Mercurial > repos > iuc > scanpy_cluster_reduce_dimension

annotate cluster_reduce_dimension.xml @ 18:7f7be140247d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 76bfefa9116713dc1078ae407ab6dd69ed14a244
author iuc
date Wed, 26 Mar 2025 09:39:39 +0000
parents f68aa37a20ab
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1 <tool id="scanpy_cluster_reduce_dimension" name="Scanpy cluster, embed" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>and infer trajectories</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="layer" type="text" value="" optional="true" label="If provided, which element of layers to use for PCA">
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8 <expand macro="sanitize_query"/>
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9 </param>
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10 <param argument="dtype" type="select" label="Numpy data type string to which to convert the result">
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11 <option value="float32" selected="true">float32</option>
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12 <option value="int32">int32</option>
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13 <option value="int64">int64</option>
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14 <option value="uint32">uint32</option>
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15 <option value="uint64">uint64</option>
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16 <option value="float16">float16</option>
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17 <option value="float64">float64</option>
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18 </param>
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19 <conditional name="pca">
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20 <param argument="chunked" type="select" label="Type of PCA?">
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21 <option value="False" selected="true">Full PCA</option>
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22 <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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23 </param>
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24 <when value="True">
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25 <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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26 </when>
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27 <when value="False">
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28 <param argument="zero_center" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Compute standard PCA from covariance matrix?" help="If not, it omits zero-centering variables (uses *TruncatedSVD* from scikit-learn), which allows to handle sparse input efficiently."/>
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29 <expand macro="svd_solver"/>
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30 <param argument="random_state" type="integer" value="0" label="Change to use different initial states for the optimization"/>
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31 </when>
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32 </conditional>
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33 <param argument="mask_var" type="text" value="" optional="true" label="To run only on a certain set of genes given by a string referring to an array in" help="By default, uses .var['highly_variable'] if available, else everything"/>
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34 </xml>
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35 <xml name="param_random_state">
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36 <param argument="random_state" type="integer" value="0" label="Random state" help="Change the initialization of the optimization."/>
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37 </xml>
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38 <xml name="param_use_weights" token_checked="">
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39 <param argument="use_weights" type="boolean" truevalue="True" falsevalue="False" checked="@CHECKED@" label="Use weights from knn graph?"/>
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40 </xml>
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41 <token name="@CMD_PCA_HELP@"><![CDATA[
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42 The PCA is computed using the implementation of *scikit-learn*.
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44 The returned AnnData object contains:
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46 - PCA coordinates in the multi-dimensional observation annotation (obsm)
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47 - Principal components containing the loadings in the multi-dimensional variable annotation (varm)
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48 - The variance decomposition in the unstructured annotation (uns)
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49 - Ratio of explained variance for PCA (variance)
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50 - Explained variance, equivalent to the eigenvalues of the covariance matrix
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51
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52 This data is accessible using the inspect tool for AnnData
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53 ]]>
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54 </token>
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55 </macros>
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56 <expand macro="bio_tools"/>
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57 <expand macro="requirements">
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58 <requirement type="package" version="0.5.6">umap-learn</requirement>
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59 <requirement type="package" version="0.10.2">leidenalg</requirement>
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60 <requirement type="package" version="0.8.2">louvain</requirement>
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61 <requirement type="package" version="1.5.1">scikit-learn</requirement>
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62 </expand>
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63 <expand macro="version_command"/>
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64 <command detect_errors="exit_code"><![CDATA[
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65 @CMD@
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66 ]]>
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67 </command>
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68 <configfiles>
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69 <configfile name="script_file"><![CDATA[
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70 @CMD_IMPORTS@
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71 @CMD_READ_INPUTS@
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73 #if $method.method == 'tl.louvain'
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74 sc.tl.louvain(
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75 adata=adata,
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76 flavor = '$method.flavor.flavor',
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77 #if $method.flavor.flavor == 'vtraag'
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78 resolution=$method.flavor.resolution,
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79 #end if
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80 random_state=$method.random_state,
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81 key_added='$method.key_added',
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82 directed=$method.directed,
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83 use_weights=$method.use_weights,
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84 @CMD_PARAM_NEIGHBORS_KEY@
0
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85 copy=False)
1
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86
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87 #else if $method.method == 'tl.leiden'
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88 sc.tl.leiden(
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89 adata=adata,
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90 resolution=$method.resolution,
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91 random_state=$method.random_state,
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92 key_added='$method.key_added',
14
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93 directed=$method.directed,
1
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94 use_weights=$method.use_weights,
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95 n_iterations=$method.n_iterations,
14
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96 @CMD_PARAM_NEIGHBORS_KEY@
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97 flavor='$method.flavor',
1
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98 copy=False)
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99
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100 #else if $method.method == 'pp.pca'
14
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101 sc.pp.pca(
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102 data=adata,
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103 n_comps=min($method.n_comps, adata.n_vars-1),
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104 #if $method.layer != ''
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105 layer='$method.layer',
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106 #end if
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107 dtype='$method.dtype',
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108 chunked=$method.pca.chunked,
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109 #if $method.pca.chunked == 'True'
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110 chunk_size=$method.pca.chunk_size,
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111 #else
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112 zero_center=$method.pca.zero_center,
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113 #if $method.pca.svd_solver != ''
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114 svd_solver='$method.pca.svd_solver',
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115 #end if
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116 random_state=$method.pca.random_state,
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117 #end if
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118 #if $method.mask_var != ''
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119 mask_var='$method.mask_var',
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120 #end if
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121 copy=False)
1
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122
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123 #else if $method.method == 'tl.diffmap'
0
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124 sc.tl.diffmap(
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125 adata=adata,
14
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126 n_comps=min($method.n_comps, adata.n_vars-1),
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127 random_state=$method.random_state,
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128 @CMD_PARAM_NEIGHBORS_KEY@
0
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129 copy =False)
1
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130
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131 #else if $method.method == 'tl.tsne'
14
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132 import os
0
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133 sc.tl.tsne(
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134 adata=adata,
12
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135 #if str($method.n_pcs) != ''
0
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136 n_pcs=$method.n_pcs,
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137 #end if
14
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138 #if $method.use_rep != ''
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139 use_rep='$method.use_rep',
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140 #end if
0
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141 perplexity=$method.perplexity,
14
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142 metric='$method.metric',
0
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143 early_exaggeration=$method.early_exaggeration,
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144 learning_rate=$method.learning_rate,
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145 random_state=$method.random_state,
14
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146 n_jobs = int(os.getenv("GALAXY_SLOTS", 4)),
0
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147 copy=False)
1
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148
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149 #else if $method.method == 'tl.umap'
0
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150 sc.tl.umap(
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151 adata=adata,
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152 min_dist=$method.min_dist,
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153 spread=$method.spread,
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154 n_components=$method.n_components,
12
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155 #if str($method.maxiter) != ''
0
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156 maxiter=$method.maxiter,
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157 #end if
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158 alpha=$method.alpha,
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159 gamma=$method.gamma,
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160 negative_sample_rate=$method.negative_sample_rate,
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161 init_pos='$method.init_pos',
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162 random_state=$method.random_state,
14
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163 @CMD_PARAM_NEIGHBORS_KEY@
0
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164 copy=False)
1
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165
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166 #else if $method.method == 'tl.draw_graph'
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167 #if str($method.adjacency) != 'None'
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168 from scipy import io
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169 adjacency = io.mmread('$method.adjacency')
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170 #end if
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171
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172 sc.tl.draw_graph(
0
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173 adata=adata,
1
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174 layout='$method.layout',
14
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175 #if str($method.root)
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176 root=$method.root,
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177 #end if
0
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178 random_state=$method.random_state,
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179 #if str($method.adjacency) != 'None'
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180 adjacency=adjacency,
0
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181 #end if
14
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182 #if $method.key_added_ext != ''
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183 key_added_ext='$method.key_added_ext',
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184 #end if
14
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185 #if $method.init_pos != ''
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186 init_pos='$method.init_pos',
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187 #end if
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188 @CMD_PARAM_NEIGHBORS_KEY@
1
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189 copy=False)
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190
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191 #else if $method.method == "tl.dpt"
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192 sc.tl.dpt(
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193 adata=adata,
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194 n_dcs=$method.n_dcs,
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195 n_branchings=$method.n_branchings,
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196 min_group_size=$method.min_group_size,
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197 allow_kendall_tau_shift=$method.allow_kendall_tau_shift,
14
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198 @CMD_PARAM_NEIGHBORS_KEY@
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199 copy=False)
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200
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201 #else if $method.method == "tl.paga"
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202 sc.tl.paga(
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203 adata=adata,
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204 #if $method.groups != '':
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205 groups='$method.groups',
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206 #end if
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207 use_rna_velocity=$method.use_rna_velocity,
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208 model='$method.model',
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209 @CMD_PARAM_NEIGHBORS_KEY@
1
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210 copy=False)
12
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211
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212 #else if $method.method == "tl.embedding_density"
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213 sc.tl.embedding_density(
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214 adata=adata,
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215 basis='$method.basis',
14
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216 #if $method.groupby != ''
12
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217 groupby='$method.groupby',
14
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218 #end if
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219 #if $method.key_added != ''
12
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220 key_added='$method.key_added',
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221 #end if
12
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222 )
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223
0
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224 #end if
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225
14
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226 @CMD_ANNDATA_WRITE_OUTPUTS@
16
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227 ]]>
14
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228 </configfile>
0
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229 </configfiles>
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230 <inputs>
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231 <expand macro="inputs_anndata"/>
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232 <conditional name="method">
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233 <param argument="method" type="select" label="Method used">
3
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234 <option value="tl.louvain">Cluster cells into subgroups, using 'tl.louvain'</option>
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235 <option value="tl.leiden">Cluster cells into subgroups, using 'tl.leiden'</option>
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236 <option value="pp.pca">Computes PCA (principal component analysis) coordinates, loadings and variance decomposition, using 'pp.pca'</option>
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237 <option value="tl.diffmap">Diffusion Maps, using 'tl.diffmap'</option>
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238 <option value="tl.tsne">t-distributed stochastic neighborhood embedding (tSNE), using 'tl.tsne'</option>
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239 <option value="tl.umap">Embed the neighborhood graph using UMAP, using 'tl.umap'</option>
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240 <option value="tl.draw_graph">Force-directed graph drawing, using 'tl.draw_graph'</option>
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241 <option value="tl.dpt">Infer progression of cells through geodesic distance along the graph, using 'tl.dpt'</option>
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242 <option value="tl.paga">Generate cellular maps of differentiation manifolds with complex topologies, using 'tl.paga'</option>
14
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243 <option value="tl.embedding_density">Calculate the density of cells in an embedding (per condition), using 'tl.embedding_density'</option>
0
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244 </param>
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245 <when value="tl.louvain">
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246 <conditional name="flavor">
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247 <param argument="flavor" type="select" label="Flavor for the clustering">
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248 <option value="vtraag" selected="true">vtraag (much more powerful than igraph)</option>
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249 <option value="igraph">Built in igraph method</option>
0
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250 </param>
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251 <when value="vtraag">
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252 <param argument="resolution" type="float" value="1.0" label="Resolution" help="Higher resolution means finding more and smaller clusters, which defaults to 1.0. See “Time as a resolution parameter” in Lambiotte et al, 2014"/>
0
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253 </when>
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254 <when value="igraph"/>
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255 </conditional>
1
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256 <expand macro="param_random_state"/>
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257 <param argument="key_added" type="text" value="louvain" optional="true" label="Key under which to add the cluster labels">
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258 <expand macro="sanitize_query"/>
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259 </param>
1
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260 <param argument="directed" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Interpret the adjacency matrix as directed graph?"/>
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261 <expand macro="param_use_weights" checked="false"/>
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262 <expand macro="param_neighbors_key"/>
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263 </when>
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264 <when value="tl.leiden">
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265 <param argument="resolution" type="float" value="1" label="Coarseness of the clusterin" help="Higher values lead to more clusters"/>
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266 <expand macro="param_random_state"/>
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267 <param argument="key_added" type="text" value="leiden" label="Key under which to add the cluster labels">
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268 <expand macro="sanitize_query"/>
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269 </param>
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270 <param argument="directed" type="boolean" truevalue="True" falsevalue="None" checked="false" label="Treat the graph as directed or undirected?"/>
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271 <expand macro="param_use_weights" checked="true"/>
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272 <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."/>
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273 <expand macro="param_neighbors_key"/>
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274 <param argument="flavor" type="select" label="Flavor for the clustering">
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275 <option value="leidenalg" selected="true">leidenalg</option>
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276 <option value="igraph">Built in igraph method</option>
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277 </param>
0
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278 </when>
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279 <when value="pp.pca">
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280 <expand macro="pca_inputs"/>
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281 </when>
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282 <when value="tl.diffmap">
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283 <param argument="n_comps" type="integer" min="0" value="15" optional="true" label="Number of dimensions of the representation"/>
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284 <param argument="random_state" type="integer" value="0" label="Seed used by the random number generator"/>
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285 <expand macro="param_neighbors_key"/>
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286 </when>
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287 <when value="tl.tsne">
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288 <param argument="n_pcs" type="integer" min="0" value="" optional="true" label="Number of PCs to use"/>
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289 <expand macro="param_use_rep"/>
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290 <param argument="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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291 <param argument="metric" type="select">
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292 <expand macro="distance_metric_options"/>
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293 </param>
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294 <param argument="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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295 <param argument="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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296 <param argument="random_state" type="integer" value="0" label="Random state" help="Change this to use different intial states for the optimization"/>
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297 </when>
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298 <when value="tl.umap">
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299 <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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300 <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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301 <param argument="n_components" type="integer" min="0" value="2" label="Number of dimensions of the embedding"/>
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302 <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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303 <param argument="alpha" type="float" value="1.0" label="Initial learning rate for the embedding optimization"/>
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304 <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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305 <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"/>
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306 <param argument="init_pos" type="select" label="How to initialize the low dimensional embedding" help="Called 'init' in the original UMAP">
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307 <option value="spectral" selected="true">Spectral embedding of the graph</option>
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308 <option value="paga">Position from paga</option>
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309 <option value="random">Initial embedding positions at random</option>
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310 </param>
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311 <param argument="random_state" type="integer" value="0" label="Seed used by the random number generator"/>
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312 <expand macro="param_neighbors_key"/>
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313 </when>
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314 <when value="tl.draw_graph">
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315 <expand macro="param_layout"/>
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316 <param argument="root" type="integer" value="" optional="true" label="Root for tree layouts"/>
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317 <param argument="random_state" type="integer" value="0" optional="true" label="Random state" help="For layouts with random initialization like 'fr', change this to use different intial states for the optimization."/>
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318 <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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319 <param argument="key_added_ext" type="text" optional="true" value="" label="External key" help="If not set, it appends 'layout'">
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320 <expand macro="sanitize_query"/>
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321 </param>
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322 <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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323 <expand macro="sanitize_query"/>
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324 </param>
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325 <expand macro="param_neighbors_key"/>
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326 </when>
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327 <when value="tl.dpt">
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328 <param argument="n_dcs" type="integer" min="0" value="10" label="Number of diffusion components to use"/>
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329 <param argument="n_branchings" type="integer" min="0" value="0" label="Number of branchings to detect"/>
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330 <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."/>
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331 <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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332 <expand macro="param_neighbors_key"/>
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333 </when>
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334 <when value="tl.paga">
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335 <param argument="groups" type="text" optional="true" value="" 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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336 <expand macro="sanitize_query"/>
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337 </param>
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338 <param argument="use_rna_velocity" type="boolean" truevalue="True" 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."/>
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339 <param argument="model" type="select" label="PAGA connectivity model">
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340 <option value="v1.2" selected="true">v1.2</option>
1
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parents: 0
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341 <option value="v1.0">v1.0</option>
0
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342 </param>
14
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343 <expand macro="param_neighbors_key"/>
0
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344 </when>
12
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345 <when value="tl.embedding_density">
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346 <param argument="basis" type="text" value="umap" label="The embedding over which the density will be calculated." help="This embedded representation should be found in adata.obsm['X_[basis]']">
14
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347 <expand macro="sanitize_query"/>
12
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348 </param>
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349 <param argument="groupby" type="text" optional="true" value="" label="Key for categorical observation/cell annotation for which densities are calculated per category." >
14
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350 <expand macro="sanitize_query"/>
12
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351 </param>
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352 <param argument="key_added" type="text" optional="true" value="" label="Name of the .obs covariate that will be added with the density estimates.">
14
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353 <expand macro="sanitize_query"/>
12
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354 </param>
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355 </when>
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356 </conditional>
6
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357 <expand macro="inputs_common_advanced"/>
0
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358 </inputs>
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359 <outputs>
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360 <expand macro="anndata_outputs"/>
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361 </outputs>
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362 <tests>
14
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diff changeset
363
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364 <!-- test 1 -->
12
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365 <test expect_num_outputs="2">
14
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366 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
0
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367 <conditional name="method">
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368 <param name="method" value="tl.louvain"/>
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369 <param name="random_state" value="10"/>
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370 </conditional>
6
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371 <section name="advanced_common">
14
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372 <param name="show_log" value="true"/>
6
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373 </section>
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374 <output name="hidden_output">
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375 <assert_contents>
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376 <has_text_matching expression="sc.tl.louvain"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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377 <has_text_matching expression="adata=adata"/>
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378 <has_text_matching expression="flavor = 'vtraag'"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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379 <has_text_matching expression="resolution=1.0"/>
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380 <has_text_matching expression="random_state=10"/>
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diff changeset
381 <has_text_matching expression="key_added='louvain'"/>
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382 <has_text_matching expression="directed=True"/>
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383 <has_text_matching expression="use_weights=False"/>
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384 </assert_contents>
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385 </output>
14
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386 <output name="anndata_out" ftype="h5ad">
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387 <assert_contents>
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388 <has_h5_keys keys="obs/louvain"/>
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389 <has_h5_keys keys="uns/louvain"/>
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390 </assert_contents>
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391 </output>
0
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392 </test>
14
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parents: 12
diff changeset
393
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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diff changeset
394 <!-- test 2 -->
12
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395 <test expect_num_outputs="2">
14
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diff changeset
396 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
1
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parents: 0
diff changeset
397 <conditional name="method">
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
398 <param name="method" value="tl.leiden"/>
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parents: 0
diff changeset
399 <param name="random_state" value="10"/>
0
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400 </conditional>
6
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parents: 5
diff changeset
401 <section name="advanced_common">
14
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diff changeset
402 <param name="show_log" value="true"/>
6
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diff changeset
403 </section>
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parents: 5
diff changeset
404 <output name="hidden_output">
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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parents: 5
diff changeset
405 <assert_contents>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
406 <has_text_matching expression="sc.tl.leiden"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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parents: 5
diff changeset
407 <has_text_matching expression="resolution=1"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
408 <has_text_matching expression="random_state=10"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
409 <has_text_matching expression="key_added='leiden'"/>
14
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parents: 12
diff changeset
410 <has_text_matching expression="use_weights=True"/>
6
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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diff changeset
411 <has_text_matching expression="n_iterations=-1"/>
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412 </assert_contents>
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diff changeset
413 </output>
14
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parents: 12
diff changeset
414 <output name="anndata_out" ftype="h5ad">
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parents: 12
diff changeset
415 <assert_contents>
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parents: 12
diff changeset
416 <has_h5_keys keys="obs/leiden"/>
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iuc
parents: 12
diff changeset
417 <has_h5_keys keys="uns/leiden"/>
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diff changeset
418 </assert_contents>
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diff changeset
419 </output>
1
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parents: 0
diff changeset
420 </test>
14
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parents: 12
diff changeset
421
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
422 <!-- test 3 -->
12
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diff changeset
423 <test expect_num_outputs="2">
14
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parents: 12
diff changeset
424 <param name="adata" value="krumsiek11.h5ad"/>
0
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iuc
parents:
diff changeset
425 <conditional name="method">
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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diff changeset
426 <param name="method" value="pp.pca"/>
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iuc
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diff changeset
427 </conditional>
6
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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diff changeset
428 <section name="advanced_common">
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
429 <param name="show_log" value="true"/>
6
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
430 </section>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
431 <output name="hidden_output">
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
432 <assert_contents>
bd6d678d0579 "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="sc.pp.pca"/>
bd6d678d0579 "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="dtype='float32'"/>
bd6d678d0579 "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="copy=False"/>
bd6d678d0579 "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="chunked=False"/>
bd6d678d0579 "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="zero_center=True"/>
bd6d678d0579 "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="random_state=0"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
439 </assert_contents>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
440 </output>
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
441 <output name="anndata_out" ftype="h5ad">
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
442 <assert_contents>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
443 <has_h5_keys keys="uns/pca"/>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
444 <has_h5_keys keys="obsm/X_pca"/>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
445 <has_h5_keys keys="varm/PCs"/>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
446 </assert_contents>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
447 </output>
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
448 </test>
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
449
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
450 <!-- test 4 -->
12
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
451 <test expect_num_outputs="2">
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
452 <param name="adata" value="krumsiek11.h5ad"/>
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
453 <conditional name="method">
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
454 <param name="method" value="pp.pca"/>
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
455 <param name="n_comps" value="20"/>
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
456 <conditional name="pca">
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
457 <param name="chunked" value="True"/>
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
458 <param name="chunk_size" value="50"/>
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
459 </conditional>
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
460 </conditional>
12
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
461 <section name="advanced_common">
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
462 <param name="show_log" value="true"/>
12
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
463 </section>
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
464 <output name="hidden_output">
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
465 <assert_contents>
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
466 <has_text_matching expression="sc.pp.pca"/>
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
467 <has_text_matching expression="data=adata"/>
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
468 <has_text_matching expression="dtype='float32'"/>
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
469 <has_text_matching expression="copy=False"/>
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
470 <has_text_matching expression="chunked=True"/>
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
471 <has_text_matching expression="chunk_size=50"/>
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
472 </assert_contents>
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
473 </output>
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
474 <output name="anndata_out" ftype="h5ad">
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
475 <assert_contents>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
476 <has_h5_keys keys="uns/pca"/>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
477 <has_h5_keys keys="obsm/X_pca"/>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
478 <has_h5_keys keys="varm/PCs"/>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
479 </assert_contents>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
480 </output>
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
481 </test>
16
f68aa37a20ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 14
diff changeset
482
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
483 <!-- test 5 -->
12
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
484 <test expect_num_outputs="2">
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
485 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
486 <conditional name="method">
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
487 <param name="method" value="tl.diffmap"/>
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
488 </conditional>
6
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
489 <section name="advanced_common">
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
490 <param name="show_log" value="true"/>
6
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
491 </section>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
492 <output name="hidden_output">
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
493 <assert_contents>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
494 <has_text_matching expression="sc.tl.diffmap"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
495 </assert_contents>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
496 </output>
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
497 <output name="anndata_out" ftype="h5ad">
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
498 <assert_contents>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
499 <has_h5_keys keys="obsm/X_diffmap"/>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
500 <has_h5_keys keys="uns/diffmap_evals"/>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
501 </assert_contents>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
502 </output>
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
503 </test>
16
f68aa37a20ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 14
diff changeset
504
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
505 <!-- test 6 -->
12
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
506 <test expect_num_outputs="2">
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
507 <param name="adata" value="krumsiek11.h5ad"/>
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
508 <conditional name="method">
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
509 <param name="method" value="tl.tsne"/>
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
510 <param name="n_pcs" value="10"/>
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
511 </conditional>
6
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
512 <section name="advanced_common">
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
513 <param name="show_log" value="true"/>
6
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
514 </section>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
515 <output name="hidden_output">
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
516 <assert_contents>
bd6d678d0579 "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="sc.tl.tsne"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
518 <has_text_matching expression="n_pcs=10"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
519 <has_text_matching expression="perplexity=30.0"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
520 <has_text_matching expression="early_exaggeration=12.0"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
521 <has_text_matching expression="learning_rate=1000.0"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
522 <has_text_matching expression="random_state=0"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
523 </assert_contents>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
524 </output>
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
525 <output name="anndata_out" ftype="h5ad">
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
526 <assert_contents>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
527 <has_h5_keys keys="uns/tsne"/>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
528 <has_h5_keys keys="obsm/X_tsne"/>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
529 </assert_contents>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
530 </output>
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
531 </test>
16
f68aa37a20ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 14
diff changeset
532
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
533 <!-- test 7 -->
12
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
534 <test expect_num_outputs="2">
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
535 <param name="adata" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
536 <conditional name="method">
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
537 <param name="method" value="tl.umap"/>
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
538 <param name="maxiter" value="2"/>
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
539 </conditional>
6
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
540 <section name="advanced_common">
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
541 <param name="show_log" value="true"/>
6
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
542 </section>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
543 <output name="hidden_output">
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
544 <assert_contents>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
545 <has_text_matching expression="sc.tl.umap"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
546 <has_text_matching expression="min_dist=0.5"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
547 <has_text_matching expression="spread=1.0"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
548 <has_text_matching expression="n_components=2"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
549 <has_text_matching expression="maxiter=2"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
550 <has_text_matching expression="alpha=1.0"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
551 <has_text_matching expression="gamma=1.0"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
552 <has_text_matching expression="negative_sample_rate=5"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
553 <has_text_matching expression="init_pos='spectral'"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
554 <has_text_matching expression="random_state=0"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
555 </assert_contents>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
556 </output>
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
557 <output name="anndata_out" ftype="h5ad">
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
558 <assert_contents>
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
559 <has_h5_keys keys="uns/umap"/>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
560 <has_h5_keys keys="obsm/X_umap"/>
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
561 </assert_contents>
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
562 </output>
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
563 </test>
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
564
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
565 <!-- test 8 -->
12
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
566 <test expect_num_outputs="2">
1
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
567 <param name="adata" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
568 <conditional name="method">
1
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
569 <param name="method" value="tl.draw_graph"/>
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
570 </conditional>
6
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
571 <section name="advanced_common">
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
572 <param name="show_log" value="true"/>
6
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
573 </section>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
574 <output name="hidden_output">
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
575 <assert_contents>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
576 <has_text_matching expression="sc.tl.draw_graph"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
577 <has_text_matching expression="layout='fa'"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
578 <has_text_matching expression="random_state=0"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
579 </assert_contents>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
580 </output>
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
581 <output name="anndata_out" ftype="h5ad">
6
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
582 <assert_contents>
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
583 <has_h5_keys keys="uns/draw_graph"/>
16
f68aa37a20ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 14
diff changeset
584 <has_h5_keys keys="obsm/X_draw_graph_fa"/>
6
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
585 </assert_contents>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
586 </output>
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
587 </test>
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
588
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
589 <!-- test 9 -->
12
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
590 <test expect_num_outputs="2">
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
591 <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
592 <conditional name="method">
1
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
593 <param name="method" value="tl.dpt"/>
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
594 <param name="n_dcs" value="15"/>
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
595 <param name="n_branchings" value="1"/>
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
596 </conditional>
6
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
597 <section name="advanced_common">
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
598 <param name="show_log" value="true"/>
6
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
599 </section>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
600 <output name="hidden_output">
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
601 <assert_contents>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
602 <has_text_matching expression="sc.tl.dpt"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
603 <has_text_matching expression="n_dcs=15"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
604 <has_text_matching expression="n_branchings=1"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
605 <has_text_matching expression="min_group_size=0.01"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
606 <has_text_matching expression="allow_kendall_tau_shift=True"/>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
607 </assert_contents>
bd6d678d0579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
608 </output>
14
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iuc
parents: 12
diff changeset
609 <output name="anndata_out" ftype="h5ad">
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
610 <assert_contents>
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iuc
parents: 12
diff changeset
611 <has_h5_keys keys="obs/dpt_groups,obs/dpt_order,obs/dpt_order_indices"/>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
612 <has_h5_keys keys="uns/dpt_changepoints,uns/dpt_grouptips"/>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
613 </assert_contents>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
614 </output>
0
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iuc
parents:
diff changeset
615 </test>
14
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iuc
parents: 12
diff changeset
616
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
617 <!-- test 10 -->
16
f68aa37a20ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
iuc
parents: 14
diff changeset
618 <test expect_num_outputs="2">
14
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iuc
parents: 12
diff changeset
619 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
620 <conditional name="method">
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
621 <param name="method" value="tl.paga"/>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
622 <param name="groups" value="paul15_clusters"/>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
623 </conditional>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
624 <section name="advanced_common">
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
625 <param name="show_log" value="true"/>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
626 </section>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
627 <output name="hidden_output">
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
628 <assert_contents>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
629 <has_text_matching expression="sc.tl.paga"/>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
630 <has_text_matching expression="groups='paul15_clusters'"/>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
631 <has_text_matching expression="use_rna_velocity=False"/>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
632 <has_text_matching expression="model='v1.2'"/>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
633 </assert_contents>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
634 </output>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
635 <output name="anndata_out" ftype="h5ad">
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
636 <assert_contents>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
637 <has_h5_keys keys="uns/paga,uns/paul15_clusters_sizes"/>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
638 </assert_contents>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
639 </output>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
640 </test>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
641
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
642 <!-- test 11 -->
12
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iuc
parents: 10
diff changeset
643 <test expect_num_outputs="2">
14
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parents: 12
diff changeset
644 <param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
12
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iuc
parents: 10
diff changeset
645 <conditional name="method">
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
646 <param name="method" value="tl.embedding_density"/>
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
647 <param name="key_added" value="umap_density"/>
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
648 </conditional>
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
649 <section name="advanced_common">
14
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iuc
parents: 12
diff changeset
650 <param name="show_log" value="true"/>
12
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parents: 10
diff changeset
651 </section>
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
652 <output name="hidden_output">
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
653 <assert_contents>
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
654 <has_text_matching expression="sc.tl.embedding_density"/>
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
655 <has_text_matching expression="basis='umap'"/>
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
656 <has_text_matching expression="key_added='umap_density'"/>
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
657 </assert_contents>
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
658 </output>
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
659 <output name="anndata_out" ftype="h5ad">
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
660 <assert_contents>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
661 <has_h5_keys keys="obs/umap_density"/>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
662 <has_h5_keys keys="uns/umap_density_params"/>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
663 </assert_contents>
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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diff changeset
664 </output>
12
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iuc
parents: 10
diff changeset
665 </test>
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
666 </tests>
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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diff changeset
667 <help><![CDATA[
16
f68aa37a20ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
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parents: 14
diff changeset
668
1
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
669 Cluster cells into subgroups (`tl.louvain`)
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
670 ===========================================
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
671
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
672 Cluster cells using the Louvain algorithm (Blondel et al, 2008) in the implementation
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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diff changeset
673 of Traag et al,2017. The Louvain algorithm has been proposed for single-cell
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
674 analysis by Levine et al, 2015.
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
675
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
676 This requires to run `pp.neighbors`, first.
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
677
5
e160e1dd7fb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
iuc
parents: 4
diff changeset
678 More details on the `tl.louvain scanpy documentation
12
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iuc
parents: 10
diff changeset
679 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.louvain.html>`_
1
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
680
14
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iuc
parents: 12
diff changeset
681
1
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
682 Cluster cells into subgroups (`tl.leiden`)
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
683 ==========================================
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
684
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
685 Cluster cells using the Leiden algorithm (Traag et al, 2018), an improved version of the Louvain algorithm (Blondel et al, 2008).
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
686
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
687 The Louvain algorithm has been proposed for single-cell analysis by Levine et al, 2015.
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
688
5
e160e1dd7fb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
iuc
parents: 4
diff changeset
689 More details on the `tl.leiden scanpy documentation
12
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iuc
parents: 10
diff changeset
690 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.leiden.html>`_
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
691
14
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
692
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
693 Computes PCA (principal component analysis) coordinates, loadings and variance decomposition, using `pp.pca`
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
694 ============================================================================================================
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
695
5
e160e1dd7fb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
iuc
parents: 4
diff changeset
696 More details on the `pp.pca scanpy documentation
12
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iuc
parents: 10
diff changeset
697 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.pca.html>`__
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
698
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iuc
parents:
diff changeset
699
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
700 Diffusion Maps, using `tl.diffmap`
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diff changeset
701 ==================================
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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parents:
diff changeset
702
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
703 Diffusion maps (Coifman et al 2005) has been proposed for visualizing single-cell
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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parents:
diff changeset
704 data by Haghverdi et al (2015). The tool uses the adapted Gaussian kernel suggested
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
705 by Haghverdi et al (2016) in the implementation of Wolf et al (2017).
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parents:
diff changeset
706
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
707 The width ("sigma") of the connectivity kernel is implicitly determined by
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
708 the number of neighbors used to compute the single-cell graph in
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
709 `pp.neighbors`. To reproduce the original implementation
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
710 using a Gaussian kernel, use `method=='gauss'` in
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
711 `pp.neighbors`. To use an exponential kernel, use the default
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
712 `method=='umap'`. Differences between these options shouldn't usually be
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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parents:
diff changeset
713 dramatic.
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iuc
parents:
diff changeset
714
12
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parents: 10
diff changeset
715 The diffusion map representation of data are added to the return AnnData in the multi-dimensional
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
iuc
parents: 10
diff changeset
716 observations annotation (obsm). It is the right eigen basis of the transition matrix with eigenvectors
1
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parents: 0
diff changeset
717 as colum. It can be accessed using the inspect tool for AnnData
0
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parents:
diff changeset
718
5
e160e1dd7fb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
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parents: 4
diff changeset
719 More details on the `tl.diffmap scanpy documentation
12
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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diff changeset
720 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.diffmap.html>`__
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
721
14
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diff changeset
722
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
723 t-distributed stochastic neighborhood embedding (tSNE), using `tl.tsne`
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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parents:
diff changeset
724 =======================================================================
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
725
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
726 t-distributed stochastic neighborhood embedding (tSNE) (Maaten et al, 2008) has been
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
727 proposed for visualizating single-cell data by (Amir et al, 2013). Here, by default,
12
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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diff changeset
728 we use the implementation of *scikit-learn* (Pedregosa et al, 2011).
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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parents:
diff changeset
729
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
730 It returns `X_tsne`, tSNE coordinates of data.
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
731
5
e160e1dd7fb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
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diff changeset
732 More details on the `tl.tsne scanpy documentation
12
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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diff changeset
733 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.tsne.html>`__
0
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diff changeset
734
14
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parents: 12
diff changeset
735
0
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
736 Embed the neighborhood graph using UMAP, using `tl.umap`
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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parents:
diff changeset
737 ========================================================
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
738
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
739 UMAP (Uniform Manifold Approximation and Projection) is a manifold learning
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
740 technique suitable for visualizing high-dimensional data. Besides tending to
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
741 be faster than tSNE, it optimizes the embedding such that it best reflects
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
742 the topology of the data, which we represent throughout Scanpy using a
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
743 neighborhood graph. tSNE, by contrast, optimizes the distribution of
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
parents:
diff changeset
744 nearest-neighbor distances in the embedding such that these best match the
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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diff changeset
745 distribution of distances in the high-dimensional space. We use the
0adf813af36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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746 implementation of `umap-learn <https://github.com/lmcinnes/umap>`__
14
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diff changeset
747 (McInnes et al, 2018). For a few comparisons of UMAP with tSNE, see this `paper
b43f391d2919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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748 <https://www.nature.com/articles/nbt.4314>`__.
0
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749
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diff changeset
750 The UMAP coordinates of data are added to the return AnnData in the multi-dimensional
1
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parents: 0
diff changeset
751 observations annotation (obsm). This data is accessible using the inspect tool for AnnData
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
752
5
e160e1dd7fb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
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753 More details on the `tl.umap scanpy documentation
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754 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.umap.html>`__
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diff changeset
755
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diff changeset
756
1
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parents: 0
diff changeset
757 Force-directed graph drawing, using `tl.draw_graph`
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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758 ===================================================
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
759
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diff changeset
760 Force-directed graph drawing describes a class of long-established algorithms for visualizing graphs.
9740d430d9f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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diff changeset
761 It has been suggested for visualizing single-cell data by Islam et al, 11.
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diff changeset
762 Many other layouts as implemented in igraph are available. Similar approaches have been used by
1
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parents: 0
diff changeset
763 Zunder et al, 2015 or Weinreb et al, 2016.
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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764
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765 This is an alternative to tSNE that often preserves the topology of the data better.
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diff changeset
766 This requires to run `pp.neighbors`, first.
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767
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parents: 0
diff changeset
768 The default layout (ForceAtlas2) uses the package fa2.
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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769
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770 The coordinates of graph layout are added to the return AnnData in the multi-dimensional
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diff changeset
771 observations annotation (obsm). This data is accessible using the inspect tool for AnnData.
0
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772
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773 More details on the `tl.draw_graph scanpy documentation
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774 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.draw_graph.html>`__
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775
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776
1
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777 Infer progression of cells through geodesic distance along the graph (`tl.dpt`)
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778 ===============================================================================
0
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779
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parents: 0
diff changeset
780 Reconstruct the progression of a biological process from snapshot
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diff changeset
781 data. `Diffusion Pseudotime` has been introduced by Haghverdi et al (2016) and
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
782 implemented within Scanpy (Wolf et al, 2017). Here, we use a further developed
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
783 version, which is able to deal with disconnected graphs (Wolf et al, 2017) and can
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
784 be run in a `hierarchical` mode by setting the parameter
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
785 `n_branchings>1`. We recommend, however, to only use
aebbe79ff418 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
786 `tl.dpt` for computing pseudotime (`n_branchings=0`) and
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787 to detect branchings via `paga`. For pseudotime, you need
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788 to annotate your data with a root cell.
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789
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790 This requires to run `pp.neighbors`, first. In order to
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791 reproduce the original implementation of DPT, use `method=='gauss'` in
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792 this. Using the default `method=='umap'` only leads to minor quantitative
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793 differences, though.
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794
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795
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796 If `n_branchings==0`, no field `dpt_groups` will be written.
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797
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798 - 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.
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799 - 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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800
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801 The tool is similar to the R package `destiny` of Angerer et al (2016).
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802
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803 More details on the `tl.dpt scanpy documentation
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804 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.dpt.html>`_
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805
1
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806
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807 Generate cellular maps of differentiation manifolds with complex topologies (`tl.paga`)
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808 =======================================================================================
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809
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810 By quantifying the connectivity of partitions (groups, clusters) of the
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811 single-cell graph, partition-based graph abstraction (PAGA) generates a much
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812 simpler abstracted graph (*PAGA graph*) of partitions, in which edge weights
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813 represent confidence in the presence of connections. By tresholding this
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814 confidence in `paga`, a much simpler representation of data
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815 can be obtained.
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816
1
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817 The confidence can be interpreted as the ratio of the actual versus the
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818 expected value of connetions under the null model of randomly connecting
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819 partitions. We do not provide a p-value as this null model does not
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820 precisely capture what one would consider "connected" in real data, hence it
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821 strongly overestimates the expected value. See an extensive discussion of
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822 this in Wolf et al (2017).
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823
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824 Together with a random walk-based distance measure, this generates a partial
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825 coordinatization of data useful for exploring and explaining its variation.
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826
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827 The returned AnnData object contains:
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828
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829 - Full adjacency matrix of the abstracted graph, weights correspond to confidence in the connectivities of partition (connectivities)
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830 - Adjacency matrix of the tree-like subgraph that best explains the topology (connectivities_tree)
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831
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832 These datasets are stored in the unstructured annotation (uns) and can be accessed using the inspect tool for AnnData objects
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833
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834 More details on the `tl.paga scanpy documentation
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835 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.paga.html>`_
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836
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837
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838 Calculates the density of cells in an embedding (per condition). (`tl.embedding_density`)
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839 =========================================================================================
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840
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841 Gaussian kernel density estimation is used to calculate the density of cells in an embedded space. This can be performed per category over a categorical cell annotation.
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842
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843 Note that density values are scaled to be between 0 and 1. Thus, the density value at each cell is only comparable to densities in the same category.
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844
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845 More details on the `tl.embedding_density scanpy documentation
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846 <https://scanpy.readthedocs.io/en/stable/generated/scanpy.tl.embedding_density.html>`_
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847 ]]>
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848 </help>
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849 <expand macro="citations"/>
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850 </tool>