annotate cluster_reduce_dimension.xml @ 9:3e4e1cf73d98 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927"
author iuc
date Mon, 12 Apr 2021 18:14:53 +0000
parents 35bc2eb568ed
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1 <tool id="scanpy_cluster_reduce_dimension" name="Cluster, infer trajectories and embed" version="@galaxy_version@" profile="@profile@">
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2 <description>with scanpy</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <xml name="pca_inputs">
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6 <param argument="n_comps" type="integer" min="0" value="50" label="Number of principal components to compute" help="If the value is larger than the number of observations the number of observations is used instead"/>
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7 <param argument="dtype" type="text" value="float32" label="Numpy data type string to which to convert the result" help="">
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8 <expand macro="sanitize_query" />
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9 </param>
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10 <conditional name="pca">
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11 <param argument="chunked" type="select" label="Type of PCA?">
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12 <option value="True">Incremental PCA on segments (incremental PCA automatically zero centers and ignores settings of 'random_seed' and 'svd_solver')</option>
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13 <option value="False" selected="true">Full PCA</option>
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14 </param>
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15 <when value="True">
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16 <param argument="chunk_size" type="integer" min="0" value="" label="chunk_size" help="Number of observations to include in each chunk"/>
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17 </when>
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18 <when value="False">
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19 <param argument="zero_center" type="boolean" truevalue="True" falsevalue="False" checked="true"
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20 label="Compute standard PCA from covariance matrix?"
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21 help="If not, it omits zero-centering variables (uses *TruncatedSVD* from scikit-learn), which allows to handle sparse input efficiently."/>
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22 <expand macro="svd_solver"/>
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23 <param argument="random_state" type="integer" value="0" label="Initial states for the optimization" help=""/>
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24 </when>
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25 </conditional>
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26 <param argument="use_highly_variable" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use highly variable genes only?" help="They should be use if they have been determined beforehand."/>
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27 </xml>
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28 <xml name="param_random_state">
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29 <param argument="random_state" type="integer" value="0" label="Random state" help="Change the initialization of the optimization."/>
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30 </xml>
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31 <xml name="param_use_weights">
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32 <param argument="use_weights" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use weights from knn graph?"/>
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33 </xml>
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34 <token name="@CMD_pca_help@"><![CDATA[
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35 The PCA is computed using the implementation of *scikit-learn*.
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36
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37 The returned AnnData object contains:
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38
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39 - PCA coordinates in the multi-dimensional observation annotation (obsm)
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40 - Principal components containing the loadings in the multi-dimensional variable annotation (varm)
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41 - The variance decomposition in the unstructured annotation (uns)
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42 - Ratio of explained variance for PCA (variance)
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43 - Explained variance, equivalent to the eigenvalues of the covariance matrix
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44
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45 This data is accessible using the inspect tool for AnnData
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46 ]]></token>
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47 <token name="@CMD_pca_params@"><![CDATA[
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48 data=adata,
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49 n_comps=min($method.n_comps, adata.n_vars),
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50 dtype='$method.dtype',
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51 copy=False,
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52 chunked=$method.pca.chunked,
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53 #if $method.pca.chunked == 'True'
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54 chunk_size=$method.pca.chunk_size,
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55 #else
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56 zero_center=$method.pca.zero_center,
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57 svd_solver='$method.pca.svd_solver',
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58 random_state=$method.pca.random_state,
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59 #end if
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60 use_highly_variable=$method.use_highly_variable
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61 ]]></token>
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62 </macros>
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63 <expand macro="requirements">
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64 <requirement type="package" version="0.7.0">louvain</requirement>
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65 </expand>
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66 <expand macro="version_command"/>
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67 <command detect_errors="exit_code"><![CDATA[
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68 @CMD@
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69 ]]></command>
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70 <configfiles>
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71 <configfile name="script_file"><![CDATA[
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72 @CMD_imports@
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73 @CMD_read_inputs@
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74
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75 #if $method.method == 'tl.louvain'
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76 sc.tl.louvain(
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77 adata=adata,
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78 flavor = '$method.flavor.flavor',
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79 #if $method.flavor.flavor == 'vtraag'
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80 resolution=$method.flavor.resolution,
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81 #end if
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82 random_state=$method.random_state,
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83 key_added='$method.key_added',
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84 directed=$method.directed,
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85 use_weights=$method.use_weights,
0
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86 copy=False)
1
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parents: 0
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87
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88 #else if $method.method == 'tl.leiden'
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iuc
parents: 0
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89 sc.tl.leiden(
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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90 adata=adata,
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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91 resolution=$method.resolution,
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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92 random_state=$method.random_state,
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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93 key_added='$method.key_added',
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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94 use_weights=$method.use_weights,
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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95 n_iterations=$method.n_iterations,
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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96 copy=False)
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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97
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98 #else if $method.method == 'pp.pca'
0
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99 sc.pp.pca(@CMD_pca_params@)
1
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100
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iuc
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101 #else if $method.method == 'tl.pca'
0
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102 sc.tl.pca(@CMD_pca_params@)
1
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103
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104 #else if $method.method == 'tl.diffmap'
0
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iuc
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105 sc.tl.diffmap(
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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106 adata=adata,
8
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107 n_comps=min($method.n_comps, adata.n_vars),
0
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108 copy =False)
1
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109
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110 #else if $method.method == 'tl.tsne'
0
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iuc
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111 sc.tl.tsne(
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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112 adata=adata,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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113 #if $method.n_pcs
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114 n_pcs=$method.n_pcs,
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115 #end if
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116 perplexity=$method.perplexity,
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117 early_exaggeration=$method.early_exaggeration,
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118 learning_rate=$method.learning_rate,
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119 random_state=$method.random_state,
1
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120 use_fast_tsne=$method.use_fast_tsne,
0
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121 copy=False)
1
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122
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123 #else if $method.method == 'tl.umap'
0
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124 sc.tl.umap(
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125 adata=adata,
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126 min_dist=$method.min_dist,
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127 spread=$method.spread,
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128 n_components=$method.n_components,
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129 #if $method.maxiter
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130 maxiter=$method.maxiter,
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131 #end if
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132 alpha=$method.alpha,
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133 gamma=$method.gamma,
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134 negative_sample_rate=$method.negative_sample_rate,
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135 init_pos='$method.init_pos',
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136 random_state=$method.random_state,
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137 copy=False)
1
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138
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139 #else if $method.method == 'tl.draw_graph'
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140
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141 #if str($method.adjacency) != 'None'
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142 from scipy import io
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143 adjacency = io.mmread('$method.adjacency')
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144 #end if
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145
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146 sc.tl.draw_graph(
0
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147 adata=adata,
1
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148 layout='$method.layout',
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149 #if str($method.root) != ''
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150 #set $root=([int(x.strip()) for x in str($method.root).split(',')])
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151 root=$root,
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152 #end if
0
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153 random_state=$method.random_state,
1
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154 #if str($method.init_pos) != ''
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155 init_pos='$method.init_pos',
0
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156 #end if
1
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157 #if str($method.adjacency) != 'None'
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158 adjacency=adjacency,
0
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159 #end if
1
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160 #if str($method.key_ext) != ''
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161 key_ext='$method.key_ext',
0
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162 #end if
1
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163 copy=False)
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164
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165 #else if $method.method == "tl.paga"
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166 sc.tl.paga(
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167 adata=adata,
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168 groups='$method.groups',
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169 use_rna_velocity=$method.use_rna_velocity,
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170 model='$method.model',
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171 copy=False)
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172
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173 #else if $method.method == "tl.dpt"
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174 sc.tl.dpt(
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175 adata=adata,
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176 n_dcs=$method.n_dcs,
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177 n_branchings=$method.n_branchings,
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178 min_group_size=$method.min_group_size,
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179 allow_kendall_tau_shift=$method.allow_kendall_tau_shift,
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180 copy=False)
0
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181 #end if
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182
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183 @CMD_anndata_write_outputs@
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184 ]]></configfile>
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185 </configfiles>
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186 <inputs>
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187 <expand macro="inputs_anndata"/>
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188 <conditional name="method">
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189 <param argument="method" type="select" label="Method used">
3
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190 <option value="tl.louvain">Cluster cells into subgroups, using 'tl.louvain'</option>
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191 <option value="tl.leiden">Cluster cells into subgroups, using 'tl.leiden'</option>
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192 <option value="pp.pca">Computes PCA (principal component analysis) coordinates, loadings and variance decomposition, using 'pp.pca'</option>
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193 <option value="tl.pca">Computes PCA (principal component analysis) coordinates, loadings and variance decomposition, using 'tl.pca'</option>
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194 <option value="tl.diffmap">Diffusion Maps, using 'tl.diffmap'</option>
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195 <option value="tl.tsne">t-distributed stochastic neighborhood embedding (tSNE), using 'tl.tsne'</option>
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196 <option value="tl.umap">Embed the neighborhood graph using UMAP, using 'tl.umap'</option>
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197 <option value="tl.draw_graph">Force-directed graph drawing, using 'tl.draw_graph'</option>
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198 <option value="tl.dpt">Infer progression of cells through geodesic distance along the graph, using 'tl.dpt'</option>
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199 <option value="tl.paga">Generate cellular maps of differentiation manifolds with complex topologies, using 'tl.paga'</option>
0
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200 </param>
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201 <when value="tl.louvain">
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202 <conditional name="flavor">
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203 <param argument="flavor" type="select" label="Flavor for the clustering" help="">
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204 <option value="vtraag">vtraag (much more powerful)</option>
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205 <option value="igraph">igraph</option>
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206 </param>
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207 <when value="vtraag">
3
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208 <param argument="resolution" type="float" value="1.0"
0
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209 label="Resolution"
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210 help="Higher resolution means finding more and smaller clusters, which defaults to 1.0. See “Time as a resolution parameter” in Lambiotte et al, 2009"/>
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211 </when>
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212 <when value="igraph"/>
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213 </conditional>
1
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214 <expand macro="param_random_state"/>
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215 <param argument="key_added" type="text" value="louvain" optional="true" label="Key under which to add the cluster labels" help="">
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216 <expand macro="sanitize_query" />
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217 </param>
1
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218 <param argument="directed" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Interpret the adjacency matrix as directed graph?"/>
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219 <expand macro="param_use_weights"/>
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220 </when>
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221 <when value="tl.leiden">
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222 <param argument="resolution" type="float" value="1" label="Coarseness of the clusterin" help="Higher values lead to more clusters"/>
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223 <expand macro="param_random_state"/>
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224 <param argument="key_added" type="text" value="leiden" label="Key under which to add the cluster labels" help="">
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225 <expand macro="sanitize_query" />
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226 </param>
1
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227 <expand macro="param_use_weights"/>
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228 <param argument="n_iterations" type="integer" value="-1" label="How many iterations of the Leiden clustering algorithm to perform." help="Positive values above 2 define the total number of iterations to perform, -1 has the algorithm run until it reaches its optimal clustering."/>
0
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229 </when>
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230 <when value="pp.pca">
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231 <expand macro="pca_inputs"/>
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232 </when>
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233 <when value="tl.pca">
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234 <expand macro="pca_inputs"/>
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235 </when>
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236 <when value="tl.diffmap">
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237 <param argument="n_comps" type="integer" min="0" value="15" optional="true" label="Number of dimensions of the representation" help=""/>
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238 </when>
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239 <when value="tl.tsne">
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240 <param name="n_pcs" type="integer" min="0" value="" optional="true" label="Number of PCs to use" help=""/>
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241 <param name="perplexity" type="float" value="30" label="Perplexity" help="The perplexity is related to the number of nearest neighbors that is used in other manifold learning algorithms. Larger datasets usually require a larger perplexity. Consider selecting a value between 5 and 50. The choice is not extremely critical since t-SNE is quite insensitive to this parameter."/>
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242 <param name="early_exaggeration" type="float" value="12.0" label="Early exaggeration" help="Controls how tight natural clusters in the original space are in the embedded space and how much space will be between them. For larger values, the space between natural clusters will be larger in the embedded space. Again, the choice of this parameter is not very critical. If the cost function increases during initial optimization, the early exaggeration factor or the learning rate might be too high."/>
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243 <param name="learning_rate" type="float" value="1000" label="Learning rate" help="The learning rate can be a critical parameter. It should be between 100 and 1000. If the cost function increases during initial optimization, the early exaggeration factor or the learning rate might be too high. If the cost function gets stuck in a bad local minimum increasing the learning rate helps sometimes."/>
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244 <param name="random_state" type="integer" value="0" label="Random state" help="Change this to use different intial states for the optimization"/>
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245 <param argument="use_fast_tsne" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Use the MulticoreTSNE package if possible?"/>
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246 </when>
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247 <when value="tl.umap">
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248 <param argument="min_dist" type="float" value="0.5" label="Effective minimum distance between embedded points" help="Smaller values will result in a more clustered/clumped embedding where nearby points on the manifold are drawn closer together, while larger values will result on a more even dispersal of points. The value should be set relative to the 'spread' value, which determines the scale at which embedded points will be spread out. The default of in the 'umap-learn' package is 0.1."/>
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249 <param argument="spread" type="float" value="1.0" label="Effective scale of embedded points" help="In combination with 'min_dist' this determines how clustered/clumped the embedded points are."/>
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250 <param argument="n_components" type="integer" min="0" value="2" label="Number of dimensions of the embedding" help=""/>
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251 <param argument="maxiter" type="integer" min="0" value="" optional="true" label="Number of iterations (epochs) of the optimization" help="Called 'n_epochs' in the original UMAP."/>
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252 <param argument="alpha" type="float" value="1.0" label="Initial learning rate for the embedding optimization" help=""/>
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253 <param argument="gamma" type="float" value="1.0" label="Weighting applied to negative samples in low dimensional embedding optimization" help="Values higher than one will result in greater weight being given to negative samples."/>
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254 <param argument="negative_sample_rate" type="integer" min="0" value="5" label="The number of negative edge/1-simplex samples to use per positive edge/1-simplex sample in optimizing the low dimensional embedding" help=""/>
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255 <param argument="init_pos" type="select" label="How to initialize the low dimensional embedding" help="Called 'init' in the original UMAP">
0
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256 <option value="paga">Position from paga</option>
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257 <option value="spectral" selected="true">Spectral embedding of the graph</option>
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258 <option value="random">Initial embedding positions at random</option>
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259 </param>
1
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260 <expand macro="param_random_state"/>
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261 </when>
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262 <when value="tl.draw_graph">
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263 <expand macro="param_layout"/>
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264 <expand macro="param_root"/>
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265 <expand macro="param_random_state"/>
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266 <param argument="init_pos" type="text" optional="true" value="" label="Precomputed coordinates for initialization" help="It should be a valid 2d observation (e.g. paga)">
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267 <expand macro="sanitize_query" />
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268 </param>
1
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269 <param argument="adjacency" type="data" format="mtx" optional="true" label="Sparse adjacency matrix of the graph" help="If not set, it uses the unstructured annotation (uns) / neighbors / connectivities"/>
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270 <param argument="key_ext" type="text" optional="true" value="" label="External key" help="If not set, it appends 'layout'">
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271 <expand macro="sanitize_query" />
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272 </param>
0
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273 </when>
1
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274 <when value="tl.dpt">
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275 <param argument="n_dcs" type="integer" min="0" value="10" label="Number of diffusion components to use" help=""/>
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276 <param argument="n_branchings" type="integer" min="0" value="0" label="Number of branchings to detect" help=""/>
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277 <param argument="min_group_size" type="float" min="0" value="0.01" label="Min group size" help="During recursive splitting of branches ('dpt groups') for 'n_branchings' &gt; 1, do not consider groups that contain less than 'min_group_size' data points. If a float, 'min_group_size' refers to a fraction of the total number of data points."/>
1
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278 <param argument="allow_kendall_tau_shift" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Allow Kendal tau shift?" help="If a very small branch is detected upon splitting, shift away from maximum correlation in Kendall tau criterion of Haghverdi et al (2016) to stabilize the splitting."/>
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279 </when>
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280 <when value="tl.paga">
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281 <param argument="groups" type="text" value="louvain" label="Key for categorical in the input" help="You can pass your predefined groups by choosing any categorical annotation of observations ('adata.obs').">
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282 <expand macro="sanitize_query" />
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283 </param>
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284 <param argument="use_rna_velocity" type="boolean" truevalue="False" falsevalue="False" checked="false" label="Use RNA velocity to orient edges in the abstracted graph and estimate transitions?" help="Requires that 'adata.uns' contains a directed single-cell graph with key '['velocyto_transitions']'. This feature might be subject to change in the future."/>
1
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285 <param argument="model" type="select" label="PAGA connectivity model" help="">
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286 <option value="v1.2">v1.2</option>
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287 <option value="v1.0">v1.0</option>
0
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288 </param>
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289 </when>
1
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290 </conditional>
6
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291 <expand macro="inputs_common_advanced"/>
0
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292 </inputs>
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293 <outputs>
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294 <expand macro="anndata_outputs"/>
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295 </outputs>
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296 <tests>
1
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297 <test>
6
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298 <!-- test 0 -->
1
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299 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
0
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300 <conditional name="method">
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301 <param name="method" value="tl.louvain"/>
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302 <conditional name="flavor">
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303 <param name="flavor" value="vtraag"/>
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304 <param name="resolution" value="1.0"/>
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305 </conditional>
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306 <param name="random_state" value="10"/>
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307 <param name="key_added" value="louvain"/>
1
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308 <param name="directed" value="true"/>
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309 <param name="use_weights" value="false"/>
0
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310 </conditional>
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311 <section name="advanced_common">
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312 <param name="show_log" value="true" />
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313 </section>
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314 <output name="hidden_output">
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315 <assert_contents>
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316 <has_text_matching expression="sc.tl.louvain"/>
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317 <has_text_matching expression="adata=adata"/>
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318 <has_text_matching expression="flavor = 'vtraag'"/>
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319 <has_text_matching expression="resolution=1.0"/>
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320 <has_text_matching expression="random_state=10"/>
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321 <has_text_matching expression="key_added='louvain'"/>
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322 <has_text_matching expression="directed=True"/>
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323 <has_text_matching expression="use_weights=False"/>
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324 </assert_contents>
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325 </output>
1
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326 <output name="anndata_out" file="tl.louvain.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
0
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327 </test>
1
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328 <test>
6
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329 <!-- test 1 -->
1
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330 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
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331 <conditional name="method">
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332 <param name="method" value="tl.leiden"/>
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333 <param name="random_state" value="1"/>
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334 <param name="random_state" value="10"/>
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335 <param name="key_added" value="leiden"/>
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diff changeset
336 <param name="use_weights" value="false"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
337 <param name="n_iterations" value="-1"/>
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
338 </conditional>
6
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
339 <section name="advanced_common">
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
340 <param name="show_log" value="true" />
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
341 </section>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
342 <output name="hidden_output">
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
343 <assert_contents>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
344 <has_text_matching expression="sc.tl.leiden"/>
77b91b9bdf52 "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="resolution=1"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
346 <has_text_matching expression="random_state=10"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
347 <has_text_matching expression="key_added='leiden'"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
348 <has_text_matching expression="use_weights=False"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
349 <has_text_matching expression="n_iterations=-1"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
350 </assert_contents>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
351 </output>
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
352 <output name="anndata_out" file="tl.leiden.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
353 </test>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
354 <test>
6
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
355 <!-- test 1 -->
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
356 <param name="adata" value="krumsiek11.h5ad" />
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
357 <conditional name="method">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
358 <param name="method" value="pp.pca"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
359 <param name="n_comps" value="50"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
360 <param name="dtype" value="float32"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
361 <conditional name="pca">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
362 <param name="chunked" value="False"/>
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
363 <param name="zero_center" value="true"/>
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
364 <param name="svd_solver" value="auto"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
365 <param name="random_state" value="0"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
366 </conditional>
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
367 <param name="use_highly_variable" value="false"/>
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
368 </conditional>
6
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
369 <section name="advanced_common">
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
370 <param name="show_log" value="true" />
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
371 </section>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
372 <output name="hidden_output">
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
373 <assert_contents>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
374 <has_text_matching expression="sc.pp.pca"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
375 <has_text_matching expression="dtype='float32'"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
376 <has_text_matching expression="copy=False"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
377 <has_text_matching expression="chunked=False"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
378 <has_text_matching expression="zero_center=True"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
379 <has_text_matching expression="svd_solver='auto'"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
380 <has_text_matching expression="random_state=0"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
381 <has_text_matching expression="use_highly_variable=False"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
382 </assert_contents>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
383 </output>
8
35bc2eb568ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec"
iuc
parents: 7
diff changeset
384 <output name="anndata_out" file="pp.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.15"/>
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
385 </test>
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
386 <!--<test>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
387 < test 3 >
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
388 <param name="adata" value="krumsiek11.h5ad" />
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
389 <conditional name="method">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
390 <param name="method" value="pp.pca"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
391 <param name="n_comps" value="20"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
392 <param name="dtype" value="float32"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
393 <conditional name="pca">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
394 <param name="chunked" value="True"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
395 <param name="chunk_size" value="50"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
396 </conditional>
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
397 <param name="use_highly_variable" value="false"/>
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
398 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
399 <assert_stdout>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
400 <has_text_matching expression="sc.pp.pca"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
401 <has_text_matching expression="data=adata"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
402 <has_text_matching expression="n_comps=20"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
403 <has_text_matching expression="dtype='float32'"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
404 <has_text_matching expression="copy=False"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
405 <has_text_matching expression="chunked=True"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
406 <has_text_matching expression="chunk_size=50"/>
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
407 <has_text_matching expression="use_highly_variable=False"/>
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
408 </assert_stdout>
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
409 <output name="anndata_out" file="pp.pca.krumsiek11_chunk.h5ad" ftype="h5ad" compare="sim_size"/>
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
410 </test>
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
411 -->
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
412 <test>
6
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
413 <!-- test 2 -->
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
414 <param name="adata" value="krumsiek11.h5ad" />
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
415 <conditional name="method">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
416 <param name="method" value="tl.pca"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
417 <param name="n_comps" value="50"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
418 <param name="dtype" value="float32"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
419 <conditional name="pca">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
420 <param name="chunked" value="False"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
421 <param name="zero_center" value="True"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
422 <param name="svd_solver" value="auto"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
423 <param name="random_state" value="0"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
424 </conditional>
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
425 <param name="use_highly_variable" value="false"/>
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
426 </conditional>
6
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
427 <section name="advanced_common">
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
428 <param name="show_log" value="true" />
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
429 </section>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
430 <output name="hidden_output">
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
431 <assert_contents>
77b91b9bdf52 "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="sc.tl.pca"/>
77b91b9bdf52 "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="dtype='float32'"/>
77b91b9bdf52 "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="copy=False"/>
77b91b9bdf52 "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="chunked=False"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
436 <has_text_matching expression="zero_center=True"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
437 <has_text_matching expression="svd_solver='auto'"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
438 <has_text_matching expression="use_highly_variable=False"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
439 </assert_contents>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
440 </output>
8
35bc2eb568ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec"
iuc
parents: 7
diff changeset
441 <output name="anndata_out" file="tl.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.15"/>
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
442 </test>
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
443 <test>
6
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
444 <!-- test 3 -->
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
445 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
446 <conditional name="method">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
447 <param name="method" value="tl.diffmap"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
448 <param name="n_comps" value="15"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
449 </conditional>
6
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
450 <section name="advanced_common">
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
451 <param name="show_log" value="true" />
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
452 </section>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
453 <output name="hidden_output">
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
454 <assert_contents>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
455 <has_text_matching expression="sc.tl.diffmap"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
456 </assert_contents>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
457 </output>
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
458 <output name="anndata_out" file="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
459 </test>
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
460 <test>
6
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
461 <!-- test 4 -->
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
462 <param name="adata" value="krumsiek11.h5ad" />
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
463 <conditional name="method">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
464 <param name="method" value="tl.tsne"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
465 <param name="n_pcs" value="10"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
466 <param name="perplexity" value="30"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
467 <param name="early_exaggeration" value="12.0"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
468 <param name="learning_rate" value="1000"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
469 <param name="random_state" value="0"/>
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
470 <param name="use_fast_tsne" value="true"/>
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
471 </conditional>
6
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
472 <section name="advanced_common">
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
473 <param name="show_log" value="true" />
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
474 </section>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
475 <output name="hidden_output">
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
476 <assert_contents>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
477 <has_text_matching expression="sc.tl.tsne"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
478 <has_text_matching expression="n_pcs=10"/>
77b91b9bdf52 "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="perplexity=30.0"/>
77b91b9bdf52 "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="early_exaggeration=12.0"/>
77b91b9bdf52 "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="learning_rate=1000.0"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
482 <has_text_matching expression="random_state=0"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
483 <has_text_matching expression="use_fast_tsne=True"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
484 </assert_contents>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
485 </output>
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
486 <output name="anndata_out" file="tl.tsne.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
487 </test>
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
488 <test>
6
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
489 <!-- test 5 -->
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
490 <param name="adata" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
491 <conditional name="method">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
492 <param name="method" value="tl.umap"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
493 <param name="min_dist" value="0.5"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
494 <param name="spread" value="1.0"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
495 <param name="n_components" value="2"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
496 <param name="maxiter" value="2"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
497 <param name="alpha" value="1.0"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
498 <param name="gamma" value="1.0"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
499 <param name="negative_sample_rate" value="5"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
500 <param name="init_pos" value="spectral"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
501 <param name="random_state" value="0"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
502 </conditional>
6
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
503 <section name="advanced_common">
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
504 <param name="show_log" value="true" />
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
505 </section>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
506 <output name="hidden_output">
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
507 <assert_contents>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
508 <has_text_matching expression="sc.tl.umap"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
509 <has_text_matching expression="min_dist=0.5"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
510 <has_text_matching expression="spread=1.0"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
511 <has_text_matching expression="n_components=2"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
512 <has_text_matching expression="maxiter=2"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
513 <has_text_matching expression="alpha=1.0"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
514 <has_text_matching expression="gamma=1.0"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
515 <has_text_matching expression="negative_sample_rate=5"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
516 <has_text_matching expression="init_pos='spectral'"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
517 <has_text_matching expression="random_state=0"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
518 </assert_contents>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
519 </output>
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
520 <output name="anndata_out" file="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size">
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
521 <assert_contents>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
522 <has_h5_keys keys="X, obs, obsm, uns, var" />
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
523 </assert_contents>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
524 </output>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
525 </test>
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
526 <test>
6
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
527 <!-- test 6 -->
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
528 <param name="adata" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
529 <conditional name="method">
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
530 <param name="method" value="tl.draw_graph"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
531 <param name="layout" value="fa"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
532 <param name="random_state" value="0"/>
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
533 </conditional>
6
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
534 <section name="advanced_common">
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
535 <param name="show_log" value="true" />
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
536 </section>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
537 <output name="hidden_output">
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
538 <assert_contents>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
539 <has_text_matching expression="sc.tl.draw_graph"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
540 <has_text_matching expression="layout='fa'"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
541 <has_text_matching expression="random_state=0"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
542 </assert_contents>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
543 </output>
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
544 <output name="anndata_out" file="tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
545 </test>
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
546 <test>
6
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
547 <!-- test 7 -->
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
548 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
549 <conditional name="method">
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
550 <param name="method" value="tl.paga"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
551 <param name="groups" value="paul15_clusters"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
552 <param name="use_rna_velocity" value="False"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
553 <param name="model" value="v1.2"/>
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
554 </conditional>
6
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
555 <section name="advanced_common">
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
556 <param name="show_log" value="true" />
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
557 </section>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
558 <output name="hidden_output">
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
559 <assert_contents>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
560 <has_text_matching expression="sc.tl.paga"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
561 <has_text_matching expression="groups='paul15_clusters'"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
562 <has_text_matching expression="use_rna_velocity=False"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
563 <has_text_matching expression="model='v1.2'"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
564 </assert_contents>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
565 </output>
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
566 <output name="anndata_out" file="tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
567 </test>
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
568 <test>
6
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
569 <!-- test 8 -->
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
570 <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
571 <conditional name="method">
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
572 <param name="method" value="tl.dpt"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
573 <param name="n_dcs" value="15"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
574 <param name="n_branchings" value="1"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
575 <param name="min_group_size" value="0.01"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
576 <param name="allow_kendall_tau_shift" value="True"/>
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
577 </conditional>
6
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
578 <section name="advanced_common">
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
579 <param name="show_log" value="true" />
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
580 </section>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
581 <output name="hidden_output">
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
582 <assert_contents>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
583 <has_text_matching expression="sc.tl.dpt"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
584 <has_text_matching expression="n_dcs=15"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
585 <has_text_matching expression="n_branchings=1"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
586 <has_text_matching expression="min_group_size=0.01"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
587 <has_text_matching expression="allow_kendall_tau_shift=True"/>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
588 </assert_contents>
77b91b9bdf52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
589 </output>
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
590 <output name="anndata_out" file="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
591 </test>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
592 </tests>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
593 <help><![CDATA[
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
594 Cluster cells into subgroups (`tl.louvain`)
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
595 ===========================================
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
596
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
597 Cluster cells using the Louvain algorithm (Blondel et al, 2008) in the implementation
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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598 of Traag et al,2017. The Louvain algorithm has been proposed for single-cell
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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599 analysis by Levine et al, 2015.
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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600
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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601 This requires to run `pp.neighbors`, first.
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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602
5
6f2d2c7f77ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
iuc
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diff changeset
603 More details on the `tl.louvain scanpy documentation
6f2d2c7f77ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
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parents: 4
diff changeset
604 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.louvain.html>`_
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
605
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
606 Cluster cells into subgroups (`tl.leiden`)
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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607 ==========================================
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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608
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
609 Cluster cells using the Leiden algorithm (Traag et al, 2018), an improved version of the Louvain algorithm (Blondel et al, 2008).
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
610
20cfb9f3dded "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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611 The Louvain algorithm has been proposed for single-cell analysis by Levine et al, 2015.
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
612
5
6f2d2c7f77ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
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diff changeset
613 More details on the `tl.leiden scanpy documentation
6f2d2c7f77ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
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614 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.leiden.html>`_
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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615
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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diff changeset
616 Computes PCA (principal component analysis) coordinates, loadings and variance decomposition, using `pp.pca`
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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617 ============================================================================================================
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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618
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
619 @CMD_pca_outputs@
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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620
5
6f2d2c7f77ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
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diff changeset
621 More details on the `pp.pca scanpy documentation
6f2d2c7f77ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
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622 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.pca.html>`__
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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623
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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624 Computes PCA (principal component analysis) coordinates, loadings and variance decomposition, using `tl.pca`
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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625 ============================================================================================================
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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626
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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627 @CMD_pca_outputs@
0
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628
5
6f2d2c7f77ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
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diff changeset
629 More details on the `tl.pca scanpy documentation
6f2d2c7f77ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
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630 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.pca.html>`__
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
631
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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632 Diffusion Maps, using `tl.diffmap`
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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633 ==================================
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
634
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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635 Diffusion maps (Coifman et al 2005) has been proposed for visualizing single-cell
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
636 data by Haghverdi et al (2015). The tool uses the adapted Gaussian kernel suggested
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
637 by Haghverdi et al (2016) in the implementation of Wolf et al (2017).
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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diff changeset
638
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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diff changeset
639 The width ("sigma") of the connectivity kernel is implicitly determined by
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
640 the number of neighbors used to compute the single-cell graph in
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
641 `pp.neighbors`. To reproduce the original implementation
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
642 using a Gaussian kernel, use `method=='gauss'` in
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
643 `pp.neighbors`. To use an exponential kernel, use the default
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
644 `method=='umap'`. Differences between these options shouldn't usually be
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
645 dramatic.
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
646
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
647 The diffusion map representation of data are added to the return AnnData in the multi-dimensional
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
648 observations annotation (obsm). It is the right eigen basis of the transition matrix with eigenvectors
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
649 as colum. It can be accessed using the inspect tool for AnnData
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
650
5
6f2d2c7f77ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
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651 More details on the `tl.diffmap scanpy documentation
6f2d2c7f77ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
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652 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.diffmap.html>`__
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
653
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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654 t-distributed stochastic neighborhood embedding (tSNE), using `tl.tsne`
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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parents:
diff changeset
655 =======================================================================
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
656
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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diff changeset
657 t-distributed stochastic neighborhood embedding (tSNE) (Maaten et al, 2008) has been
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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parents:
diff changeset
658 proposed for visualizating single-cell data by (Amir et al, 2013). Here, by default,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
659 we use the implementation of *scikit-learn* (Pedregosa et al, 2011).
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660
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
661 It returns `X_tsne`, tSNE coordinates of data.
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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662
5
6f2d2c7f77ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
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663 More details on the `tl.tsne scanpy documentation
6f2d2c7f77ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
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664 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.tsne.html>`__
0
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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665
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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666 Embed the neighborhood graph using UMAP, using `tl.umap`
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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667 ========================================================
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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668
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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669 UMAP (Uniform Manifold Approximation and Projection) is a manifold learning
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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670 technique suitable for visualizing high-dimensional data. Besides tending to
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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671 be faster than tSNE, it optimizes the embedding such that it best reflects
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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672 the topology of the data, which we represent throughout Scanpy using a
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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673 neighborhood graph. tSNE, by contrast, optimizes the distribution of
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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674 nearest-neighbor distances in the embedding such that these best match the
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675 distribution of distances in the high-dimensional space. We use the
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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676 implementation of `umap-learn <https://github.com/lmcinnes/umap>`__
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677 (McInnes et al, 2018). For a few comparisons of UMAP with tSNE, see this `preprint
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678 <https://doi.org/10.1101/298430>`__.
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679
1
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680 The UMAP coordinates of data are added to the return AnnData in the multi-dimensional
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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681 observations annotation (obsm). This data is accessible using the inspect tool for AnnData
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
682
5
6f2d2c7f77ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
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683 More details on the `tl.umap scanpy documentation
6f2d2c7f77ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
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diff changeset
684 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.umap.html>`__
1
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685
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686 Force-directed graph drawing, using `tl.draw_graph`
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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687 ===================================================
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688
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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689 Force-directed graph drawing describes a class of long-established algorithms for visualizing graphs.
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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690 It has been suggested for visualizing single-cell data by Islam et al, 11.
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691 Many other layouts as implemented in igraph are available. Similar approaches have been used by
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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692 Zunder et al, 2015 or Weinreb et al, 2016.
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693
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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694 This is an alternative to tSNE that often preserves the topology of the data better.
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695 This requires to run `pp.neighbors`, first.
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696
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697 The default layout (ForceAtlas2) uses the package fa2.
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
698
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
699 The coordinates of graph layout are added to the return AnnData in the multi-dimensional
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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700 observations annotation (obsm). This data is accessible using the inspect tool for AnnData.
0
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701
5
6f2d2c7f77ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
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diff changeset
702 More details on the `tl.draw_graph scanpy documentation
6f2d2c7f77ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
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703 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.draw_graph.html>`__
1
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diff changeset
704
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
705 Infer progression of cells through geodesic distance along the graph (`tl.dpt`)
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
706 ===============================================================================
0
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707
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
708 Reconstruct the progression of a biological process from snapshot
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
709 data. `Diffusion Pseudotime` has been introduced by Haghverdi et al (2016) and
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
710 implemented within Scanpy (Wolf et al, 2017). Here, we use a further developed
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
711 version, which is able to deal with disconnected graphs (Wolf et al, 2017) and can
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
712 be run in a `hierarchical` mode by setting the parameter
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
713 `n_branchings>1`. We recommend, however, to only use
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
714 `tl.dpt` for computing pseudotime (`n_branchings=0`) and
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
715 to detect branchings via `paga`. For pseudotime, you need
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
716 to annotate your data with a root cell.
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717
1
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diff changeset
718 This requires to run `pp.neighbors`, first. In order to
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
719 reproduce the original implementation of DPT, use `method=='gauss'` in
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
720 this. Using the default `method=='umap'` only leads to minor quantitative
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diff changeset
721 differences, though.
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diff changeset
722
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
723
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diff changeset
724 If `n_branchings==0`, no field `dpt_groups` will be written.
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
725
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
726 - dpt_pseudotime : Array of dim (number of samples) that stores the pseudotime of each cell, that is, the DPT distance with respect to the root cell.
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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727 - dpt_groups : Array of dim (number of samples) that stores the subgroup id ('0','1', ...) for each cell. The groups typically correspond to 'progenitor cells', 'undecided cells' or 'branches' of a process.
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parents: 0
diff changeset
728
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
729 The tool is similar to the R package `destiny` of Angerer et al (2016).
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diff changeset
730
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
731 More details on the `tl.dpt scanpy documentation
5
6f2d2c7f77ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
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732 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.dpt.html>`_
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diff changeset
733
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
734
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
735 Generate cellular maps of differentiation manifolds with complex topologies (`tl.paga`)
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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736 =======================================================================================
0
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737
1
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
738 By quantifying the connectivity of partitions (groups, clusters) of the
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
739 single-cell graph, partition-based graph abstraction (PAGA) generates a much
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740 simpler abstracted graph (*PAGA graph*) of partitions, in which edge weights
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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741 represent confidence in the presence of connections. By tresholding this
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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742 confidence in `paga`, a much simpler representation of data
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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743 can be obtained.
0
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744
1
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745 The confidence can be interpreted as the ratio of the actual versus the
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
746 expected value of connetions under the null model of randomly connecting
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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747 partitions. We do not provide a p-value as this null model does not
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748 precisely capture what one would consider "connected" in real data, hence it
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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749 strongly overestimates the expected value. See an extensive discussion of
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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750 this in Wolf et al (2017).
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751
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752 Together with a random walk-based distance measure, this generates a partial
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753 coordinatization of data useful for exploring and explaining its variation.
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754
1
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755 The returned AnnData object contains:
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756
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757 - Full adjacency matrix of the abstracted graph, weights correspond to confidence in the connectivities of partition (connectivities)
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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758 - Adjacency matrix of the tree-like subgraph that best explains the topology (connectivities_tree)
0
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759
1
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760 These datasets are stored in the unstructured annotation (uns) and can be accessed using the inspect tool for AnnData objects
0
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761
1
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762 More details on the `tl.paga scanpy documentation
5
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763 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.paga.html>`_
0
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764 ]]></help>
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765 <expand macro="citations"/>
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766 </tool>