Mercurial > repos > iuc > snapatac2_clustering

annotate dimension_reduction_clustering.xml @ 4:d60c2415e7ba draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
author iuc
date Tue, 25 Nov 2025 16:39:49 +0000
parents 1e61bebe64d5
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1 <tool id="snapatac2_clustering" name="SnapATAC2 Clustering" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>and dimension reduction</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
3
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6 <expand macro="xrefs"/>
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7 <requirements>
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8 <expand macro="requirements"/>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 export NUMBA_CACHE_DIR="\${TEMP:-/tmp}";
4
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12 #if $method.method == 'tl.multi_spectral'
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13 #for $i in range(len($method.adata))
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14 cp $method.adata[$i] 'adata_${i}.h5ad' &&
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15 #end for
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16 #else
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17 @CMD_PREP_ADATA@
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18 #end if
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19 @CMD@
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20 ]]></command>
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21 <configfiles>
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22 <configfile name="script_file"><![CDATA[
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23
4
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24 @CONF_IMPORTS@
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25 #if $method.method == 'tl.multi_spectral'
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26 ## read all files ending with .h5ad in the working directory
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27 import glob
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28 files = sorted(glob.glob('adata_*.h5ad'))
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29
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30 adata_list = []
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31 for fn in files:
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32 ad = snap.read(fn, backed=None)
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33 adata_list.append(ad)
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34 #else
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35 @CONF_READ_INPUTS@
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36 #end if
0
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37
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38 #if $method.method == 'tl.spectral'
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39 #if $method.features
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40 with open('$method.features') as f:
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41 features_mask = [x.lower().capitalize() == "True" for x in f.read().splitlines()]
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42 #end if
4
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43
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44 ## somewhere in the SnapATAC2 code, a pandas Series is being passed where a numpy array is expected.
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45 ## This is a workaround to add the nonzero method back to pandas Series.
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46 ## Add the nonzero method back to pandas Series
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47 import pandas as pd
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48 def series_nonzero(self):
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49 return (self != 0).values.nonzero()
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50
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51 pd.Series.nonzero = series_nonzero
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52
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53
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54 snap.tl.spectral(
0
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55 adata,
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56 n_comps = $method.n_comps,
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57 #if $method.features
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58 features = features_mask,
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59 #end if
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60 random_state = $method.random_state,
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61 #if $method.sample_size
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62 sample_size = $method.sample_size,
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63 #end if
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64 chunk_size = $method.chunk_size,
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65 distance_metric = '$method.distance_metric',
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66 weighted_by_sd = $method.weighted_by_sd,
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67 inplace = True
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68 )
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69
4
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70 #else if $method.method == 'tl.multi_spectral'
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71 #if $method.features
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72 with open('$method.features') as f:
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73 features_mask = [x.lower().capitalize() == "True" for x in f.read().splitlines()]
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74 #end if
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75
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76 embedding = snap.tl.multi_spectral(
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77 adatas = adata_list,
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78 n_comps = $method.n_comps,
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79 #if $method.features
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80 features = features_mask,
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81 #else
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82 features = None,
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83 #end if
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84 weights = None, # Will enable if requested by users
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85 random_state = $method.random_state,
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86 weighted_by_sd = $method.weighted_by_sd,
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87 )
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88
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89 adata = adata_list[0].copy()
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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90 adata.uns['spectral_eigenvalue_joint'] = embedding[0]
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91 adata.obsm['X_joint'] = embedding[1]
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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92
0
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93 #else if $method.method == 'tl.umap'
4
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94 snap.tl.umap(
0
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95 adata,
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96 n_comps = $method.n_comps,
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97 #if $method.use_dims != ''
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98 #set $dims = ([x.strip() for x in str($method.use_dims).split(',')])
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99 use_dims=$dims,
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100 #end if
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101 use_rep = '$method.use_rep',
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102 key_added = '$method.key_added',
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103 random_state = $method.random_state,
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104 inplace = True
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105 )
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106
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107 #else if $method.method == 'pp.knn'
4
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108 snap.pp.knn(
0
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109 adata,
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110 n_neighbors = $method.n_neighbors,
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111 #if $method.use_dims != ''
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112 #set $dims = ([x.strip() for x in str($method.use_dims).split(',')])
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113 use_dims=$dims,
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114 #end if
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115 use_rep = '$method.use_rep',
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116 method = '$method.algorithm',
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117 inplace = True,
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118 random_state = $method.random_state
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119 )
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120
4
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121 #else if $method.method == 'tl.leiden'
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122 snap.tl.leiden(
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123 adata,
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124 resolution = $method.resolution,
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125 objective_function = '$method.objective_function',
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126 min_cluster_size = $method.min_cluster_size,
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127 n_iterations = $method.n_iterations,
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128 random_state = $method.random_state,
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129 key_added = '$method.key_added',
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130 use_leidenalg = $method.use_leidenalg,
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131 weighted = $method.weighted,
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132 inplace = True
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133 )
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134
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135 #else if $method.method == 'tl.kmeans'
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136 snap.tl.kmeans(
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137 adata,
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138 n_clusters = $method.n_clusters,
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139 n_iterations = $method.n_iterations,
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140 random_state = $method.random_state,
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141 use_rep = '$method.use_rep',
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142 key_added = '$method.key_added'
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143 )
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144
0
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145 #else if $method.method == 'tl.dbscan'
4
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146 snap.tl.dbscan(
0
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147 adata,
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148 eps = $method.eps,
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149 min_samples = $method.min_samples,
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150 leaf_size = $method.leaf_size,
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151 use_rep = '$method.use_rep',
4
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152 key_added = '$method.key_added',
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153 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
0
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154 )
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155
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156 #else if $method.method == 'tl.hdbscan'
4
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157 snap.tl.hdbscan(
0
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158 adata,
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159 min_cluster_size = $method.min_cluster_size,
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160 #if $method.min_samples
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161 min_samples = $method.min_samples,
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162 #end if
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163 cluster_selection_epsilon = $method.cluster_selection_epsilon,
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164 alpha = $method.alpha,
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165 cluster_selection_method = '$method.cluster_selection_method',
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166 random_state = $method.random_state,
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167 use_rep = '$method.use_rep',
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168 key_added = '$method.key_added'
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169 )
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170
4
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171 ## It is implemented in select_feature function, and it is problematic if the user don't select a groupby (will return an array). i think this can be skipped unless needed
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172 ## #else if $method.method == 'tl.aggregate_X'
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173 ## snap.tl.aggregate_X(
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174 ## adata,
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175 ## #if $method.groupby != ''
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176 ## groupby = '$method.groupby',
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177 ## #end if
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178 ## normalize = '$method.normalize'
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179 ## )
0
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180
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181 #else if $method.method == 'tl.aggregate_cells'
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182 snap.tl.aggregate_cells(
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183 adata,
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184 use_rep = '$method.use_rep',
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185 #if $method.target_num_cells
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186 target_num_cells = $method.target_num_cells,
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187 #end if
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188 min_cluster_size = $method.min_cluster_size,
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189 random_state = $method.random_state,
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190 key_added = '$method.key_added',
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191 inplace = True
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192 )
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193 #end if
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194
4
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195 @CONF_ANNDATA_WRITE_OUTPUTS@
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196 ]]></configfile>
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197 </configfiles>
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198 <inputs>
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199 <conditional name="method">
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200 <param name="method" type="select" label="Dimension reduction and Clustering">
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201 <option value="tl.spectral">Perform dimension reduction using Laplacian Eigenmap, using 'tl.spectral'</option>
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202 <option value="tl.multi_spectral">similar to 'tl.multi_spectral' but it can work on multiple modalities.</option>
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203 <option value="tl.umap">Compute Umap, using 'tl.umap'</option>
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204 <option value="pp.knn">Compute a neighborhood graph of observations, using 'pp.knn'</option>
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205 <option value="tl.leiden">Cluster cells into subgroups, using 'tl.leiden'</option>
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206 <option value="tl.kmeans">Cluster cells into subgroups using the K-means algorithm, using 'tl.kmeans'</option>
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207 <option value="tl.dbscan">Cluster cells into subgroups using the DBSCAN algorithm, using 'tl.dbscan'</option>
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208 <option value="tl.hdbscan">Cluster cells into subgroups using the HDBSCAN algorithm, using 'tl.hdbscan'</option>
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209 <!-- It is implemented in select_feature function in preprocessing.xml tool (implemented in upstream code, not in the xml). It is problematic if the user don't select a groupby (will return an array). i think this can be skipped unless needed -->
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210 <!-- <option value="tl.aggregate_X">Aggregate values in adata.X in a row-wise fashion, using 'tl.aggregate_X'</option> -->
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211 <option value="tl.aggregate_cells">Aggregate cells into pseudo-cells, using 'tl.aggregate_cells'</option>
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212 </param>
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213 <when value="tl.spectral">
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214 <expand macro="param_inputs_anndata"/>
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215 <expand macro="param_n_comps"/>
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216 <param argument="features" type="data" format="txt,tabular" optional="true" label="Text file indicating features to keep. Each line contains only word (True/False)." help="True means that the feature is kept. False means the feature is removed"/>
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217 <expand macro="param_random_state"/>
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218 <param argument="sample_size" type="float" min="0" max="1" optional="true" label="Approximate the embedding using the Nystrom algorithm by selecting a subset of cells" help="Using this only when the number of cells is too large, e.g. &gt; 10,000,000, or the `distance_metric` is “jaccard”"/>
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219 <param argument="chunk_size" type="integer" value="20000" label="chunk size"/>
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220 <param argument="distance_metric" type="select" label="distance metric: “jaccard”, “cosine“">
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221 <option value="jaccard">jaccard</option>
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222 <option value="cosine" selected="true">cosine</option>
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223 </param>
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224 <param argument="weighted_by_sd" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Whether to weight the result eigenvectors by the square root of eigenvalues"/>
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225 </when>
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226 <when value="tl.multi_spectral">
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227 <expand macro="param_inputs_anndata" multiple="true" label="list of Anndatas to use for multi_spectral" help="Please note that the embedding will be saved in the first Anndata"/>
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228 <!-- Will enable if requested by users -->
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229 <!-- <param name="weights" type="data" format="tabular" optional="true" label="Weights" help="Text file indicating weights for each modality. Each line contains only floats.If not provided, all modalities are weighted equally" /> -->
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230 <expand macro="param_n_comps"/>
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231 <param argument="features" type="data" format="txt,tabular" optional="true" label="Text file indicating features to keep. Each line contains only word (True/False)." help="True means that the feature is kept. False means the feature is removed"/>
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232 <expand macro="param_random_state"/>
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233 <param argument="weighted_by_sd" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Whether to weight the result eigenvectors by the square root of eigenvalues"/>
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234 </when>
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235 <when value="tl.umap">
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236 <expand macro="param_inputs_anndata"/>
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237 <expand macro="param_n_comps" value="2" label="Number of components" help=""/>
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238 <param argument="use_dims" type="text" optional="true" label="Use these dimensions in `use_rep`" help="comma separated list of dimensions">
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239 <expand macro="sanitize_query"/>
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240 </param>
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241 <expand macro="param_use_rep"/>
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242 <expand macro="param_key_added" key_added="umap"/>
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243 <expand macro="param_random_state"/>
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244 </when>
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245 <when value="pp.knn">
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246 <expand macro="param_inputs_anndata"/>
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247 <param argument="n_neighbors" type="integer" value="50" label="The number of nearest neighbors to be searched"/>
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248 <param argument="use_dims" type="text" value="" optional="true" label="The dimensions used for computation">
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249 <expand macro="sanitize_query"/>
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250 </param>
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251 <expand macro="param_use_rep" label="The key for the matrix"/>
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252 <param argument="algorithm" type="select" label="Choose method">
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253 <option value="kdtree" selected="true">'kdtree': use the kdtree algorithm to find the nearest neighbors</option>
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254 <option value="hora">'hora': use the HNSW algorithm to find the approximate nearest neighbors</option>
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255 <option value="pynndescent">'pynndescent': use the pynndescent algorithm to find the approximate nearest neighbors</option>
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256 </param>
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257 <expand macro="param_random_state" label="Random seed for approximate nearest neighbor search" help="Note that this is only used when method='pynndescent'. Currently hora does not support random seed, so the result of hora is not reproducible."/>
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258 </when>
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259 <when value="tl.leiden">
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260 <expand macro="param_inputs_anndata"/>
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261 <param argument="resolution" type="float" value="1" label="Parameter value controlling the coarseness of the clustering" help="Higher values lead to more clusters"/>
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262 <param argument="objective_function" type="select" label="Whether to use the Constant Potts Model (CPM) or modularity">
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263 <option value="CPM">CPM</option>
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264 <option value="modularity" selected="true">modularity</option>
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265 <option value="RBConfiguration">RBConfiguration</option>
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266 </param>
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267 <param argument="min_cluster_size" type="integer" value="5" label="The minimum size of clusters"/>
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268 <expand macro="param_n_iterations"/>
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269 <expand macro="param_random_state"/>
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270 <expand macro="param_key_added" key_added="leiden"/>
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271 <param argument="use_leidenalg" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Whether to use the leidenalg package for Leiden clustering"/>
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272 <param argument="weighted" type="boolean" truevalue="True" falsevalue="False" label="Whether to use the edge weights in the graph"/>
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273 </when>
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274 <when value="tl.kmeans">
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275 <expand macro="param_inputs_anndata"/>
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276 <param argument="n_clusters" type="integer" value="5" label="Number of clusters to return"/>
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277 <expand macro="param_n_iterations"/>
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278 <expand macro="param_random_state"/>
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279 <expand macro="param_use_rep"/>
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280 <expand macro="param_key_added" key_added="kmeans"/>
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281 </when>
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282 <when value="tl.dbscan">
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283 <expand macro="param_inputs_anndata"/>
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284 <param argument="eps" type="float" value="0.5" label=" The maximum distance between two samples for one to be considered as in the neighborhood of the other" help="This is not a maximum bound on the distances of points within a cluster. This is the most important DBSCAN parameter to choose appropriately for your data set and distance function."/>
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285 <param argument="min_samples" type="integer" value="5" label="The number of samples (or total weight) in a neighborhood for a point to be considered as a core point."/>
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286 <param argument="leaf_size" type="integer" value="30" label="Leaf size passed to BallTree or cKDTree" help="This can affect the speed of the construction and query, as well as the memory required to store the tree."/>
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287 <expand macro="param_use_rep"/>
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288 <expand macro="param_key_added" key_added="dbscan"/>
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289 </when>
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290 <when value="tl.hdbscan">
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291 <expand macro="param_inputs_anndata"/>
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292 <param argument="min_cluster_size" type="integer" value="5" label="The minimum size of clusters"/>
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293 <param argument="min_samples" type="integer" value="" optional="true" label="The number of samples in a neighborhood for a point to be considered a core point"/>
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294 <param argument="cluster_selection_epsilon" type="float" value="0.0" label="A distance threshold. Clusters below this value will be merged"/>
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295 <param argument="alpha" type="float" value="1.0" label="A distance scaling parameter as used in robust single linkage"/>
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296 <param argument="cluster_selection_method" type="select" label="The method used to select clusters from the condensed tree">
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297 <option value="eom">Excess of Mass algorithm to find the most persistent clusters</option>
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298 <option value="leaf">Select the clusters at the leaves of the tree - this provides the most fine grained and homogeneous clusters</option>
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299 </param>
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300 <expand macro="param_random_state"/>
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301 <expand macro="param_use_rep"/>
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302 <expand macro="param_key_added" key_added="hdbscan"/>
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303 </when>
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304 <!-- <when value="tl.aggregate_X">
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305 <expand macro="param_inputs_anndata"/>
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306 <expand macro="param_groupby"/>
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307 <param argument="normalize" type="select" optional="true" label="normalization method">
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308 <option value="RPM">RPM</option>
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309 <option value="RPKM">RPKM</option>
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310 </param>
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311 </when> -->
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312 <when value="tl.aggregate_cells">
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313 <expand macro="param_inputs_anndata"/>
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314 <expand macro="param_use_rep"/>
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315 <param argument="target_num_cells" type="integer" value="" optional="true" label="target_num_cells" help="If None, `target_num_cells = num_cells / min_cluster_size`"/>
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316 <param argument="min_cluster_size" type="integer" value="50" label="The minimum size of clusters"/>
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317 <expand macro="param_random_state"/>
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318 <expand macro="param_key_added" key_added="pseudo_cell"/>
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319 </when>
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320 </conditional>
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321 <expand macro="param_common_advanced"/>
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322 </inputs>
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323 <outputs>
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324 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad.gz" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/>
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325 <data name="hidden_output" format="txt" label="Log file">
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326 <filter>advanced_common['show_log']</filter>
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327 </data>
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328 </outputs>
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329 <tests>
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330 <test expect_num_outputs="2">
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331 <!-- tl.spectral -->
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332 <conditional name="method">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
333 <param name="method" value="tl.spectral"/>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
334 <param name="adata" location="https://zenodo.org/records/17512085/files/pp.select_features.pbmc_500_chr21.h5ad"/>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
335 <param name="n_comps" value="30"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
336 <param name="random_state" value="0"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
337 <param name="chunk_size" value="20000"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
338 <param name="distance_metric" value="jaccard"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
339 <param name="weighted_by_sd" value="True"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
340 </conditional>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
341 <section name="advanced_common">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
342 <param name="show_log" value="true"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
343 </section>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
344 <output name="hidden_output">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
345 <assert_contents>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
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diff changeset
346 <has_text_matching expression="snap.tl.spectral"/>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
347 <has_text_matching expression="random_state = 0"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
348 <has_text_matching expression="n_comps = 30"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
349 <has_text_matching expression="chunk_size = 20000"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
350 <has_text_matching expression="distance_metric = 'jaccard'"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
351 <has_text_matching expression="weighted_by_sd = True"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
352 </assert_contents>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
353 </output>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
354 <output name="anndata_out" ftype="h5ad">
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
355 <assert_contents>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
356 <has_h5_keys keys="uns/spectral_eigenvalue"/>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
357 <has_h5_keys keys="obsm/X_spectral"/>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
358 </assert_contents>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
359 </output>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
360 </test>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
361 <test expect_num_outputs="2">
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
362 <!-- tl.multi_spectral -->
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
363 <conditional name="method">
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
364 <param name="method" value="tl.multi_spectral"/>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
365 <param name="adata" location="https://zenodo.org/records/17512085/files/snap_datasets_pbmc10k_multiome_RNA.h5ad.gz,https://zenodo.org/records/17512085/files/snap_datasets_pbmc10k_multiome_ATAC.h5ad.gz"/>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
366 <param name="n_comps" value="30"/>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
367 <param name="random_state" value="0"/>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
368 <param name="weighted_by_sd" value="True"/>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
369 </conditional>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
370 <section name="advanced_common">
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
371 <param name="show_log" value="true"/>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
372 </section>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
373 <output name="hidden_output">
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
374 <assert_contents>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
375 <has_text_matching expression="snap.tl.multi_spectral"/>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
376 <has_text_matching expression="random_state = 0"/>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
377 <has_text_matching expression="n_comps = 30"/>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
378 <has_text_matching expression="weighted_by_sd = True"/>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
379 <has_text_matching expression="features = None"/>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
380 </assert_contents>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
381 </output>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
382 <output name="anndata_out" ftype="h5ad">
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
383 <assert_contents>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
384 <has_h5_keys keys="uns/spectral_eigenvalue_joint"/>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
385 <has_h5_keys keys="obsm/X_joint"/>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
386 </assert_contents>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
387 </output>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
388 </test>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
389 <test expect_num_outputs="2">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
390 <!-- tl.umap -->
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
391 <conditional name="method">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
392 <param name="method" value="tl.umap"/>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
393 <param name="adata" location="https://zenodo.org/records/17512085/files/tl.spectral.pbmc_500_chr21.h5ad"/>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
394 <param name="n_comps" value="2"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
395 <param name="use_rep" value="X_spectral"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
396 <param name="key_added" value="umap"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
397 <param name="random_state" value="0"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
398 </conditional>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
399 <section name="advanced_common">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
400 <param name="show_log" value="true"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
401 </section>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
402 <output name="hidden_output">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
403 <assert_contents>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
404 <has_text_matching expression="snap.tl.umap"/>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
405 <has_text_matching expression="n_comps = 2"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
406 <has_text_matching expression="use_rep = 'X_spectral'"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
407 <has_text_matching expression="key_added = 'umap'"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
408 <has_text_matching expression="random_state = 0"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
409 </assert_contents>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
410 </output>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
411 <output name="anndata_out" ftype="h5ad">
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
412 <assert_contents>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
413 <has_h5_keys keys="obsm/X_umap"/>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
414 </assert_contents>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
415 </output>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
416 </test>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
417 <test expect_num_outputs="2">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
418 <!-- pp.knn -->
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
419 <conditional name="method">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
420 <param name="method" value="pp.knn"/>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
421 <param name="adata" location="https://zenodo.org/records/17512085/files/tl.umap.pbmc_500_chr21.h5ad"/>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
422 <param name="n_neighbors" value="50"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
423 <param name="use_rep" value="X_spectral"/>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
424 <param name="algorithm" value="kdtree"/>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
425 <param name="random_state" value="0"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
426 </conditional>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
427 <section name="advanced_common">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
428 <param name="show_log" value="true"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
429 </section>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
430 <output name="hidden_output">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
431 <assert_contents>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
432 <has_text_matching expression="snap.pp.knn"/>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
433 <has_text_matching expression="n_neighbors = 50"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
434 <has_text_matching expression="use_rep = 'X_spectral'"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
435 <has_text_matching expression="method = 'kdtree'"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
436 <has_text_matching expression="inplace = True"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
437 <has_text_matching expression="random_state = 0"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
438 </assert_contents>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
439 </output>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
440 <output name="anndata_out" ftype="h5ad">
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
441 <assert_contents>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
442 <has_h5_keys keys="obsp/distances"/>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
443 </assert_contents>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
444 </output>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
445 </test>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
446 <test expect_num_outputs="2">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
447 <!-- tl.leiden -->
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
448 <conditional name="method">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
449 <param name="method" value="tl.leiden"/>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
450 <param name="adata" location="https://zenodo.org/records/17512085/files/pp.knn.pbmc_500_chr21.h5ad"/>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
451 <param name="resolution" value="2"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
452 <param name="objective_function" value="modularity"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
453 <param name="min_cluster_size" value="3"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
454 <param name="n_iterations" value="-1"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
455 <param name="random_state" value="0"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
456 <param name="key_added" value="leiden"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
457 <param name="weighted" value="False"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
458 </conditional>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
459 <section name="advanced_common">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
460 <param name="show_log" value="true"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
461 </section>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
462 <output name="hidden_output">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
463 <assert_contents>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
464 <has_text_matching expression="snap.tl.leiden"/>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
465 <has_text_matching expression="resolution = 2"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
466 <has_text_matching expression="objective_function = 'modularity'"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
467 <has_text_matching expression="min_cluster_size = 3"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
468 <has_text_matching expression="n_iterations = -1"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
469 <has_text_matching expression="random_state = 0"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
470 <has_text_matching expression="key_added = 'leiden'"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
471 <has_text_matching expression="weighted = False"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
472 </assert_contents>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
473 </output>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
474 <output name="anndata_out" ftype="h5ad">
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
475 <assert_contents>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
476 <has_h5_keys keys="obs/leiden"/>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
477 </assert_contents>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
478 </output>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
479 </test>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
480 <test expect_num_outputs="2">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
481 <!-- tl.leiden -->
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
482 <conditional name="method">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
483 <param name="method" value="tl.leiden"/>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
484 <param name="adata" location="https://zenodo.org/records/17512085/files/pp.knn.pbmc_500_chr21.h5ad"/>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
485 <param name="resolution" value="2"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
486 <param name="objective_function" value="RBConfiguration"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
487 <param name="min_cluster_size" value="3"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
488 <param name="n_iterations" value="-1"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
489 <param name="random_state" value="0"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
490 <param name="key_added" value="leiden"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
491 <param name="weighted" value="False"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
492 </conditional>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
493 <section name="advanced_common">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
494 <param name="show_log" value="true"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
495 </section>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
496 <output name="hidden_output">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
497 <assert_contents>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
498 <has_text_matching expression="snap.tl.leiden"/>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
499 <has_text_matching expression="resolution = 2"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
500 <has_text_matching expression="objective_function = 'RBConfiguration'"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
501 <has_text_matching expression="min_cluster_size = 3"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
502 <has_text_matching expression="n_iterations = -1"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
503 <has_text_matching expression="random_state = 0"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
504 <has_text_matching expression="key_added = 'leiden'"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
505 <has_text_matching expression="weighted = False"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
506 </assert_contents>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
507 </output>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
508 <output name="anndata_out" ftype="h5ad">
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
509 <assert_contents>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
510 <has_h5_keys keys="obs/leiden"/>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
511 </assert_contents>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
512 </output>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
513 </test>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
514 <test expect_num_outputs="2">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
515 <!-- tl.kmeans -->
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
516 <conditional name="method">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
517 <param name="method" value="tl.kmeans"/>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
518 <param name="adata" location="https://zenodo.org/records/17512085/files/tl.spectral.pbmc_500_chr21.h5ad"/>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
519 <param name="n_iterations" value="-1"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
520 <param name="random_state" value="0"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
521 <param name="use_rep" value="X_spectral"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
522 <param name="key_added" value="kmeans"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
523 </conditional>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
524 <section name="advanced_common">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
525 <param name="show_log" value="true"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
526 </section>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
527 <output name="hidden_output">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
528 <assert_contents>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
529 <has_text_matching expression="snap.tl.kmeans"/>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
530 <has_text_matching expression="n_iterations = -1"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
531 <has_text_matching expression="random_state = 0"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
532 <has_text_matching expression="use_rep = 'X_spectral'"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
533 <has_text_matching expression="key_added = 'kmeans'"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
534 </assert_contents>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
535 </output>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
536 <output name="anndata_out" ftype="h5ad">
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
537 <assert_contents>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
538 <has_h5_keys keys="obs/kmeans"/>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
539 </assert_contents>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
540 </output>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
541 </test>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
542 <test expect_num_outputs="2">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
543 <!-- tl.dbscan -->
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
544 <conditional name="method">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
545 <param name="method" value="tl.dbscan"/>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
546 <param name="adata" location="https://zenodo.org/records/17512085/files/tl.spectral.pbmc_500_chr21.h5ad"/>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
547 <param name="eps" value="0.5"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
548 <param name="min_samples" value="3"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
549 <param name="leaf_size" value="5"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
550 <param name="use_rep" value="X_spectral"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
551 <param name="key_added" value="dbscan"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
552 </conditional>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
553 <section name="advanced_common">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
554 <param name="show_log" value="true"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
555 </section>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
556 <output name="hidden_output">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
557 <assert_contents>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
558 <has_text_matching expression="snap.tl.dbscan"/>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
559 <has_text_matching expression="eps = 0.5"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
560 <has_text_matching expression="min_samples = 3"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
561 <has_text_matching expression="leaf_size = 5"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
562 <has_text_matching expression="use_rep = 'X_spectral'"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
563 <has_text_matching expression="key_added = 'dbscan'"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
564 </assert_contents>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
565 </output>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
566 <output name="anndata_out" ftype="h5ad">
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
567 <assert_contents>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
568 <has_h5_keys keys="obs/dbscan"/>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
569 </assert_contents>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
570 </output>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
571 </test>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
572 <test expect_num_outputs="2">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
573 <!-- tl.hdbscan -->
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
574 <conditional name="method">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
575 <param name="method" value="tl.hdbscan"/>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
576 <param name="adata" location="https://zenodo.org/records/17512085/files/tl.spectral.pbmc_500_chr21.h5ad"/>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
577 <param name="min_cluster_size" value="3"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
578 <param name="min_samples" value="3"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
579 <param name="cluster_selection_method" value="eom"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
580 <param name="random_state" value="0"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
581 <param name="use_rep" value="X_spectral"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
582 <param name="key_added" value="hdbscan"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
583 </conditional>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
584 <section name="advanced_common">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
585 <param name="show_log" value="true"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
586 </section>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
587 <output name="hidden_output">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
588 <assert_contents>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
589 <has_text_matching expression="snap.tl.hdbscan"/>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
590 <has_text_matching expression="min_cluster_size = 3"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
591 <has_text_matching expression="min_samples = 3"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
592 <has_text_matching expression="cluster_selection_method = 'eom'"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
593 <has_text_matching expression="random_state = 0"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
594 <has_text_matching expression="use_rep = 'X_spectral'"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
595 <has_text_matching expression="key_added = 'hdbscan'"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
596 </assert_contents>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
597 </output>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
598 <output name="anndata_out" ftype="h5ad">
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
599 <assert_contents>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
600 <has_h5_keys keys="obs/hdbscan"/>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
601 </assert_contents>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
602 </output>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
603 </test>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
604 <!-- <test expect_num_outputs="2">
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
605 tl.aggregate_X
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
606 <conditional name="method">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
607 <param name="method" value="tl.aggregate_X"/>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
608 <param name="adata" location="https://zenodo.org/records/17512085/files/tl.spectral.pbmc_500_chr21.h5ad"/>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
609 <param name="normalize" value="RPKM"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
610 </conditional>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
611 <section name="advanced_common">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
612 <param name="show_log" value="true"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
613 </section>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
614 <output name="hidden_output">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
615 <assert_contents>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
616 <has_text_matching expression="snap.tl.aggregate_X"/>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
617 <has_text_matching expression="normalize = 'RPKM'"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
618 </assert_contents>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
619 </output>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
620 <output name="anndata_out" ftype="h5ad">
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
621 <assert_contents>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
622 <has_h5_keys keys="obs/n_fragment"/>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
623 </assert_contents>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
624 </output>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
625 </test> -->
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
626 <test expect_num_outputs="2">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
627 <!-- tl.aggregate_cells -->
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
628 <conditional name="method">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
629 <param name="method" value="tl.aggregate_cells"/>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
630 <param name="adata" location="https://zenodo.org/records/17512085/files/tl.spectral.pbmc_500_chr21.h5ad"/>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
631 <param name="use_rep" value="X_spectral"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
632 <param name="target_num_cells" value="5"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
633 <param name="min_cluster_size" value="3"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
634 <param name="random_state" value="0"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
635 <param name="key_added" value="pseudo_cell"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
636 </conditional>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
637 <section name="advanced_common">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
638 <param name="show_log" value="true"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
639 </section>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
640 <output name="hidden_output">
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
641 <assert_contents>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
642 <has_text_matching expression="snap.tl.aggregate_cells"/>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
643 <has_text_matching expression="use_rep = 'X_spectral'"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
644 <has_text_matching expression="target_num_cells = 5"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
645 <has_text_matching expression="min_cluster_size = 3"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
646 <has_text_matching expression="random_state = 0"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
647 <has_text_matching expression="key_added = 'pseudo_cell'"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
648 </assert_contents>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
649 </output>
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
650 <output name="anndata_out" ftype="h5ad">
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
651 <assert_contents>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
652 <has_h5_keys keys="obs/pseudo_cell"/>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
653 </assert_contents>
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
654 </output>
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
655 </test>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
656 </tests>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
657 <help><![CDATA[
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
658 Perform dimension reduction using Laplacian Eigenmap, using `tl.spectral`
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
659 =========================================================================
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
660
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
661 Perform dimension reduction using Laplacian Eigenmaps.
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
662
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
663 Convert the cell-by-feature count matrix into lower dimensional representations using the spectrum of the normalized graph Laplacian defined by pairwise similarity between cells. This function utilizes the matrix-free spectral embedding algorithm to compute the embedding when `distance_metric` is “cosine”, which scales linearly with the number of cells. For other types of similarity metrics, the time and space complexity scale quadratically with the number of cells.
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
664
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
665 More details on the `SnapATAC2 documentation
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
666 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.tl.spectral.html>`__
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
667
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
668 Compute Laplacian Eigenmaps simultaneously on multiple modalities, with linear space and time complexity, using `tl.multi_spectral`
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
669 ===================================================================================================================================
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
670
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
671 This is similar to `spectral`, but it can work on multiple modalities.
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
672
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
673 More details on the `SnapATAC2 documentation
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
674 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.tl.multi_spectral.html>`__
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
675
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
676 Compute Umap, using `tl.umap`
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
677 =============================
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
678
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
679 Compute Umap
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
680
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
681 More details on the `SnapATAC2 documentation
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
682 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.tl.umap.html>`__
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
683
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
684 Compute a neighborhood graph of observations, using `pp.knn`
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
685 ============================================================
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
686
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
687 Compute a neighborhood graph of observations.
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
688
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
689 Computes a neighborhood graph of observations stored in adata using the method specified by method. The distance metric used is Euclidean.
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
690
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
691 More details on the `SnapATAC2 documentation
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
692 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.knn.html>`__
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
693
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
694 Cluster cells into subgroups, using `tl.leiden`
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
695 ===============================================
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
696
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
697 Cluster cells into subgroups.
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
698
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
699 Cluster cells using the Leiden algorithm, an improved version of the Louvain algorithm. It has been proposed for single-cell analysis by. This requires having ran `knn`.
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
700
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
701 More details on the `SnapATAC2 documentation
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
702 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.tl.leiden.html>`__
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
703
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
704 Cluster cells into subgroups using the K-means algorithm, using `tl.kmeans`
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
705 ===========================================================================
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
706
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
707 Cluster cells into subgroups using the K-means algorithm, a classical algorithm in data mining.
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
708
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
709 More details on the `SnapATAC2 documentation
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
710 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.tl.kmeans.html>`__
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
711
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
712 Cluster cells into subgroups using the DBSCAN algorithm, using `tl.dbscan`
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
713 ==========================================================================
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
714
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
715 Cluster cells into subgroups using the DBSCAN algorithm.
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
716
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
717 More details on the `SnapATAC2 documentation
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
718 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.tl.dbscan.html>`__
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
719
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
720 Cluster cells into subgroups using the HDBSCAN algorithm, using `tl.hdbscan`
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
721 ============================================================================
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
722
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
723 Cluster cells into subgroups using the HDBSCAN algorithm.
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
724
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
725 More details on the `SnapATAC2 documentation
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
726 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.tl.hdbscan.html>`__
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
727
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
728 .. Aggregate values in adata.X in a row-wise fashion, using `tl.aggregate_X`
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
729 .. =========================================================================
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
730
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
731 .. Aggregate values in adata.X in a row-wise fashion.
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
732
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
733 .. Aggregate values in adata.X in a row-wise fashion. This is used to compute RPKM or RPM values stratified by user-provided groupings.
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
734
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
735 .. More details on the `SnapATAC2 documentation
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
736 .. <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.tl.aggregate_X.html>`__
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
737
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
738 Aggregate cells into pseudo-cells, using `tl.aggregate_cells`
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
739 =============================================================
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
740
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
741 Aggregate cells into pseudo-cells.
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
742
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
743 Aggregate cells into pseudo-cells by iterative clustering.
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
744
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
745 More details on the `SnapATAC2 documentation
4
d60c2415e7ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
746 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.tl.aggregate_cells.html>`__
0
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
747 ]]></help>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
748 <expand macro="citations"/>
6eb1e0ef8f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
749 </tool>