Mercurial > repos > iuc > scanpy_normalize

annotate normalize.xml @ 11:c9cb76cf8d6c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
author iuc
date Wed, 08 Nov 2023 14:49:18 +0000
parents ab55fe8030b6
children 94c19fb1281c
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8e0f141c8c66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit e6675eff6b4d49386c2a9e4dde0011ba33aedbcc"
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1 <tool id="scanpy_normalize" name="Normalize" version="@galaxy_version@" profile="@profile@">
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a9f14e2d1655 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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2 <description>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>
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5 </macros>
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c9cb76cf8d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
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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@
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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@
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15 @CMD_read_inputs@
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16
1
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17 #if $method.method == "pp.normalize_total"
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18 sc.pp.normalize_total(
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19 adata,
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20 #if str($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 str($method.key_added) != ''
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28 key_added='$method.key_added',
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29 #end if
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30 #if str($method.layers) != ''
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31 #if str($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($method.layer_norm) != "None"
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38 layer_norm='$method.layer_norm',
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39 #end if
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40 inplace=True)
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41
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42 #else if $method.method == "pp.recipe_zheng17"
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43 sc.pp.recipe_zheng17(
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44 adata=adata,
ed64c90a9b93 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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45 n_top_genes=$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,
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47 plot=False,
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48 copy=False)
1
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49
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50 #else if $method.method == "pp.recipe_weinreb17"
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51 sc.pp.recipe_weinreb17(
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52 adata=adata,
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53 log=$method.log,
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54 mean_threshold=$method.mean_threshold,
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55 cv_threshold=$method.cv_threshold,
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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)
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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)
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67
0
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68 #end if
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69
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70 @CMD_anndata_write_outputs@
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71
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72 ]]></configfile>
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73 </configfiles>
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74 <inputs>
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75 <expand macro="inputs_anndata"/>
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76 <conditional name="method">
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77 <param argument="method" type="select" label="Method used for normalization">
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78 <option value="pp.normalize_total">Normalize counts per cell, using 'pp.normalize_total'</option>
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79 <option value="pp.recipe_zheng17">Normalization and filtering as of Zheng et al. (2017), using 'pp.recipe_zheng17'</option>
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80 <option value="pp.recipe_weinreb17">Normalization and filtering as of Weinreb et al (2017), using 'pp.recipe_weinreb17'</option>
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81 <option value="pp.recipe_seurat">Normalization and filtering as of Seurat et al (2015), using 'pp.recipe_seurat'</option>
0
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82 </param>
1
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83 <when value="pp.normalize_total">
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84 <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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85 <conditional name="exclude_highly_expressed">
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86 <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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87 <option value="True">Yes</option>
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88 <option value="False" selected="true">No</option>
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89 </param>
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90 <when value="True">
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91 <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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92 </when>
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93 <when value="False"/>
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94 </conditional>
7
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95 <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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96 <expand macro="sanitize_query" />
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97 </param>
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98 <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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99 <expand macro="sanitize_query" />
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100 </param>
1
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101 <param argument="layer_norm" type="select" label="How to normalize layers?">
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102 <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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103 <option value="after">After: for each layer in layers each cell has a total count equal to target_sum.</option>
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104 <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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105 </param>
0
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106 </when>
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107 <when value="pp.recipe_zheng17">
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108 <param argument="n_top_genes" type="integer" min="0" value="1000" label="Number of genes to keep" help=""/>
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109 <expand macro="param_log"/>
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110 </when>
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111 <when value="pp.recipe_weinreb17">
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112 <expand macro="param_log"/>
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113 <param argument="mean_threshold" type="float" value="0.01" label="Mean threshold" help=""/>
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114 <param argument="cv_threshold" type="float" value="2" label="CV threshold" help=""/>
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115 <param argument="n_pcs" type="integer" min="0" value="50" label="Number of principal component" help=""/>
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116 <expand macro="svd_solver"/>
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117 <expand macro="pca_random_state"/>
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118 </when>
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119 <when value="pp.recipe_seurat">
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120 <expand macro="param_log"/>
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121 </when>
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122 </conditional>
6
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123 <expand macro="inputs_common_advanced"/>
0
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124 </inputs>
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125 <outputs>
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126 <expand macro="anndata_outputs"/>
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127 </outputs>
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128 <tests>
11
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129 <test expect_num_outputs="2">
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130 <!-- test 1 -->
1
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131 <param name="adata" value="krumsiek11.h5ad" />
0
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132 <conditional name="method">
1
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133 <param name="method" value="pp.normalize_total"/>
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134 <conditional name="exclude_highly_expressed">
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135 <param name="exclude_highly_expressed" value="False"/>
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136 </conditional>
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137 <param name="key_added" value="n_counts"/>
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138 <param name="layers" value="all"/>
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139 <param name="layer_norm" value="None"/>
0
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140 </conditional>
6
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141 <section name="advanced_common">
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142 <param name="show_log" value="true" />
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143 </section>
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144 <output name="hidden_output">
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145 <assert_contents>
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146 <has_text_matching expression="sc.pp.normalize_total"/>
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147 <has_text_matching expression="exclude_highly_expressed=False"/>
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148 <has_text_matching expression="key_added='n_counts'"/>
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149 <has_text_matching expression="layers='all'"/>
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150 </assert_contents>
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151 </output>
1
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152 <output name="anndata_out" file="pp.normalize_total.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
0
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153 </test>
11
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154 <test expect_num_outputs="2">
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155 <!-- test 2 -->
1
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156 <param name="adata" value="random-randint.h5ad"/>
0
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157 <conditional name="method">
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158 <param name="method" value="pp.recipe_zheng17"/>
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159 <param name="n_top_genes" value="1000"/>
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160 <param name="log" value="True"/>
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161 </conditional>
6
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162 <section name="advanced_common">
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163 <param name="show_log" value="true" />
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164 </section>
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165 <output name="hidden_output">
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166 <assert_contents>
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167 <has_text_matching expression="sc.pp.recipe_zheng17"/>
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168 <has_text_matching expression="n_top_genes=1000"/>
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169 <has_text_matching expression="log=True"/>
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170 </assert_contents>
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171 </output>
10
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172 <output name="anndata_out" file="pp.recipe_zheng17.random-randint.h5ad" ftype="h5ad" compare="sim_size" delta="1000000" delta_frac="0.15"/>
0
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173 </test>
11
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174 <test expect_num_outputs="2">
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175 <!-- test 3 -->
1
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176 <param name="adata" value="paul15_subsample.h5ad" />
0
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177 <conditional name="method">
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178 <param name="method" value="pp.recipe_weinreb17"/>
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179 <param name="log" value="True"/>
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180 <param name="mean_threshold" value="0.01"/>
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181 <param name="cv_threshold" value="2.0"/>
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182 <param name="n_pcs" value="50"/>
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183 <param name="svd_solver" value="randomized"/>
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184 <param name="random_state" value="0"/>
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185 </conditional>
6
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186 <section name="advanced_common">
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187 <param name="show_log" value="true" />
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188 </section>
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189 <output name="hidden_output">
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190 <assert_contents>
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191 <has_text_matching expression="sc.pp.recipe_weinreb17"/>
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192 <has_text_matching expression="log=True"/>
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193 <has_text_matching expression="mean_threshold=0.01"/>
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194 <has_text_matching expression="cv_threshold=2.0"/>
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195 <has_text_matching expression="n_pcs=50"/>
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196 <has_text_matching expression="svd_solver='randomized'"/>
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197 <has_text_matching expression="random_state=0"/>
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198 </assert_contents>
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199 </output>
1
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200 <output name="anndata_out" file="pp.recipe_weinreb17.paul15_subsample.updated.h5ad" ftype="h5ad" compare="sim_size"/>
0
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201 </test>
11
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202 <test expect_num_outputs="2">
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203 <!-- test 4 -->
1
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204 <param name="adata" value="pp.recipe_zheng17.random-randint.h5ad" />
0
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205 <conditional name="method">
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206 <param name="method" value="pp.recipe_seurat"/>
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207 <param name="log" value="True"/>
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208 </conditional>
6
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209 <section name="advanced_common">
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210 <param name="show_log" value="true" />
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211 </section>
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212 <output name="hidden_output">
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213 <assert_contents>
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214 <has_text_matching expression="sc.pp.recipe_seurat"/>
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215 <has_text_matching expression="log=True"/>
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216 </assert_contents>
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217 </output>
10
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218 <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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219 </test>
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220 </tests>
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221 <help><![CDATA[
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222 Normalize total counts per cell (`pp.normalize_per_cell`)
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223 =========================================================
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224
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225 Normalize each cell by total counts over all genes, so that every cell has
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226 the same total count after normalization.
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227
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228 Similar functions are used, for example, by Seurat, Cell Ranger or SPRING.
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229
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230 More details on the `scanpy documentation
11
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231 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.normalize_per_cell.html>`__
0
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232
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233
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234 Normalization and filtering as of Zheng et al. (2017), the Cell Ranger R Kit of 10x Genomics (`pp.recipe_zheng17`)
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235 ==================================================================================================================
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236
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237 Expects non-logarithmized data. If using logarithmized data, pass `log=False`.
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238
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239 The recipe runs the following steps:
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240
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241 - only consider genes with more than 1 count
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242 - normalize with total UMI count per cell
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243 - select highly-variable genes
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244 - subset the genes
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245 - renormalize after filtering
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246 - log transform (if needed)
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247 - scale to unit variance and shift to zero mean
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248
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249 More details on the `scanpy documentation
11
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250 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.recipe_zheng17.html>`__
0
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251
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252
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253 Normalization and filtering as of Weinreb et al (2017) (`pp.recipe_weinreb17`)
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254 ==============================================================================
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255
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256 Expects non-logarithmized data. If using logarithmized data, pass `log=False`.
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257
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258 More details on the `scanpy documentation
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259 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.recipe_weinreb17.html>`__
0
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260
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262 Normalization and filtering as of Seurat et al (2015) (`pp.recipe_seurat`)
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263 ==========================================================================
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264
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265 This uses a particular preprocessing.
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267 Expects non-logarithmized data. If using logarithmized data, pass `log=False`.
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269 More details on the `scanpy documentation
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270 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.recipe_seurat.html>`__
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272 ]]></help>
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273 <expand macro="citations"/>
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274 </tool>