Mercurial > repos > iuc > scanpy_normalize

annotate normalize.xml @ 15:f3ad813a58a3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
author iuc
date Wed, 31 Jul 2024 18:13:07 +0000
parents d844935c906c
children 5dada6f76047
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94c19fb1281c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0
iuc
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1 <tool id="scanpy_normalize" name="Normalize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@">
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2 <description>and impute with scanpy</description>
0
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3 <macros>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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4 <import>macros.xml</import>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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5 </macros>
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
ed64c90a9b93 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"/>
ed64c90a9b93 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[
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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10 @CMD@
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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11 ]]></command>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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12 <configfiles>
ed64c90a9b93 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[
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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14 @CMD_imports@
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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15 @CMD_read_inputs@
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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16
1
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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17 #if $method.method == "pp.normalize_total"
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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18 sc.pp.normalize_total(
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19 adata,
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20 #if str($method.target_sum) != ''
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21 target_sum=$method.target_sum,
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22 #end if
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23 exclude_highly_expressed=$method.exclude_highly_expressed.exclude_highly_expressed,
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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24 #if $method.exclude_highly_expressed.exclude_highly_expressed == "True"
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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25 max_fraction=$method.exclude_highly_expressed.max_fraction,
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26 #end if
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27 #if $method.key_added
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28 key_added='$method.key_added',
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29 #end if
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30 #if $method.layers
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31 #if str($method.layers) != 'all'
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32 layers[str(x.strip()) for x in str($method.layers).split(',')],
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33 #else
1
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34 layers='$method.layers',
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35 #end if
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36 #end if
1
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37 #if str($method.layer_norm) != "None"
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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38 layer_norm='$method.layer_norm',
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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39 #end if
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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40 inplace=True)
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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41
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42 #else if $method.method == "pp.recipe_zheng17"
0
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43 sc.pp.recipe_zheng17(
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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44 adata=adata,
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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45 n_top_genes=$method.n_top_genes,
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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46 log=$method.log,
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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47 plot=False,
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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48 copy=False)
1
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49
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50 #else if $method.method == "pp.recipe_weinreb17"
0
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51 sc.pp.recipe_weinreb17(
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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52 adata=adata,
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53 log=$method.log,
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54 mean_threshold=$method.mean_threshold,
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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55 cv_threshold=$method.cv_threshold,
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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56 n_pcs=$method.n_pcs,
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57 svd_solver='$method.svd_solver',
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58 random_state=$method.random_state,
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59 copy=False)
1
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60
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61 #else if $method.method == "pp.recipe_seurat"
0
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62 sc.pp.recipe_seurat(
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63 adata=adata,
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64 log=$method.log,
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65 plot=False,
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66 copy=False)
1
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67
13
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68 #else if $method.method == "external.pp.magic"
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69 sc.external.pp.magic(
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70 adata=adata,
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71 name_list='$method.name_list',
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72 knn=$method.knn,
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73 #if str($method.decay) != ''
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74 decay=$method.decay,
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75 #end if
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76 #if str($method.knn_max) != ''
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77 knn_max=$method.knn_max,
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78 #end if
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79 #if $method.t == -1
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80 t='auto',
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81 #else
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82 t=$method.t,
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83 #end if
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84 #if str($method.n_pca) != ''
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85 n_pca=$method.n_pca,
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86 #end if
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87 solver='$method.solver',
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88 knn_dist='$method.knn_dist',
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89 random_state=$method.random_state,
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90 copy=False)
0
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91 #end if
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92
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93 @CMD_anndata_write_outputs@
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94
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95 ]]></configfile>
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96 </configfiles>
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97 <inputs>
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98 <expand macro="inputs_anndata"/>
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99 <conditional name="method">
1
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100 <param argument="method" type="select" label="Method used for normalization">
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101 <option value="pp.normalize_total">Normalize counts per cell, using 'pp.normalize_total'</option>
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102 <option value="pp.recipe_zheng17">Normalization and filtering as of Zheng et al. (2017), using 'pp.recipe_zheng17'</option>
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103 <option value="pp.recipe_weinreb17">Normalization and filtering as of Weinreb et al (2017), using 'pp.recipe_weinreb17'</option>
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104 <option value="pp.recipe_seurat">Normalization and filtering as of Seurat et al (2015), using 'pp.recipe_seurat'</option>
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105 <option value="external.pp.magic">Denoising using Markov Affinity-based Graph Imputation of Cells (MAGIC) API 'external.pp.magic'</option>
0
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106 </param>
1
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107 <when value="pp.normalize_total">
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108 <param argument="target_sum" type="float" value="" optional="true" label="Target sum" help="If not provided, after normalization, each observation (cell) has a total count equal to the median of the total counts (cells) before normalization."/>
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109 <conditional name="exclude_highly_expressed">
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110 <param argument="exclude_highly_expressed" type="select" label="Exclude (very) highly expressed genes for the computation of the normalization factor (size factor) for each cell" help=" A gene is considered highly expressed, if it has more than max_fraction of the total counts in at least one cell. The not-excluded genes will sum up to target_sum">
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111 <option value="True">Yes</option>
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112 <option value="False" selected="true">No</option>
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113 </param>
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114 <when value="True">
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115 <param argument="max_fraction" type="float" value="0.05" label="Target sum" help="If not provided, after normalization, each observation (cell) has a total count equal to the median of the total counts (cells) before normalization."/>
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116 </when>
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117 <when value="False"/>
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118 </conditional>
7
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119 <param argument="key_added" type="text" value="" optional="true" label="Name of the field in 'adata.obs' where the normalization factor is stored" help="">
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120 <expand macro="sanitize_query" />
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121 </param>
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122 <param argument="layers" type="text" value="" optional="true" label="List of layers to normalize" help="'All' will normalize all layers. The list should be comma-separated.">
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123 <expand macro="sanitize_query" />
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124 </param>
1
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125 <param argument="layer_norm" type="select" label="How to normalize layers?">
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126 <option value="None">None: after normalization, for each layer in layers each cell has a total count equal to the median of the median of the total counts (cells) before normalization of the layer.</option>
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127 <option value="after">After: for each layer in layers each cell has a total count equal to target_sum.</option>
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128 <option value="X">X: for each layer in layers each cell has a total count equal to the median of total counts for observations (cells) of adata.X before normalization.</option>
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129 </param>
0
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130 </when>
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131 <when value="pp.recipe_zheng17">
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132 <param argument="n_top_genes" type="integer" min="0" value="1000" label="Number of genes to keep" help=""/>
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133 <expand macro="param_log"/>
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134 </when>
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135 <when value="pp.recipe_weinreb17">
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136 <expand macro="param_log"/>
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137 <param argument="mean_threshold" type="float" value="0.01" label="Mean threshold" help=""/>
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138 <param argument="cv_threshold" type="float" value="2" label="CV threshold" help=""/>
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139 <param argument="n_pcs" type="integer" min="0" value="50" label="Number of principal component" help=""/>
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140 <expand macro="svd_solver"/>
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141 <expand macro="pca_random_state"/>
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142 </when>
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143 <when value="pp.recipe_seurat">
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144 <expand macro="param_log"/>
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145 </when>
13
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146 <when value="external.pp.magic">
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147 <param name="name_list" type="select" label="Denoised genes to return" help="Selecting all genes may require a large amount of memory">
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148 <option value="all_genes">All genes</option>
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149 <option value="pca_only">PCA only</option>
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150 </param>
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151 <param argument="knn" type="integer" min="1" value="5" label="Number of nearest neighbors on which to build kernel" help=""/>
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152 <param argument="decay" type="integer" optional="true" value="1" label="Set decay rate of kernel tails"
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153 help="If not set, alpha decaying kernel is not used" />
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154 <param argument="knn_max" type="integer" min="1" optional="true" value="" label="Maximum number of nearest neighbors with nonzero connection"
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155 help="If not set, will be set to 3 * knn" />
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156 <param argument="t" type="integer" min="-1" value="3" label="Power to which the diffusion operator is powered. This sets the level of diffusion"
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157 help="If ‘-1’, this parameter is selected according to the Procrustes disparity of the diffused data." />
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158 <param argument="n_pca" type="integer" value="100" optional="true" label="Number of principal components to use for calculating neighborhoods"
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159 help="For extremely large datasets, using n_pca less than 20 allows neighborhoods to be calculated in roughly log(n_samples) time. If not set, no PCA is performed." />
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160 <param name="solver" type="select" label="Which solver to use" help="Selecting all genes may require a large amount of memory">
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161 <option value="exact">"exact", the implementation described in van Dijk et al. (2018) </option>
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162 <option value="approximate">"approximate", is faster that performs imputation in the PCA space and then projects back to the gene space</option>
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163 </param>
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164 <param name="knn_dist" type="select" label="Distance metric to use for the data" help="See scipy.spatial.distance.pdist documentation for more options https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.pdist.html">
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165 <expand macro="distance_metric_options"/>
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166 </param>
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167 <expand macro="param_random_state"/>
7b9fafe32c86 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3974c0ff86bb1d6633281f29dfb4c605a74e1e6e
iuc
parents: 12
diff changeset
168 </when>
0
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
169 </conditional>
6
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
170 <expand macro="inputs_common_advanced"/>
0
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iuc
parents:
diff changeset
171 </inputs>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
172 <outputs>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
173 <expand macro="anndata_outputs"/>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
174 </outputs>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
175 <tests>
11
c9cb76cf8d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
176 <test expect_num_outputs="2">
c9cb76cf8d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
177 <!-- test 1 -->
1
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
178 <param name="adata" value="krumsiek11.h5ad" />
0
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
179 <conditional name="method">
1
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
180 <param name="method" value="pp.normalize_total"/>
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
181 <conditional name="exclude_highly_expressed">
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
182 <param name="exclude_highly_expressed" value="False"/>
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
183 </conditional>
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
184 <param name="key_added" value="n_counts"/>
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
185 <param name="layers" value="all"/>
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
186 <param name="layer_norm" value="None"/>
0
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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diff changeset
187 </conditional>
6
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
188 <section name="advanced_common">
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
189 <param name="show_log" value="true" />
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
190 </section>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
191 <output name="hidden_output">
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
192 <assert_contents>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
193 <has_text_matching expression="sc.pp.normalize_total"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
194 <has_text_matching expression="exclude_highly_expressed=False"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
195 <has_text_matching expression="key_added='n_counts'"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
196 <has_text_matching expression="layers='all'"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
197 </assert_contents>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
198 </output>
1
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
199 <output name="anndata_out" file="pp.normalize_total.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
0
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
200 </test>
11
c9cb76cf8d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
201 <test expect_num_outputs="2">
c9cb76cf8d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
202 <!-- test 2 -->
1
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
203 <param name="adata" value="random-randint.h5ad"/>
0
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
204 <conditional name="method">
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
205 <param name="method" value="pp.recipe_zheng17"/>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
206 <param name="n_top_genes" value="1000"/>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
207 <param name="log" value="True"/>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
208 </conditional>
6
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
209 <section name="advanced_common">
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
210 <param name="show_log" value="true" />
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
211 </section>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
212 <output name="hidden_output">
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
213 <assert_contents>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
214 <has_text_matching expression="sc.pp.recipe_zheng17"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
215 <has_text_matching expression="n_top_genes=1000"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
216 <has_text_matching expression="log=True"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
217 </assert_contents>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
218 </output>
10
ab55fe8030b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 806c15e8f3ae7acea300ebeb83222162c42eca14"
iuc
parents: 8
diff changeset
219 <output name="anndata_out" file="pp.recipe_zheng17.random-randint.h5ad" ftype="h5ad" compare="sim_size" delta="1000000" delta_frac="0.15"/>
0
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
220 </test>
11
c9cb76cf8d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
221 <test expect_num_outputs="2">
c9cb76cf8d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
222 <!-- test 3 -->
1
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
223 <param name="adata" value="paul15_subsample.h5ad" />
0
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
224 <conditional name="method">
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
225 <param name="method" value="pp.recipe_weinreb17"/>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
226 <param name="log" value="True"/>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
227 <param name="mean_threshold" value="0.01"/>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
228 <param name="cv_threshold" value="2.0"/>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
229 <param name="n_pcs" value="50"/>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
230 <param name="svd_solver" value="randomized"/>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
231 <param name="random_state" value="0"/>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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diff changeset
232 </conditional>
6
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
233 <section name="advanced_common">
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
234 <param name="show_log" value="true" />
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
235 </section>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
236 <output name="hidden_output">
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
237 <assert_contents>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
238 <has_text_matching expression="sc.pp.recipe_weinreb17"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
239 <has_text_matching expression="log=True"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
240 <has_text_matching expression="mean_threshold=0.01"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
241 <has_text_matching expression="cv_threshold=2.0"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
242 <has_text_matching expression="n_pcs=50"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
243 <has_text_matching expression="svd_solver='randomized'"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
244 <has_text_matching expression="random_state=0"/>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
245 </assert_contents>
3bcd5445cd7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
246 </output>
1
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
247 <output name="anndata_out" file="pp.recipe_weinreb17.paul15_subsample.updated.h5ad" ftype="h5ad" compare="sim_size"/>
0
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
248 </test>
11
c9cb76cf8d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
249 <test expect_num_outputs="2">
c9cb76cf8d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
iuc
parents: 10
diff changeset
250 <!-- test 4 -->
1
a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
251 <param name="adata" value="pp.recipe_zheng17.random-randint.h5ad" />
0
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
252 <conditional name="method">
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
253 <param name="method" value="pp.recipe_seurat"/>
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
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254 <param name="log" value="True"/>
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255 </conditional>
6
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256 <section name="advanced_common">
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257 <param name="show_log" value="true" />
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258 </section>
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259 <output name="hidden_output">
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260 <assert_contents>
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261 <has_text_matching expression="sc.pp.recipe_seurat"/>
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262 <has_text_matching expression="log=True"/>
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263 </assert_contents>
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264 </output>
10
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265 <output name="anndata_out" file="pp.recipe_seurat.recipe_zheng17.h5ad" ftype="h5ad" compare="sim_size" delta="1000000" delta_frac="0.25"/>
0
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266 </test>
13
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267 <test expect_num_outputs="2">
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268 <!-- test 5 -->
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269 <param name="adata" value="krumsiek11.h5ad" />
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270 <conditional name="method">
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271 <param name="method" value="external.pp.magic"/>
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272 <param name="name_list" value="all_genes"/>
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273 <param name="t" value="-1"/>
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274 <param name="n_pca" value="5"/>
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275 </conditional>
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276 <section name="advanced_common">
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277 <param name="show_log" value="true" />
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278 </section>
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279 <output name="hidden_output">
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280 <assert_contents>
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281 <has_text_matching expression="external.pp.magic"/>
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282 <has_text_matching expression="name_list='all_genes'"/>
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283 <has_text_matching expression="t='auto'"/>
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284 <has_text_matching expression="n_pca=5"/>
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285 </assert_contents>
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286 </output>
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287 <output name="anndata_out" file="external.pp.magic.all_genes.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
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288 </test>
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289 <test expect_num_outputs="2">
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290 <!-- test 6 -->
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291 <param name="adata" value="krumsiek11.h5ad" />
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292 <conditional name="method">
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293 <param name="method" value="external.pp.magic"/>
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294 <param name="name_list" value="pca_only"/>
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295 <param name="t" value="3"/>
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296 <param name="n_pca" value="5"/>
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297 </conditional>
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298 <section name="advanced_common">
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299 <param name="show_log" value="true" />
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300 </section>
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301 <output name="hidden_output">
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302 <assert_contents>
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303 <has_text_matching expression="external.pp.magic"/>
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304 <has_text_matching expression="name_list='pca_only'"/>
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305 <has_text_matching expression="t=3"/>
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306 <has_text_matching expression="n_pca=5"/>
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307 </assert_contents>
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308 </output>
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309 <output name="anndata_out" file="external.pp.magic.pca_only.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
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310 <assert_stdout>
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311 <has_text text="X_magic"/>
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312 </assert_stdout>
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313 </test>
0
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314 </tests>
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315 <help><![CDATA[
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316 Normalize total counts per cell (`pp.normalize_per_cell`)
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317 =========================================================
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318
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319 Normalize each cell by total counts over all genes, so that every cell has
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320 the same total count after normalization.
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321
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322 Similar functions are used, for example, by Seurat, Cell Ranger or SPRING.
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323
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324 More details on the `scanpy documentation
14
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325 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.normalize_per_cell.html>`__
0
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326
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327
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328 Normalization and filtering as of Zheng et al. (2017), the Cell Ranger R Kit of 10x Genomics (`pp.recipe_zheng17`)
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329 ==================================================================================================================
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330
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331 Expects non-logarithmized data. If using logarithmized data, pass `log=False`.
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332
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333 The recipe runs the following steps:
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334
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335 - only consider genes with more than 1 count
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336 - normalize with total UMI count per cell
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337 - select highly-variable genes
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338 - subset the genes
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339 - renormalize after filtering
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340 - log transform (if needed)
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341 - scale to unit variance and shift to zero mean
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342
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343 More details on the `scanpy documentation
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344 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.recipe_zheng17.html>`__
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345
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346
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347 Normalization and filtering as of Weinreb et al (2017) (`pp.recipe_weinreb17`)
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348 ==============================================================================
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349
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350 Expects non-logarithmized data. If using logarithmized data, pass `log=False`.
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351
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352 More details on the `scanpy documentation
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353 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.recipe_weinreb17.html>`__
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354
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355
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356 Normalization and filtering as of Seurat et al (2015) (`pp.recipe_seurat`)
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357 ==========================================================================
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358
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359 This uses a particular preprocessing.
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360
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361 Expects non-logarithmized data. If using logarithmized data, pass `log=False`.
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362
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363 More details on the `scanpy documentation
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364 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.recipe_seurat.html>`__
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365
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366
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367 Markov Affinity-based Graph Imputation of Cells (MAGIC) as of Van Dijk D et al. (2018) (`external.pp.magic`)
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368 ============================================================================================================
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369
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370 MAGIC is an algorithm for denoising and transcript recover of single cells applied to single-cell sequencing data. MAGIC builds a graph from the data and uses diffusion to smooth out noise and recover the data manifold.
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371
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372 The algorithm implemented here has changed primarily in two ways compared to the algorithm described in Van Dijk D et al. (2018).
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373
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374 - Firstly, we use the adaptive kernel described in Moon et al, (2019) for improved stability.
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375 - Secondly, data diffusion is applied in the PCA space, rather than the data space, for speed and memory improvements.
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376
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377 More details on the `scanpy documentation
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378 <https://scanpy.readthedocs.io/en/stable/api/scanpy.external.pp.magic.html>`__
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379
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380 ]]></help>
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381 <expand macro="citations"/>
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382 </tool>