDATA[
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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536
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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537 Filter cells outliers based on counts and numbers of genes expressed (`pp.filter_cells`)
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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538 ========================================================================================
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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539
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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540 For instance, only keep cells with at least `min_counts` counts or
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
541 `min_genes` genes expressed. This is to filter measurement outliers, i.e.,
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
542 "unreliable" observations.
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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543
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
544 Only provide one of the optional parameters `min_counts`, `min_genes`,
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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545 `max_counts`, `max_genes` per call.
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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546
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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547 More details on the `scanpy documentation
12
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548 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.filter_cells.html>`__
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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549
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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550
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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diff changeset
551 Filter genes based on number of cells or counts (`pp.filter_genes`)
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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552 ===================================================================
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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553
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
554 Keep genes that have at least `min_counts` counts or are expressed in at
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
555 least `min_cells` cells or have at most `max_counts` counts or are expressed
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
556 in at most `max_cells` cells.
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
557
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
558 Only provide one of the optional parameters `min_counts`, `min_cells`,
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
559 `max_counts`, `max_cells` per call.
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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560
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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561 More details on the `scanpy documentation
12
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562 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.filter_genes.html>`__
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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563
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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564
1
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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565 Filters out genes based on fold change and fraction of genes expressing the gene within and outside the groupby categories (`tl.filter_rank_genes_groups`)
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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566 ==========================================================================================================================================================
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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567
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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568 More details on the `scanpy documentation
12
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569 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.filter_rank_genes_groups.html>`__
1
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
570
0
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571
1
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
572 Annotate highly variable genes (`pp.highly_variable_genes`)
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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573 ===========================================================
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
574
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
575 It expects logarithmized data.
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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576
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
577 Depending on flavor, this reproduces the R-implementations of Seurat or Cell Ranger. The normalized dispersion is obtained by scaling with the mean and standard deviation of the dispersions for genes falling into a given bin for mean expression of genes. This means that for each bin of mean expression, highly variable genes are selected.
0
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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578
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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579
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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580 Subsample to a fraction of the number of observations (`pp.subsample`)
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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581 ======================================================================
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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582
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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583 More details on the `scanpy documentation
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584 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.subsample.html>`__
1
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585
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
586 Downsample counts (`pp.downsample_counts`)
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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587 ==========================================
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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588
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
589 Downsample counts so that each cell has no more than `target_counts`. Cells with fewer counts than `target_counts` are unaffected by this. This
deeb0203d693 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
590 has been implemented by M. D. Luecken.
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591
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592
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diff changeset
593 Filter marker genes (`filter_marker`)
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594 ======================================================================
d600e0947468 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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595
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diff changeset
596 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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597
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598 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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599
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600 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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601
1
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602 More details on the `scanpy documentation
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603 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.downsample_counts.html>`__
0
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604
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605
7edb8980267d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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606 ]]></help>
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607 <expand macro="citations"/>
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608 </tool>