Mercurial > repos > iuc > anndata_manipulate

annotate manipulate.xml @ 13:7e8c677a7b71 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
author iuc
date Sat, 14 Sep 2024 19:58:00 +0000
parents ed4996a16f7f
children
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13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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1 <tool id="anndata_manipulate" name="Manipulate AnnData" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>object</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <xml name="param_join">
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6 <param name="join" type="select" label="The connecting string between name and integer">
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7 <option value="-">-</option>
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8 <option value="_">_</option>
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9 <option value=" "> </option>
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10 <option value="/">/</option>
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11 </param>
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12 </xml>
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13 </macros>
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14 <expand macro="requirements"/>
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15 <expand macro="version_command"/>
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16 <command detect_errors="exit_code"><![CDATA[
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17 @CMD@
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18 ]]></command>
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19 <configfiles>
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20 <configfile name="script_file"><![CDATA[
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21 @CMD_imports@
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22
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23 adata = ad.read_h5ad('$input')
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25 #if $manipulate.function == 'concatenate'
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26 #for i, filepath in enumerate($manipulate.other_adatas)
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27 adata_$i = ad.read_h5ad('$filepath')
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28 #end for
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29 adata = adata.concatenate(
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30 #for i, filepath in enumerate($manipulate.other_adatas)
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31 adata_$i,
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32 #end for
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33 join='$manipulate.join',
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34 #if str($manipulate.index_unique) != ''
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35 index_unique='$manipulate.index_unique',
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36 #else
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37 index_unique=None,
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38 #end if
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39 batch_key='$manipulate.batch_key')
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40
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41 #else if $manipulate.function == 'var_names_make_unique'
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42 adata.var_names_make_unique(join='$manipulate.join')
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43
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44 #else if $manipulate.function == 'obs_names_make_unique'
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45 adata.obs_names_make_unique(join='$manipulate.join')
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46
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47 #else if $manipulate.function == 'rename_categories'
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48 #set $categories = [x.strip() for x in str($manipulate.categories).split(',')]
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49 adata.rename_categories(
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50 key='$manipulate.key',
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51 categories=$categories)
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52
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53 #else if $manipulate.function == 'remove_keys'
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54 #if $manipulate.obs_keys
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55 #set $keys = [x.strip() for x in str($manipulate.obs_keys).split(',')]
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56 adata.obs = adata.obs.drop(columns=$keys)
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57 #end if
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58
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59 #if $manipulate.var_keys
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60 #set $keys = [x.strip() for x in str($manipulate.var_keys).split(',')]
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61 adata.var = adata.vars.drop(columns=$keys)
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62 #end if
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63
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64 #else if $manipulate.function == 'flag_genes'
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65 ## adapted from anndata operations
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66 #for $flag in $manipulate.gene_flags
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67 k_cat = adata.var_names.str.startswith('${flag.startswith}')
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68 if k_cat.sum() > 0:
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69 adata.var['${flag.col_name}'] = k_cat
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70 else:
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71 print(f'No genes starting with {'${flag.startswith}'} found.')
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72 #end for
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73
0
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74 #else if $manipulate.function == 'strings_to_categoricals'
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75 adata.strings_to_categoricals()
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76
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77 #else if $manipulate.function == 'transpose'
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78 adata = adata.transpose()
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79
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80 #else if $manipulate.function == 'add_annotation'
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81 import pandas as pd
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82 extra_annot_t = pd.read_csv('$manipulate.new_annot', sep='\t').reset_index(drop=True)
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83 #if $manipulate.var_obs == 'var'
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84 var_index = adata.var_names
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85 var = pd.concat([adata.var.reset_index(drop=True), extra_annot_t], axis=1)
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86 var.index = var_index
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87 adata.var = var
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88 #else if $manipulate.var_obs == 'obs'
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89 obs_index = adata.obs.index
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90 obs = pd.concat([adata.obs.reset_index(drop=True), extra_annot_t], axis=1)
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91 obs.index = obs_index
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92 adata.obs = obs
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93 #end if
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94
13
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95 #else if $manipulate.function == 'split_on_obs'
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96 import os
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97 res_dir = "output_split"
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98 os.makedirs(res_dir, exist_ok=True)
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99 for s,field_value in enumerate(adata.obs["${manipulate.key}"].unique()):
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100 ad_s = adata[adata.obs.${manipulate.key} == field_value]
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101 ad_s.write(f"{res_dir}/${manipulate.key}_{s}.h5ad", compression='gzip')
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102
1
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103 #else if $manipulate.function == 'filter'
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104 #if $manipulate.filter.filter == 'key'
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105 #if $manipulate.var_obs == 'var'
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106 filtered = adata.var['$manipulate.filter.key']
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107 #else if $manipulate.var_obs == 'obs'
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108 filtered = adata.obs['$manipulate.filter.key']
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109 #end if
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110
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111 #if $manipulate.filter.filter_key.type == 'number'
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112 #if $manipulate.filter.filter_key.filter == 'equal'
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113 filtered = filtered == $manipulate.filter.filter_key.value
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114 #else if $manipulate.filter.filter_key.filter == 'equal'
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115 filtered = filtered != $manipulate.filter.filter_key.value
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116 #else if $manipulate.filter.filter_key.filter == 'less'
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117 filtered = filtered < $manipulate.filter.filter_key.value
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118 #else if $manipulate.filter.filter_key.filter == 'less_or_equal'
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119 filtered = filtered <= $manipulate.filter.filter_key.value
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120 #else if $manipulate.filter.filter_key.filter == 'greater'
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121 filtered = filtered > $manipulate.filter.filter_key.value
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122 #else if $manipulate.filter.filter_key.filter == 'greater_or_equal'
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123 filtered = filtered >= $manipulate.filter.filter_key.value
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124 #end if
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125 #else if $manipulate.filter.filter_key.type == 'text'
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126 #if $manipulate.filter.filter_key.filter == 'equal'
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127 filtered = filtered == '$manipulate.filter.filter_key.value'
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128 #else
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129 filtered = filtered != '$manipulate.filter.filter_key.value'
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130 #end if
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131 #else if $manipulate.filter.filter_key.type == 'boolean'
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132 filtered = filtered == $manipulate.filter.filter_key.value
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133 #end if
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134
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135 #else if $manipulate.filter.filter == 'index'
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136 #if str($manipulate.filter.index.format) == 'file'
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137 with open('$manipulate.filter.index.file', 'r') as filter_f:
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138 filters = [str(x.strip()) for x in filter_f.readlines()]
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139 filtered = filters
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140 #else
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141 #set $filters = [str(x.strip()) for x in $manipulate.filter.index.text.split(',')]
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142 filtered = $filters
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143 #end if
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144 #end if
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145 print(filtered)
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146
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147 #if $manipulate.var_obs == 'var'
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148 adata = adata[:,filtered]
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149 #else if $manipulate.var_obs == 'obs'
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150 adata = adata[filtered, :]
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151 #end if
2
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152
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153 #else if $manipulate.function == 'save_raw'
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154 adata.raw = adata
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155
0
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156 #end if
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157
13
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158 #if $manipulate.function != 'split_on_obs'
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159 adata.write('anndata.h5ad', compression='gzip')
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160 print(adata)
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161 #end if
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162
0
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163 ]]></configfile>
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164 </configfiles>
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165 <inputs>
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166 <param name="input" type="data" format="h5ad" label="Annotated data matrix"/>
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167 <conditional name="manipulate">
6
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168 <param name="function" type="select" label="Function to manipulate the object">
0
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169 <option value="concatenate">Concatenate along the observations axis</option>
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170 <option value="obs_names_make_unique">Makes the obs index unique by appending '1', '2', etc</option>
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171 <option value="var_names_make_unique">Makes the var index unique by appending '1', '2', etc</option>
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172 <option value="rename_categories">Rename categories of annotation</option>
13
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173 <option value="remove_keys">Remove keys from obs or var annotations</option>
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174 <option value="flag_genes">Flag genes start with a pattern</option><!--adapted from EBI anndata operations tool -->
0
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175 <option value="strings_to_categoricals">Transform string annotations to categoricals</option>
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176 <option value="transpose">Transpose the data matrix, leaving observations and variables interchanged</option>
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177 <option value="add_annotation">Add new annotation(s) for observations or variables</option>
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178 <option value="split_on_obs">Split the AnnData object into multiple AnnData objects based on the values of a given obs key</option><!--adapted from EBI anndata operations tool-->
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179 <option value="filter">Filter observations or variables</option>
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180 <option value="save_raw">Freeze the current state into the 'raw' attribute</option>
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181 </param>
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182 <when value="concatenate">
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183 <param name="other_adatas" type="data" format="h5ad" multiple="true" label="Annotated data matrix to add"/>
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184 <param name="join" type="select" label="Join method">
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185 <option value="inner">Intersection of variables</option>
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186 <option value="outer">Union of variables</option>
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187 </param>
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188 <param name="batch_key" type="text" value="batch" label="Key to add the batch annotation to obs"/>
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189 <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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190 <option value="-">-</option>
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191 <option value="_">_</option>
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192 <option value=" "> </option>
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193 <option value="/">/</option>
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194 </param>
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195 </when>
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196 <when value="obs_names_make_unique">
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197 <expand macro="param_join"/>
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198 </when>
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199 <when value="var_names_make_unique">
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200 <expand macro="param_join"/>
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201 </when>
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202 <when value="rename_categories">
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203 <param name="key" type="text" value="" label="Key for observations or variables annotation" help="Annotation key in obs or var"/>
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204 <param name="categories" type="text" value="" label="Comma-separated list of new categories" help="It should be the same number as the old categories"/>
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205 </when>
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206 <when value="remove_keys">
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207 <param name="obs_keys" type="text" value="" optional="true" label="Keys/fields to remove from observations (obs)">
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208 <expand macro="sanitize_query"/>
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209 </param>
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210 <param name="var_keys" type="text" value="" optional="true" label="Keys/fields to remove from variables (var)">
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211 <expand macro="sanitize_query"/>
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212 </param>
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213 </when>
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214 <when value="flag_genes">
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215 <repeat name="gene_flags" title="Flag genes that start with these names">
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216 <param name="startswith" type="text" label="Text that you expect the genes to be flagged to start with" help="For example, 'MT-' for mito genes">
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217 <sanitizer invalid_char="">
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218 <valid initial="string.ascii_letters,string.digits,string.punctuation">
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219 <remove value="&apos;" />
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220 </valid>
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221 </sanitizer>
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222 </param>
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223 <param name="col_name" type="text" label="Name of the column in var.names where this boolean flag is stored" help="For example, name this column as 'mito' for mitochondrial genes."/>
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224 </repeat>
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225 </when>
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226 <when value="strings_to_categoricals" ></when>
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227 <when value="transpose" ></when>
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228 <when value="add_annotation">
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229 <param name="var_obs" type="select" label="What to annotate?">
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230 <option value="var">Variables (var)</option>
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231 <option value="obs">Observations (obs)</option>
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232 </param>
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233 <param name="new_annot" type="data" format="tabular" label="Table with new annotations"
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234 help="The new table should have the same number of rows and same order than obs or var. The key names should be in the header (1st line)"/>
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235 </when>
13
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236 <when value="split_on_obs">
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237 <param name="key" type="text" label="The obs key to split on" help="For example, if you want to split on cluster annotation, you can use the key 'louvain'. The output will be a collection of anndata objects">
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238 <sanitizer invalid_char="">
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239 <valid initial="string.ascii_letters,string.digits,string.punctuation">
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240 <remove value="&apos;" />
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241 </valid>
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242 </sanitizer>
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243 </param>
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244 </when>
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245 <when value="filter">
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246 <param name="var_obs" type="select" label="What to filter?">
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247 <option value="var">Variables (var)</option>
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248 <option value="obs">Observations (obs)</option>
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249 </param>
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250 <conditional name="filter">
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251 <param name="filter" type="select" label="Type of filtering?">
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252 <option value="key">By key (column) values</option>
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253 <option value="index">By index (row)</option>
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254 </param>
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255 <when value="key">
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256 <param name="key" type="text" value="n_genes" label="Key to filter"/>
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257 <conditional name="filter_key">
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258 <param name="type" type="select" label="Type of value to filter">
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259 <option value="number">Number</option>
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260 <option value="text">Text</option>
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parents: 0
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261 <option value="boolean">Boolean</option>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
262 </param>
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parents: 0
diff changeset
263 <when value="number">
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parents: 0
diff changeset
264 <param name="filter" type="select" label="Filter">
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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265 <option value="equal">equal to</option>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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266 <option value="not_equal">not equal to</option>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
267 <option value="less">less than</option>
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iuc
parents: 0
diff changeset
268 <option value="less_or_equal">less than or equal to</option>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
269 <option value="greater">greater than</option>
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iuc
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270 <option value="greater_or_equal">greater than or equal to</option>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
271 </param>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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272 <param name="value" type="float" value="2500" label="Value"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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273 </when>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
274 <when value="text">
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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275 <param name="filter" type="select" label="Filter">
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
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276 <option value="equal">equal to</option>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
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277 <option value="not_equal">not equal to</option></param>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
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278 <param name="value" type="text" value="2500" label="Value"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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279 </when>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
diff changeset
280 <when value="boolean">
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parents: 0
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281 <param name="value" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Value to keep"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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282 </when>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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283 </conditional>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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284 </when>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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285 <when value="index">
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iuc
parents: 0
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286 <conditional name="index">
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
287 <param name="format" type="select" label="Format for the filter by index">
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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288 <option value="file">File</option>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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289 <option value="text" selected="true">Text</option>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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290 </param>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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291 <when value="text">
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parents: 0
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292 <param name="text" type="text" value="" label="List of index to keep" help="Indexes separated by a comma"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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293 </when>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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294 <when value="file">
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parents: 0
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295 <param name="file" type="data" format="txt" label="File with the list of index to keep" help="One index per line"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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296 </when>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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297 </conditional>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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298 </when>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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299 </conditional>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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300 </when>
7
43cb7b5a6fe7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 033c2d20a0c73cd84c5c3aee73ae224183a9c1c2"
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301 <when value="save_raw"></when>
0
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302 </conditional>
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303 </inputs>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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304 <outputs>
13
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305 <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${manipulate.function}) on ${on_string}">
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306 <filter>manipulate['function'] != 'split_on_obs'</filter>
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307 </data>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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308 <collection name="output_h5ad_split" type="list" label="${tool.name} (${manipulate.function}) on ${on_string} Collection">
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309 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.h5" directory="output_split" format="h5ad" visible="true"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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310 <filter>manipulate['function'] == 'split_on_obs'</filter>
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311 </collection>
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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312 </outputs>
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313 <tests>
13
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314 <test expect_num_outputs="1">
1
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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parents: 0
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315 <!-- test 1 -->
8
b85871dd69f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6497f5415b57bedd849b876883574b3f0050741a"
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316 <param name="input" value="import.csv.h5ad"/>
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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317 <conditional name="manipulate">
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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318 <param name="function" value="concatenate"/>
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319 <param name="other_adatas" value="import.csv.h5ad"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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320 <param name="join" value="inner"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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321 <param name="batch_key" value="batch"/>
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322 <param name="index_unique" value="-"/>
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323 </conditional>
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324 <assert_stdout>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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325 <has_text_matching expression="adata_0"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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326 <has_text_matching expression="adata.concatenate"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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diff changeset
327 <has_text_matching expression="join='inner'"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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328 <has_text_matching expression="index_unique='-'"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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329 <has_text_matching expression="batch_key='batch'"/>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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330 <has_text_matching expression="6 × 2"/>
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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331 </assert_stdout>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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diff changeset
332 <output name="anndata" ftype="h5ad">
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333 <assert_contents>
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diff changeset
334 <has_h5_keys keys="obs/batch"/>
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335 </assert_contents>
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336 </output>
0
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337 </test>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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338 <test expect_num_outputs="1">
1
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iuc
parents: 0
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339 <!-- test 2 -->
0
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340 <param name="input" value="krumsiek11.h5ad"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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341 <conditional name="manipulate">
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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342 <param name="function" value="obs_names_make_unique"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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343 <param name="join" value="-"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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344 </conditional>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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345 <assert_stdout>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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346 <has_text_matching expression="adata.obs_names_make_unique\(join='-'\)"/>
13
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diff changeset
347 <has_text_matching expression="500 × 11"/>
0
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348 </assert_stdout>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
349 <output name="anndata" ftype="h5ad">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
350 <assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
351 <has_h5_keys keys="obs/cell_type"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
352 <has_h5_keys keys="uns/highlights"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
353 <has_h5_keys keys="uns/iroot"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
354 </assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
355 </output>
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
356 </test>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
357 <test expect_num_outputs="1">
1
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
358 <!-- test 3 -->
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
359 <param name="input" value="krumsiek11.h5ad"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
360 <conditional name="manipulate">
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
361 <param name="function" value="var_names_make_unique"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
362 <param name="join" value="-"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
363 </conditional>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
364 <assert_stdout>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
365 <has_text_matching expression="adata.var_names_make_unique\(join='-'\)"/>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
366 <has_text_matching expression="500 × 11"/>
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
367 </assert_stdout>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
368 <output name="anndata" ftype="h5ad">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
369 <assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
370 <has_h5_keys keys="obs/cell_type"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
371 <has_h5_keys keys="uns/highlights"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
372 <has_h5_keys keys="uns/iroot"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
373 </assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
374 </output>
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
375 </test>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
376 <test expect_num_outputs="1">
1
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
377 <!-- test 4 -->
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
378 <param name="input" value="krumsiek11.h5ad"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
379 <conditional name="manipulate">
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
380 <param name="function" value="rename_categories"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
381 <param name="key" value="cell_type"/>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
382 <param name="categories" value="ery, mk, mo, progenitor"/>
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
383 </conditional>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
384 <assert_stdout>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
385 <has_text_matching expression="adata.rename_categories"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
386 <has_text_matching expression="key='cell_type'"/>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
387 <has_text_matching expression="categories=\['ery', 'mk', 'mo', 'progenitor'\]"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
388 <has_text_matching expression="500 × 11"/>
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
389 </assert_stdout>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
390 <output name="anndata" ftype="h5ad">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
391 <assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
392 <has_h5_keys keys="obs/cell_type"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
393 <has_h5_keys keys="uns/highlights"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
394 <has_h5_keys keys="uns/iroot"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
395 </assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
396 </output>
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
397 </test>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
398 <test expect_num_outputs="1">
1
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
399 <!-- test 5 -->
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
400 <param name="input" value="krumsiek11.h5ad"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
401 <conditional name="manipulate">
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
402 <param name="function" value="strings_to_categoricals"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
403 </conditional>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
404 <assert_stdout>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
405 <has_text_matching expression="adata.strings_to_categoricals"/>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
406 <has_text_matching expression="500 × 11"/>
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
407 </assert_stdout>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
408 <output name="anndata" ftype="h5ad">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
409 <assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
410 <has_h5_keys keys="obs/cell_type"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
411 <has_h5_keys keys="uns/highlights"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
412 <has_h5_keys keys="uns/iroot"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
413 </assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
414 </output>
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
415 </test>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
416 <test expect_num_outputs="1">
1
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
417 <!-- test 6 -->
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
418 <param name="input" value="krumsiek11.h5ad"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
419 <conditional name="manipulate">
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
420 <param name="function" value="transpose"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
421 </conditional>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
422 <assert_stdout>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
423 <has_text_matching expression="adata.transpose"/>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
424 <has_text_matching expression="11 × 500"/>
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
425 </assert_stdout>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
426 <output name="anndata" ftype="h5ad">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
427 <assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
428 <has_h5_keys keys="var/cell_type"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
429 <has_h5_keys keys="uns/highlights"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
430 <has_h5_keys keys="uns/iroot"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
431 </assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
432 </output>
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
433 </test>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
434 <test expect_num_outputs="1">
1
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
435 <!-- test 7 -->
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
436 <param name="input" value="krumsiek11.h5ad"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
437 <conditional name="manipulate">
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
438 <param name="function" value="add_annotation"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
439 <param name="var_obs" value="var"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
440 <param name="new_annot" value="var_add_annotation.tabular"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
441 </conditional>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
442 <assert_stdout>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
443 <has_text_matching expression="500 × 11"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
444 </assert_stdout>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
445 <output name="anndata" ftype="h5ad">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
446 <assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
447 <has_h5_keys keys="obs/cell_type"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
448 <has_h5_keys keys="var/annot1"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
449 <has_h5_keys keys="var/annot2"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
450 <has_h5_keys keys="uns/highlights"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
451 <has_h5_keys keys="uns/iroot"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
452 </assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
453 </output>
1
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
454 </test>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
455 <test expect_num_outputs="1">
1
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
456 <!-- test 8 -->
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
457 <param name="input" value="krumsiek11.h5ad"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
458 <conditional name="manipulate">
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
459 <param name="function" value="add_annotation"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
460 <param name="var_obs" value="obs"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
461 <param name="new_annot" value="obs_add_annotation.tabular"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
462 </conditional>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
463 <assert_stdout>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
464 <has_text_matching expression="500 × 11"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
465 </assert_stdout>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
466 <output name="anndata" ftype="h5ad">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
467 <assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
468 <has_h5_keys keys="obs/cell_type"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
469 <has_h5_keys keys="obs/annot1"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
470 <has_h5_keys keys="obs/annot2"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
471 <has_h5_keys keys="uns/highlights"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
472 <has_h5_keys keys="uns/iroot"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
473 </assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
474 </output>
1
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
475 </test>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
476 <test expect_num_outputs="1">
1
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
477 <!-- test 9 -->
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
478 <param name="input" value="krumsiek11.h5ad"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
479 <conditional name="manipulate">
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
480 <param name="function" value="filter"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
481 <param name="var_obs" value="var"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
482 <conditional name="filter">
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
483 <param name="filter" value="index"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
484 <conditional name="index">
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
485 <param name="format" value="text"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
486 <param name="text" value="Gata2,EKLF"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
487 </conditional>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
488 </conditional>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
489 </conditional>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
490 <assert_stdout>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
491 <has_text_matching expression="500 × 2"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
492 </assert_stdout>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
493 <output name="anndata" ftype="h5ad">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
494 <assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
495 <has_h5_keys keys="obs/cell_type"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
496 <has_h5_keys keys="uns/highlights"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
497 <has_h5_keys keys="uns/iroot"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
498 </assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
499 </output>
1
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
500 </test>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
501 <test expect_num_outputs="1">
1
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
502 <!-- test 10 -->
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
503 <param name="input" value="krumsiek11.h5ad"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
504 <conditional name="manipulate">
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
505 <param name="function" value="filter"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
506 <param name="var_obs" value="obs"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
507 <conditional name="filter">
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
508 <param name="filter" value="key"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
509 <param name="key" value="cell_type"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
510 <conditional name="filter_key">
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
511 <param name="type" value="text"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
512 <param name="filter" value="equal"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
513 <param name="value" value="progenitor"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
514 </conditional>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
515 </conditional>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
516 </conditional>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
517 <assert_stdout>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
518 <has_text_matching expression="260 × 11"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
519 </assert_stdout>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
520 <output name="anndata" ftype="h5ad">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
521 <assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
522 <has_h5_keys keys="obs/cell_type"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
523 <has_h5_keys keys="uns/highlights"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
524 <has_h5_keys keys="uns/iroot"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
525 </assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
526 </output>
1
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
527 </test>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
528 <test expect_num_outputs="1">
2
a56baceb1900 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 1
diff changeset
529 <!-- test 11 -->
a56baceb1900 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 1
diff changeset
530 <param name="input" value="krumsiek11.h5ad"/>
a56baceb1900 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 1
diff changeset
531 <conditional name="manipulate">
a56baceb1900 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 1
diff changeset
532 <param name="function" value="save_raw"/>
a56baceb1900 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 1
diff changeset
533 </conditional>
13
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
534 <assert_stdout>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
535 <has_text_matching expression="500 × 11"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
536 </assert_stdout>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
537 <output name="anndata" ftype="h5ad">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
538 <assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
539 <has_h5_keys keys="obs/cell_type"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
540 <has_h5_keys keys="uns/highlights"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
541 <has_h5_keys keys="uns/iroot"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
542 </assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
543 </output>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
544 </test>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
545 <test expect_num_outputs="1">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
546 <!-- test 12 remove_keys -->
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
547 <param name="input" value="krumsiek11.h5ad"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
548 <conditional name="manipulate">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
549 <param name="function" value="remove_keys"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
550 <param name="obs_keys" value="cell_type"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
551 </conditional>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
552 <assert_stdout>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
553 <has_text_matching expression="500 × 11"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
554 </assert_stdout>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
555 <output name="anndata" ftype="h5ad">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
556 <assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
557 <has_h5_keys keys="uns/highlights"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
558 <has_h5_keys keys="uns/iroot"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
559 </assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
560 </output>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
561 </test>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
562 <test expect_num_outputs="1">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
563 <!-- test 13 flag_genes -->
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
564 <param name="input" value="krumsiek11.h5ad"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
565 <conditional name="manipulate">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
566 <param name="function" value="flag_genes"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
567 <repeat name="gene_flags">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
568 <param name="startswith" value="Gata"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
569 <param name="col_name" value="Gata_TF"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
570 </repeat>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
571 <repeat name="gene_flags">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
572 <param name="startswith" value="Gf"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
573 <param name="col_name" value="GF"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
574 </repeat>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
575 </conditional>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
576 <assert_stdout>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
577 <has_text_matching expression="500 × 11"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
578 </assert_stdout>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
579 <output name="anndata" ftype="h5ad">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
580 <assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
581 <has_h5_keys keys="var/Gata_TF"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
582 <has_h5_keys keys="var/GF"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
583 </assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
584 </output>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
585 </test>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
586 <test expect_num_outputs="1">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
587 <!-- test 14 split_on_obs -->
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
588 <param name="input" value="krumsiek11.h5ad"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
589 <conditional name="manipulate">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
590 <param name="function" value="split_on_obs"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
591 <param name="key" value="cell_type"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
592 </conditional>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
593 <output_collection name="output_h5ad_split" type="list">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
594 <element name="cell_type_0">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
595 <assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
596 <has_h5_keys keys="obs/cell_type"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
597 <has_h5_keys keys="uns/highlights"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
598 <has_h5_keys keys="uns/iroot"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
599 </assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
600 </element>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
601 <element name="cell_type_1">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
602 <assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
603 <has_h5_keys keys="obs/cell_type"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
604 <has_h5_keys keys="uns/highlights"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
605 <has_h5_keys keys="uns/iroot"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
606 </assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
607 </element>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
608 <element name="cell_type_2">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
609 <assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
610 <has_h5_keys keys="obs/cell_type"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
611 <has_h5_keys keys="uns/highlights"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
612 <has_h5_keys keys="uns/iroot"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
613 </assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
614 </element>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
615 <element name="cell_type_3">
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
616 <assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
617 <has_h5_keys keys="obs/cell_type"/>
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618 <has_h5_keys keys="uns/highlights"/>
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619 <has_h5_keys keys="uns/iroot"/>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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620 </assert_contents>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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621 </element>
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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622 </output_collection>
2
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623 </test>
0
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624 </tests>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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625 <help><![CDATA[
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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626 **What it does**
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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627
13
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628 This tool takes a AnnData dataset, manipulates it and returns it.
0
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629
13
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630 The possible manipulations are:
0
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631
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9bd945a03d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d"
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632 - Concatenate along the observations axis (`concatenate method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.concatenate.html>`__)
0
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633
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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634 The `uns`, `varm` and `obsm` attributes are ignored.
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635
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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636 If you use `join='outer'` this fills 0s for sparse data when variables are absent in a batch. Use this with care. Dense data is filled with `NaN`
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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637
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638 - Makes the obs index unique by appending '1', '2', etc (`obs_names_make_unique method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.obs_names_make_unique.html>`__)
0
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639
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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640 The first occurance of a non-unique value is ignored.
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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641
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9bd945a03d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d"
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642 - Makes the var index unique by appending '1', '2', etc (`var_names_make_unique method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.var_names_make_unique.html>`__)
0
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643
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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644 The first occurance of a non-unique value is ignored.
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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645
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9bd945a03d7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d"
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646 - Rename categories of annotation `key` in `obs`, `var` and `uns` (`rename_categories method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.rename_categories.html>`__)
0
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647
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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648 Besides calling `self.obs[key].cat.categories = categories` - similar for `var` - this also renames categories in unstructured annotation that uses the categorical annotation `key`
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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649
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650 - Remove keys from obs or var annotations
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651
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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652 Helps in cleaning up andata with many annotations. For example, helps in removing qc metrics calculated during the preprocesing or already existing cluster annotations.
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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653
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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654 - Flag genes start with a pattern
7e8c677a7b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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655
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656 Useful for flagging the mitochoncdrial or ribosomal protein genes
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657
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658 - Transform string annotations to categoricals (`strings_to_categoricals method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.strings_to_categoricals.html>`__)
0
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659
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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660 Only affects string annotations that lead to less categories than the total number of observations.
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661
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662 - Transpose the data matrix, leaving observations and variables interchanged (`transpose method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.transpose.html>`__)
0
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663
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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664 Data matrix is transposed, observations and variables are interchanged.
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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665
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666 - Add annotation for variables or
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667
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668 - Split the AnnData object into multiple AnnData objects based on the values of a given obs key
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669
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670 For example, helps in splitting an anndata objects based on cluster annotation. This function generates a collection with number of elements equal to the number of categories in the input obs key.
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671
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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672 - Filter data variables or observations, by index or key
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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673
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a56baceb1900 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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674 - Freeze the current state into the 'raw' attribute
a56baceb1900 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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675
0
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676 @HELP@
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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677 ]]></help>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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678 <expand macro="citations"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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679 </tool>