Mercurial > repos > iuc > scanpy_remove_confounders

annotate remove_confounders.xml @ 19:cb5846ad91ff draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy commit a6bd86a67a159906ff55e8b2dedda71d019d3caf
author iuc
date Wed, 03 Dec 2025 09:59:56 +0000
parents e078f7503d29
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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1 <tool id="scanpy_remove_confounders" name="Scanpy remove confounders" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>with scanpy</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements">
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8 <requirement type="package" version="1.6.0">bbknn</requirement>
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9 <requirement type="package" version="0.0.10">harmonypy</requirement>
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10 <requirement type="package" version="1.7.4">scanorama</requirement>
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11 <requirement type="package" version="0.5.13">pynndescent</requirement>
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12 </expand>
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13 <command detect_errors="exit_code"><![CDATA[
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14 @CMD@
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15 ]]></command>
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16 <configfiles>
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17 <configfile name="script_file"><![CDATA[
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18 @CMD_IMPORTS@
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19 @CMD_READ_INPUTS@
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21 #if str($method.method) == 'pp.regress_out':
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22 print("stats before regress_out:", "min=", adata.X.min(), "max=", adata.X.max(), "mean=", adata.X.mean())
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24 import os
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25 sc.pp.regress_out(
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26 adata=adata,
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27 #if str($method.layer) != '':
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28 layer='$method.layer',
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29 #end if
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30 #set $keys = [str(x.strip()) for x in str($method.keys).split(',')]
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31 keys=$keys,
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32 n_jobs = int(os.getenv("GALAXY_SLOTS", 4)),
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33 copy=False)
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34
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35 print("stats after regress_out:", "min=", adata.X.min(), "max=", adata.X.max(), "mean=", adata.X.mean())
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36
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37 ## This function is commented out because the conda package is not working. Please add this if there is user demand and the conda package is fixed. If not please remove in the next update.
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38 ## #else if str($method.method) == 'external.pp.mnn_correct':
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39 ## #if $method.extra_adata:
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40 ## #for i, filepath in enumerate($method.extra_adata)
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41 ## adata_$i = sc.read_h5ad('$filepath')
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42 ## #end for
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43 ## #end if
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44 ## import os
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45 ## corrected = sc.external.pp.mnn_correct(
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46 ## adata,
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47 ## #if $method.extra_adata:
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48 ## #for i, filepath in enumerate($method.extra_adata)
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49 ## adata_$i,
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50 ## #end for
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51 ## #end if
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52 ## #if str($method.var_subset) != '':
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53 ## #set $var_subset=([x.strip() for x in str($method.var_subset).split(',')])
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54 ## var_subset=$var_subset,
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55 ## #end if
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56 ## batch_key='$method.batch_key',
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57 ## index_unique='$method.index_unique',
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58 ## #if str($method.batch_categories) != '':
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59 ## #set $batch_categories=([x.strip() for x in str($method.batch_categories).split(',')])
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60 ## batch_categories=$batch_categories,
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61 ## #end if
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62 ## k=$method.k,
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63 ## sigma=$method.sigma,
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64 ## cos_norm_in=$method.cos_norm_in,
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65 ## cos_norm_out=$method.cos_norm_out,
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66 ## #if str($method.svd_dim) != '':
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67 ## svd_dim=$method.svd_dim,
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68 ## #end if
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69 ## var_adj=$method.var_adj,
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70 ## compute_angle=$method.compute_angle,
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71 ## #if str($method.mnn_order) != '':
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72 ## mnn_order='$method.mnn_order',
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73 ## #end if
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74 ## #if str($method.svd_mode) != '':
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75 ## svd_mode='$method.svd_mode',
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76 ## #end if
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77 ## do_concatenate=True,
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78 ## save_raw=True,
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79 ## n_jobs = int(os.getenv("GALAXY_SLOTS", 4)))
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81 ## adata = corrected[0]
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84 #else if str($method.method) == 'pp.combat':
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85 print("stats before combat:", "min=", adata.X.min(), "max=", adata.X.max(), "mean=", adata.X.mean())
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86
1
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87 sc.pp.combat(
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88 adata,
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89 key='$method.key',
14
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90 #if str($method.covariates) != '':
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91 #set $covariates = [str(x.strip()) for x in str($method.covariates).split(',')]
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92 covariates=$covariates,
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93 #end if
1
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94 inplace=True)
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95
14
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96 print("stats after combat:", "min=", adata.X.min(), "max=", adata.X.max(), "mean=", adata.X.mean())
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97
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98 #else if str($method.method) == 'external.pp.bbknn':
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99 sc.external.pp.bbknn(
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100 adata,
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101 batch_key='$method.batch_key',
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102 use_rep='$method.use_rep',
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103 #if str($method.approx.approx_method) == 'no':
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104 approx=False,
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105 #else if str($method.approx.approx_method) == 'annoy':
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106 approx=True,
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107 use_annoy=True,
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108 annoy_n_trees=$method.approx.annoy_n_trees,
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109 #else if str($method.approx.approx_method) == 'pyNNDescent':
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110 approx=True,
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111 use_annoy=False,
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112 pynndescent_n_neighbors=$method.approx.pynndescent_n_neighbors,
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113 pynndescent_random_state=$method.approx.pynndescent_random_state,
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114 #end if
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115 metric='$method.metric',
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116 neighbors_within_batch=$method.neighbors_within_batch,
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117 n_pcs=$method.n_pcs,
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118 #if str($method.trim) != '':
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119 trim=$method.trim,
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120 #end if
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121 set_op_mix_ratio=$method.set_op_mix_ratio,
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122 local_connectivity=$method.local_connectivity,
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123 copy=False)
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124
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125 #else if str($method.method) == 'external.pp.harmony_integrate':
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126 sc.external.pp.harmony_integrate(
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127 adata,
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128 key='$method.key',
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129 basis='$method.basis',
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130 adjusted_basis='$method.adjusted_basis',
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131 #if str($method.theta) != '':
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132 theta=$method.theta,
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133 #end if
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134 #if str($method.lamb) != '':
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135 lamb=$method.lamb,
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136 #end if
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137 sigma=$method.sigma,
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138 #if str($method.nclust) != '':
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139 nclust=$method.nclust,
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140 #end if
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141 tau=$method.tau,
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142 block_size=$method.block_size,
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143 max_iter_harmony=$method.max_iter_harmony,
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144 max_iter_kmeans=$method.max_iter_kmeans,
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145 epsilon_cluster=$method.epsilon_cluster,
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146 epsilon_harmony=$method.epsilon_harmony)
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147
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148 #else if str($method.method) == 'external.pp.scanorama_integrate':
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149 sc.external.pp.scanorama_integrate(
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150 adata,
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151 key='$method.key',
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152 basis='$method.basis',
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153 adjusted_basis='$method.adjusted_basis',
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154 knn=$method.knn,
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155 sigma=$method.sigma,
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156 approx=$method.approx,
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157 alpha=$method.alpha,
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158 batch_size=$method.batch_size)
0
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159 #end if
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160
14
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161 @CMD_ANNDATA_WRITE_OUTPUTS@
0
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162 ]]></configfile>
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163 </configfiles>
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164 <inputs>
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165 <expand macro="inputs_anndata"/>
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166 <conditional name="method">
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167 <param argument="method" type="select" label="Method used for plotting">
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168 <option value="pp.regress_out">Regress out unwanted sources of variation, using 'pp.regress_out'</option>
14
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169 <!-- This function is commented out because the conda package is not working. Please add this if there is user demand and the conda package is fixed. If not please remove in the next update. -->
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170 <!-- <option value="external.pp.mnn_correct">Correct batch effects by matching mutual nearest neighbors, using 'pp.mnn_correct'</option> -->
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171 <option value="pp.combat">Correct batch effects with ComBat function, using 'pp.combat'</option>
14
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172 <option value="external.pp.bbknn">Batch effect removal with Batch balanced KNN (BBKNN), using 'external.pp.bbknn'</option>
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173 <option value="external.pp.harmony_integrate">Integrate multiple single-cell experiments with Harmony, using 'external.pp.harmony_integrate'</option>
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174 <option value="external.pp.scanorama_integrate">Integrate multiple single-cell experiments with Scanorama, using 'external.pp.scanorama_integrate'</option>
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175 </param>
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176 <when value="pp.regress_out">
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177 <param argument="layer" type="text" value="" label="Which element of layers to regress on">
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178 <expand macro="sanitize_query"/>
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179 </param>
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180 <param argument="keys" type="text" value="" label="Keys for observation annotation on which to regress on" help="Keys separated by a comma">
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181 <expand macro="sanitize_query"/>
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182 </param>
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183 </when>
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184 <!-- This function is commented out because the conda package is not working. Please add this if there is user demand and the conda package is fixed. If not please remove in the next update. -->
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185 <!-- <when value="external.pp.mnn_correct">
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186 <param name="extra_adata" type="data" multiple="true" optional="true" format="h5ad" label="Extra annotated data matrix" help="They should have same number of variables."/>
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187 <param argument="var_subset" type="text" value="" optional="true" label="The subset of vars to be used when performing MNN correction" help="List of comma-separated key from '.var_names'. If not set, all vars are used">
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188 <expand macro="sanitize_query"/>
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189 </param>
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190 <param argument="batch_key" type="text" value="batch" label="Batch key for the concatenate">
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191 <expand macro="sanitize_query"/>
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192 </param>
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193 <param name="index_unique" type="select" label="Separator to join the existing index names with the batch category" help="Leave it empty to keep existing indices">
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194 <option value="-">-</option>
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195 <option value="_">_</option>
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196 <option value=" "> </option>
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197 <option value="/">/</option>
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198 </param>
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199 <param argument="batch_categories" type="text" value="" optional="true" label="Batch categories for the concatenate" help="List of comma-separated key">
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200 <expand macro="sanitize_query"/>
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201 </param>
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202 <param argument="k" type="integer" value="20" label="Number of mutual nearest neighbors"/>
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203 <param argument="sigma" type="float" value="1" label="The bandwidth of the Gaussian smoothing kernel used to compute the correction vectors"/>
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204 <param argument="cos_norm_in" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Should cosine normalization be performed on the input data prior to calculating distances between cells?"/>
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205 <param argument="cos_norm_out" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Should cosine normalization be performed prior to computing corrected expression values?"/>
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206 <param argument="svd_dim" type="integer" value="" optional="true" label="Number of dimensions to use for summarizing biological substructure within each batch" help="If not set, biological components will not be removed from the correction vectors."/>
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207 <param argument="var_adj" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Adjust variance of the correction vectors?" help="This step takes most computing time."/>
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208 <param argument="compute_angle" type="boolean" truevalue="True" falsevalue="False" checked="false" label="compute the angle between each cell’s correction vector and the biological subspace of the reference batch?"/>
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209 <param argument="mnn_order" type="text" value="" optional="true" label="The order in which batches are to be corrected" help="List of comma-separated key. If not set, datas are corrected sequentially">
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210 <expand macro="sanitize_query"/>
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211 </param>
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212 <param name="svd_mode" type="select" label="SVD mode">
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213 <option value="svd">svd: SVD using a non-randomized SVD-via-ID algorithm</option>
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214 <option value="rsvd" selected="true">rsvd: SVD using a randomized SVD-via-ID algorithm</option>
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215 <option value="irlb">irlb: truncated SVD by implicitly restarted Lanczos bidiagonalization</option>
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216 </param>
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217 </when> -->
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218 <when value="pp.combat">
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219 <param argument="key" type="text" value="batch" label="Key to a categorical annotation from adata.obs that will be used for batch effect removal">
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220 <expand macro="sanitize_query"/>
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221 </param>
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222 <param argument="covariates" type="text" value="" optional="true" label="Additional covariates besides the batch variable such as adjustment variables or biological condition.">
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223 <expand macro="sanitize_query"/>
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224 </param>
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225 </when>
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226 <when value="external.pp.bbknn">
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227 <param argument="batch_key" type="text" value="batch" label="Batch key for the concatenate">
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228 <expand macro="sanitize_query"/>
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229 </param>
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230 <param argument="use_rep" type="text" value="X_pca" label="The dimensionality reduction in .obsm to use for neighbour detection">
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231 <expand macro="sanitize_query"/>
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232 </param>
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233 <conditional name="approx">
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234 <param name="approx_method" type="select" label="Approximate neighbour finding">
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235 <option value="annoy" selected="true">Yes, using ANNOY algorithm</option>
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236 <option value="pyNNDescent">Yes, using pyNNDescent</option>
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237 <option value="no">Do not use approximate neighbor finding</option>
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238 </param>
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239 <when value="annoy">
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240 <param argument="annoy_n_trees" type="integer" value="10" label="The number of trees to construct in the annoy forest" help="More trees give higher precision when querying, at the cost of increased run time and resource intensity"/>
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241 </when>
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242 <when value="pyNNDescent">
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243 <param argument="pynndescent_n_neighbors" type="integer" value="30" label="The number of neighbours to include in the approximate neighbour graph" help="More neighbours give higher precision when querying, at the cost of increased run time and resource intensity"/>
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244 <param argument="pynndescent_random_state" type="integer" value="0" label="The RNG seed to use when creating the graph"/>
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245 </when>
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246 <when value="no"/>
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247 </conditional>
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248 <param name="metric" type="select" label="Distance metric to use for the data">
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249 <expand macro="distance_metric_options"/>
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250 </param>
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251 <param argument="neighbors_within_batch" type="integer" value="3" label="Number of top neighbours to report for each batch" help="total number of neighbours in the initial k-nearest-neighbours computation will be this number times the number of batches. This then serves as the basis for the construction of a symmetrical matrix of connectivities"/>
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252 <param argument="n_pcs" type="integer" value="50" label="Number of dimensions to use in the analysis" help="in case of PCA, principal components"/>
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253 <param argument="trim" type="integer" value="" optional="true" label="Trim the neighbours of each cell to these many top connectivities" help=" The lower the value the more independent the individual populations, at the cost of more conserved batch effect. If not set, sets the parameter value automatically to 10 times neighbors_within_batch times the number of batches. Set to 0 to skip."/>
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254 <param argument="set_op_mix_ratio" type="float" value="1.0" min="0" max="1" label="UMAP connectivity computation parameter" help="controlling the blend between a connectivity matrix formed exclusively from mutual nearest neighbour pairs (0) and a union of all observed neighbour relationships with the mutual pairs emphasised (1)"/>
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255 <param argument="local_connectivity" type="integer" value="1" label="Number of nearest neighbors of each cell are assumed to be fully connected"/>
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256 </when>
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257 <when value="external.pp.harmony_integrate">
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258 <param argument="key" type="text" value="batch" label="The name of the column in adata.obs that differentiates among experiments/batches">
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259 <expand macro="sanitize_query"/>
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260 </param>
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261 <param argument="basis" type="text" value="X_pca" label="The name of the field in adata.obsm where the PCA table is stored">
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262 <expand macro="sanitize_query"/>
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263 </param>
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264 <param argument="adjusted_basis" type="text" value="X_pca_harmony" label="The name of the field in adata.obsm where the adjusted PCA table will be stored after running this function">
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265 <expand macro="sanitize_query"/>
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266 </param>
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267 <param argument="theta" type="integer" value="" optional="true" label="Diversity clustering penalty parameter" help="Default theta=2. theta=0 does not encourage any diversity. Larger values of theta result in more diverse clusters."/>
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268 <param argument="lamb" type="integer" value="" optional="true" min="1" label="Ridge regression penalty parameter" help="Default lamb=1. Lambda must be strictly positive. Smaller values result in more aggressive correction."/>
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269 <param argument="sigma" type="float" value="0.1" label="Width of soft kmeans clusters" help="Sigma scales the distance from a cell to cluster centroids. Larger values of sigma result in cells assigned to more clusters. Smaller values of sigma make soft kmeans cluster approach hard clustering."/>
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270 <param argument="nclust" type="integer" value="" optional="true" label="Number of clusters in model" help="nclust=1 equivalent to simple linear regression."/>
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271 <param argument="tau" type="integer" value="0" label="Expected number of cells per cluster" help="Protection against overclustering small datasets with large ones"/>
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272 <param argument="block_size" type="float" value="0.05" min="0" max="1" label="Proportion of cells to update during clustering" help="Larger values may be faster but less accurate"/>
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273 <param argument="max_iter_harmony" type="integer" value="10" label="Maximum number of rounds to run Harmony" help="One round of Harmony involves one clustering and one correction step"/>
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274 <param argument="max_iter_kmeans" type="integer" value="20" label="Maximum number of rounds to run clustering at each round of Harmony"/>
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275 <param argument="epsilon_cluster" type="float" value="1e-5" label="Convergence tolerance for clustering round of Harmony"/>
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276 <param argument="epsilon_harmony" type="float" value="1e-4" label="Convergence tolerance for Harmony"/>
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277 </when>
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278 <when value="external.pp.scanorama_integrate">
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279 <param argument="key" type="text" value="batch" label="The name of the column in adata.obs that differentiates among experiments/batches">
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280 <expand macro="sanitize_query"/>
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281 </param>
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282 <param argument="basis" type="text" value="X_pca" label="The name of the field in adata.obsm where the PCA table is stored">
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283 <expand macro="sanitize_query"/>
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284 </param>
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285 <param argument="adjusted_basis" type="text" value="X_scanorama" label="The name of the field in adata.obsm where the adjusted PCA table will be stored after running this function">
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286 <expand macro="sanitize_query"/>
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287 </param>
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288 <param argument="knn" type="integer" value="20" label="Number of nearest neighbors to use for matching"/>
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289 <param argument="sigma" type="integer" value="15" label="Correction smoothing parameter on Gaussian kernel"/>
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290 <param argument="approx" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Use approximate nearest neighbors with Python annoy" help="greatly speeds up matching runtime"/>
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291 <param argument="alpha" type="float" value="0.1" label="Alignment score minimum cutoff"/>
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292 <param argument="batch_size" type="integer" value="5000" label="The batch size used in the alignment vector computation" help="Useful when integrating very large (>100k samples) datasets. Set to large value that runs within available memory."/>
0
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293 </when>
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294 </conditional>
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295 <expand macro="inputs_common_advanced"/>
0
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296 </inputs>
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297 <outputs>
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298 <expand macro="anndata_outputs"/>
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299 </outputs>
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300 <tests>
14
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301
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302 <!-- test 1 -->
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303 <test expect_num_outputs="2">
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304 <param name="adata" value="pp.pca.krumsiek11.batch.h5ad"/>
0
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305 <conditional name="method">
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306 <param name="method" value="pp.regress_out"/>
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307 <param name="keys" value="batch"/>
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308 </conditional>
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309 <section name="advanced_common">
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310 <param name="show_log" value="true"/>
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311 </section>
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312 <output name="hidden_output">
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313 <assert_contents>
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314 <has_text_matching expression="sc.pp.regress_out"/>
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315 <has_text_matching expression="keys=\['batch'\]"/>
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316 <has_text_matching expression="stats before regress_out: min= -0.0163 max= 1.0106 mean= 0.2864376"/>
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317 <has_text_matching expression="stats after regress_out: min= -0.7017021868145134 max= 0.7091581022301392 mean= -1.730938624756494e-16"/>
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318 </assert_contents>
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319 </output>
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320 <output name="anndata_out" ftype="h5ad">
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321 <assert_contents>
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322 <has_h5_keys keys="varm/PCs"/>
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323 </assert_contents>
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324 </output>
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325 </test>
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326
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327 <!-- This function is commented out because the conda package is not working. Please add this if there is user demand and the conda package is fixed. If not please remove in the next update. -->
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328 <!-- test 2 -->
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329 <!-- <test expect_num_outputs="2">
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330 <param name="adata" value="pp.pca.krumsiek11.batch.h5ad"/>
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331 <param name="extra_adata" value="pp.pca.krumsiek11.batch.h5ad"/>
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332 <conditional name="method">
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333 <param name="method" value="external.pp.mnn_correct"/>
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334 <param name="batch_key" value="batch"/>
0
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335 </conditional>
14
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336 <section name="advanced_common">
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337 <param name="show_log" value="true"/>
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parents: 12
diff changeset
338 </section>
0
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iuc
parents:
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339 <assert_stdout>
14
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diff changeset
340 <has_text_matching expression="I_have_to_check"/>
0
b1ce2f94a938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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341 </assert_stdout>
14
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342 <output name="hidden_output">
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iuc
parents: 12
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343 <assert_contents>
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iuc
parents: 12
diff changeset
344 <has_text_matching expression="sc.external.pp.mnn_correct"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
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345 <has_text_matching expression="batch_key='batch'"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 12
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346 </assert_contents>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 12
diff changeset
347 </output>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 12
diff changeset
348 <output name="anndata_out" file="external.pp.mnn_correct.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
349 </test> -->
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
350
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
351 <!-- test 3 -->
12
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iuc
parents: 10
diff changeset
352 <test expect_num_outputs="2">
14
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iuc
parents: 12
diff changeset
353 <param name="adata" value="pp.pca.krumsiek11.batch.h5ad"/>
0
b1ce2f94a938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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354 <conditional name="method">
1
22bcfed2afc0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
355 <param name="method" value="pp.combat"/>
0
b1ce2f94a938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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356 </conditional>
6
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iuc
parents: 5
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357 <section name="advanced_common">
14
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parents: 12
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358 <param name="show_log" value="true"/>
6
c0fab89336d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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parents: 5
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359 </section>
c0fab89336d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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parents: 5
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360 <output name="hidden_output">
c0fab89336d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
diff changeset
361 <assert_contents>
c0fab89336d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
iuc
parents: 5
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362 <has_text_matching expression="sc.pp.combat"/>
14
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iuc
parents: 12
diff changeset
363 <has_text_matching expression="key='batch'"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
364 <has_text_matching expression="stats before combat: min= -0.0163 max= 1.0106 mean= 0.2864376"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
365 <has_text_matching expression="stats after combat: min= -0.07474318799213325 max= 1.2280063438242503 mean= 0.2870530757430964"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
366 </assert_contents>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
367 </output>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
368 <output name="anndata_out" ftype="h5ad">
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
369 <assert_contents>
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iuc
parents: 12
diff changeset
370 <has_h5_keys keys="obsm/X_pca"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
371 </assert_contents>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
372 </output>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
373 </test>
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iuc
parents: 12
diff changeset
374
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
375 <!-- test 4 -->
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
376 <test expect_num_outputs="2">
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
377 <param name="adata" value="pp.pca.krumsiek11.batch.h5ad"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
378 <conditional name="method">
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
379 <param name="method" value="external.pp.bbknn"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
380 <param name="n_pcs" value="10"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
381 <param name="set_op_mix_ratio" value="0.5"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
382 </conditional>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
383 <section name="advanced_common">
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
384 <param name="show_log" value="true"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
385 </section>
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iuc
parents: 12
diff changeset
386 <output name="hidden_output">
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
387 <assert_contents>
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iuc
parents: 12
diff changeset
388 <has_text_matching expression="external.pp.bbknn"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
389 <has_text_matching expression="batch_key='batch'"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
390 <has_text_matching expression="use_rep='X_pca'"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
391 <has_text_matching expression="use_annoy=True"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
392 <has_text_matching expression="annoy_n_trees=10"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
393 <has_text_matching expression="neighbors_within_batch=3"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
394 <has_text_matching expression="n_pcs=10"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
395 <has_text_matching expression="set_op_mix_ratio=0.5"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
396 </assert_contents>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
397 </output>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
398 <output name="anndata_out" ftype="h5ad">
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
399 <assert_contents>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
400 <has_h5_keys keys="uns/neighbors"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
401 <has_h5_keys keys="obsp/distances,obsp/connectivities"/>
6
c0fab89336d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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parents: 5
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402 </assert_contents>
c0fab89336d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
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parents: 5
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403 </output>
14
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parents: 12
diff changeset
404 </test>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
405
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
406 <!-- test 5 -->
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
407 <test expect_num_outputs="2">
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
408 <param name="adata" value="pp.pca.krumsiek11.batch.h5ad"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
409 <conditional name="method">
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
410 <param name="method" value="external.pp.bbknn"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
411 <conditional name="approx">
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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diff changeset
412 <param name="approx_method" value="pyNNDescent"/>
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iuc
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diff changeset
413 <param name="pynndescent_n_neighbors" value="10"/>
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iuc
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diff changeset
414 </conditional>
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diff changeset
415 <param name="n_pcs" value="10"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
416 <param name="set_op_mix_ratio" value="0.5"/>
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iuc
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diff changeset
417 </conditional>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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diff changeset
418 <section name="advanced_common">
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
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419 <param name="show_log" value="true"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
420 </section>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
421 <output name="hidden_output">
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
422 <assert_contents>
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iuc
parents: 12
diff changeset
423 <has_text_matching expression="external.pp.bbknn"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
424 <has_text_matching expression="batch_key='batch'"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
425 <has_text_matching expression="use_rep='X_pca'"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
426 <has_text_matching expression="use_annoy=False"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
427 <has_text_matching expression="pynndescent_n_neighbors=10"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
428 <has_text_matching expression="pynndescent_random_state=0"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
429 <has_text_matching expression="neighbors_within_batch=3"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
430 <has_text_matching expression="n_pcs=10"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
431 <has_text_matching expression="set_op_mix_ratio=0.5"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
432 </assert_contents>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
433 </output>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
434 <output name="anndata_out" ftype="h5ad">
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
435 <assert_contents>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
436 <has_h5_keys keys="uns/neighbors"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
437 <has_h5_keys keys="obsp/distances,obsp/connectivities"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
438 </assert_contents>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
439 </output>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
440 </test>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
441
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
442 <!-- test 6 -->
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
443 <test expect_num_outputs="2">
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
444 <param name="adata" value="pp.pca.krumsiek11.batch.h5ad"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
445 <conditional name="method">
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
446 <param name="method" value="external.pp.harmony_integrate"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
447 <param name="theta" value="2"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
448 <param name="lamb" value="1"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
449 <param name="block_size" value="0.1"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
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450 </conditional>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
451 <section name="advanced_common">
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
452 <param name="show_log" value="true"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
453 </section>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
454 <output name="hidden_output">
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
455 <assert_contents>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
456 <has_text_matching expression="external.pp.harmony_integrate"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
457 <has_text_matching expression="key='batch'"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
458 <has_text_matching expression="basis='X_pca'"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
459 <has_text_matching expression="adjusted_basis='X_pca_harmony'"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
460 <has_text_matching expression="theta=2"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
461 <has_text_matching expression="lamb=1"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
462 <has_text_matching expression="block_size=0.1"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
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463 </assert_contents>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
464 </output>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
465 <output name="anndata_out" ftype="h5ad">
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
466 <assert_contents>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
467 <has_h5_keys keys="obsm/X_pca_harmony"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
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468 </assert_contents>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
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469 </output>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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diff changeset
470 </test>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
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471
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
472 <!-- test 7 -->
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
473 <test expect_num_outputs="2">
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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diff changeset
474 <param name="adata" value="pp.pca.krumsiek11.batch.h5ad"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
475 <conditional name="method">
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
476 <param name="method" value="external.pp.scanorama_integrate"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
diff changeset
477 <param name="knn" value="2"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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diff changeset
478 <param name="sigma" value="10"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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479 <param name="batch_size" value="100"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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480 </conditional>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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diff changeset
481 <section name="advanced_common">
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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482 <param name="show_log" value="true"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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483 </section>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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484 <output name="hidden_output">
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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485 <assert_contents>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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486 <has_text_matching expression="external.pp.scanorama_integrate"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
parents: 12
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487 <has_text_matching expression="key='batch'"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 12
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488 <has_text_matching expression="basis='X_pca'"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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489 <has_text_matching expression="adjusted_basis='X_scanorama'"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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490 <has_text_matching expression="knn=2"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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491 <has_text_matching expression="sigma=1"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
iuc
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492 <has_text_matching expression="batch_size=100"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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493 </assert_contents>
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diff changeset
494 </output>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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parents: 12
diff changeset
495 <output name="anndata_out" ftype="h5ad">
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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496 <assert_contents>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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497 <has_h5_keys keys="obsm/X_scanorama"/>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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498 </assert_contents>
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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499 </output>
0
b1ce2f94a938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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500 </test>
b1ce2f94a938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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501 </tests>
b1ce2f94a938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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502 <help><![CDATA[
b1ce2f94a938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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503 Regress out unwanted sources of variation, using `pp.regress_out`
b1ce2f94a938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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504 =================================================================
b1ce2f94a938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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505
14
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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506 Regress out unwanted sources of variation, using simple linear regression. This is
0
b1ce2f94a938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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507 inspired by Seurat's `regressOut` function in R.
b1ce2f94a938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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508
b1ce2f94a938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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509 More details on the `scanpy documentation
12
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510 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.regress_out.html>`__
0
b1ce2f94a938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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511
14
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512 .. This function is commented out because the conda package is not working. Please add this if there is user demand and the conda package is fixed. If not please remove in the next update.
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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513 .. Correct batch effects by matching mutual nearest neighbors, using `external.pp.mnn_correct`
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514 .. ===========================================================================================
0
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515
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516 .. This uses the implementation of mnnpy. Depending on do_concatenate, it returns AnnData objects in the
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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517 .. original order containing corrected expression values or a concatenated matrix or AnnData object.
0
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518
14
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519 .. Be reminded that it is not advised to use the corrected data matrices for differential expression testing.
0
b1ce2f94a938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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520
14
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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521 .. More details on the `scanpy documentation
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522 .. <https://scanpy.readthedocs.io/en/stable/generated/scanpy.external.pp.mnn_correct.html>`__
1
22bcfed2afc0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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523
0
b1ce2f94a938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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524
1
22bcfed2afc0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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525 Correct batch effects with ComBat function (`pp.combat`)
22bcfed2afc0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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526 ========================================================
0
b1ce2f94a938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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527
1
22bcfed2afc0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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528 Corrects for batch effects by fitting linear models, gains statistical power via an EB framework where information is borrowed across genes. This uses the implementation of ComBat
0
b1ce2f94a938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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529
b1ce2f94a938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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530 More details on the `scanpy documentation
12
25ab7843ad7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
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531 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.combat.html>`__
1
22bcfed2afc0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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532
22bcfed2afc0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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533
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534 Correct batch effects with bbknn function (`external.pp.bbknn`)
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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535 ===============================================================
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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536
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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537 Batch balanced kNN alters the kNN procedure to identify each cell’s top neighbours in each batch separately instead of the entire cell pool with no accounting for batch. The nearest neighbours for each batch are then merged to create a final list of neighbours for the cell. Aligns batches in a quick and lightweight manner.
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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538
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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539 More details on the `scanpy documentation
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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540 <https://scanpy.readthedocs.io/en/stable/generated/scanpy.external.pp.bbknn.html>`__
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541
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542
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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543 Correct batch effects with harmony function (`external.pp.harmony_integrate`)
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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544 =============================================================================
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545
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546 Harmony is an algorithm for integrating single-cell data from multiple experiments.
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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547 As Harmony works by adjusting the principal components, this function should be run after performing PCA but before computing the neighbor graph.
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548
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549 More details on the `scanpy documentation
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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550 <https://scanpy.readthedocs.io/en/stable/generated/scanpy.external.pp.harmony_integrate.html>`__
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551
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552
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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553 Correct batch effects with scanprama function (`external.pp.scanorama_integrate`)
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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554 =================================================================================
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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555
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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556 Scanprama is an algorithm for integrating single-cell data from multiple experiments stored in an AnnData object. This function should be run after performing PCA but before computing the neighbor graph.
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557
e078f7503d29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb
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558 More details on the `scanpy documentation
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559 <https://scanpy.readthedocs.io/en/stable/generated/scanpy.external.pp.scanorama_integrate.html>`__
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560
0
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561 ]]></help>
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562 <expand macro="citations"/>
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563 </tool>