Mercurial > repos > iuc > anndata_manipulate

annotate manipulate.xml @ 6:d4af736e7b83 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
author iuc
date Mon, 10 Feb 2020 05:21:44 -0500
parents a56baceb1900
children 43cb7b5a6fe7
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0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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1 <tool id="anndata_manipulate" name="Manipulate AnnData" version="@VERSION@+@GALAXY_VERSION@">
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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('$input')
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24
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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_$i = ad.read('$filepath')
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28 #end for
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29 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
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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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
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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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 == 'strings_to_categoricals'
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54 adata.strings_to_categoricals()
1
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55
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56 #else if $manipulate.function == 'transpose'
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57 adata = adata.transpose()
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58
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59 #else if $manipulate.function == 'add_annotation'
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60 import pandas as pd
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61 extra_annot_t = pd.read_csv('$manipulate.new_annot', sep='\t').reset_index(drop=True)
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62 #if $manipulate.var_obs == 'var'
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63 var_index = adata.var_names
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64 var = pd.concat([adata.var.reset_index(drop=True), extra_annot_t], axis=1)
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65 var.index = var_index
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66 adata.var = var
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67 #else if $manipulate.var_obs == 'obs'
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68 obs_index = adata.obs.index
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69 obs = pd.concat([adata.obs.reset_index(drop=True), extra_annot_t], axis=1)
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70 obs.index = obs_index
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71 adata.obs = obs
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72 #end if
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73
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74 #else if $manipulate.function == 'filter'
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75 #if $manipulate.filter.filter == 'key'
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76 #if $manipulate.var_obs == 'var'
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77 filtered = adata.var['$manipulate.filter.key']
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78 #else if $manipulate.var_obs == 'obs'
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79 filtered = adata.obs['$manipulate.filter.key']
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80 #end if
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81
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82 #if $manipulate.filter.filter_key.type == 'number'
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83 #if $manipulate.filter.filter_key.filter == 'equal'
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84 filtered = filtered == $manipulate.filter.filter_key.value
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85 #else if $manipulate.filter.filter_key.filter == 'equal'
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86 filtered = filtered != $manipulate.filter.filter_key.value
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87 #else if $manipulate.filter.filter_key.filter == 'less'
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88 filtered = filtered < $manipulate.filter.filter_key.value
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89 #else if $manipulate.filter.filter_key.filter == 'less_or_equal'
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90 filtered = filtered <= $manipulate.filter.filter_key.value
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91 #else if $manipulate.filter.filter_key.filter == 'greater'
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92 filtered = filtered > $manipulate.filter.filter_key.value
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93 #else if $manipulate.filter.filter_key.filter == 'greater_or_equal'
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94 filtered = filtered >= $manipulate.filter.filter_key.value
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95 #end if
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96 #else if $manipulate.filter.filter_key.type == 'text'
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97 #if $manipulate.filter.filter_key.filter == 'equal'
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98 filtered = filtered == '$manipulate.filter.filter_key.value'
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99 #else
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100 filtered = filtered != '$manipulate.filter.filter_key.value'
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101 #end if
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102 #else if $manipulate.filter.filter_key.type == 'boolean'
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103 filtered = filtered == $manipulate.filter.filter_key.value
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104 #end if
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105
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106 #else if $manipulate.filter.filter == 'index'
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107 #if str($manipulate.filter.index.format) == 'file'
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108 with open('$manipulate.filter.index.file', 'r') as filter_f:
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109 filters = [str(x.strip()) for x in filter_f.readlines()]
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110 filtered = filters
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111 #else
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112 #set $filters = [str(x.strip()) for x in $manipulate.filter.index.text.split(',')]
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113 filtered = $filters
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114 #end if
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115 #end if
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116 print(filtered)
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117
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118 #if $manipulate.var_obs == 'var'
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119 adata = adata[:,filtered]
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120 #else if $manipulate.var_obs == 'obs'
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121 adata = adata[filtered, :]
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122 #end if
2
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123
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124 #else if $manipulate.function == 'save_raw'
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125 adata.raw = adata
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126
0
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127 #end if
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128
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129 adata.write('anndata.h5ad')
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130 ]]></configfile>
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131 </configfiles>
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132 <inputs>
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133 <param name="input" type="data" format="h5ad" label="Annotated data matrix"/>
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134 <conditional name="manipulate">
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135 <param name="function" type="select" label="Function to manipulate the object">
0
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136 <option value="concatenate">Concatenate along the observations axis</option>
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137 <option value="obs_names_make_unique">Makes the obs index unique by appending '1', '2', etc</option>
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138 <option value="var_names_make_unique">Makes the var index unique by appending '1', '2', etc</option>
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139 <option value="rename_categories">Rename categories of annotation</option>
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140 <option value="strings_to_categoricals">Transform string annotations to categoricals</option>
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141 <option value="transpose">Transpose the data matrix, leaving observations and variables interchanged</option>
1
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142 <option value="add_annotation">Add new annotation(s) for observations or variables</option>
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143 <option value="filter">Filter observations or variables</option>
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144 <option value="save_raw">Freeze the current state into the 'raw' attribute</option>
0
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145 </param>
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146 <when value="concatenate">
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147 <param name="other_adatas" type="data" format="h5ad" multiple="true" label="Annotated data matrix to add"/>
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148 <param name="join" type="select" label="Join method">
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149 <option value="inner">Intersection of variables</option>
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150 <option value="outer">Union of variables</option>
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151 </param>
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152 <param name="batch_key" type="text" value="batch" label="Key to add the batch annotation to obs"/>
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153 <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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154 <option value="-">-</option>
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155 <option value="_">_</option>
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156 <option value=" "> </option>
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157 <option value="/">/</option>
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158 </param>
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159 </when>
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160 <when value="obs_names_make_unique">
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161 <expand macro="param_join"/>
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162 </when>
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163 <when value="var_names_make_unique">
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164 <expand macro="param_join"/>
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165 </when>
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166 <when value="rename_categories">
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167 <param name="key" type="text" value="" label="Key for observations or variables annotation" help="Annotation key in obs or var"/>
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168 <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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169 </when>
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170 <when value="strings_to_categoricals"/>
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171 <when value="transpose"/>
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172 <when value="add_annotation">
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173 <param name="var_obs" type="select" label="What to annotate?">
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174 <option value="var">Variables (var)</option>
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175 <option value="obs">Observations (obs)</option>
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176 </param>
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177 <param name="new_annot" type="data" format="tabular" label="Table with new annotations"
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178 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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179 </when>
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180 <when value="filter">
2
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181 <param name="var_obs" type="select" label="What to filter?">
1
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182 <option value="var">Variables (var)</option>
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183 <option value="obs">Observations (obs)</option>
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184 </param>
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185 <conditional name="filter">
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186 <param name="filter" type="select" label="Type of filtering?">
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187 <option value="key">By key (column) values</option>
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188 <option value="index">By index (row)</option>
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189 </param>
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190 <when value="key">
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191 <param name="key" type="text" value="n_genes" label="Key to filter"/>
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192 <conditional name="filter_key">
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193 <param name="type" type="select" label="Type of value to filter">
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194 <option value="number">Number</option>
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195 <option value="text">Text</option>
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196 <option value="boolean">Boolean</option>
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197 </param>
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198 <when value="number">
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199 <param name="filter" type="select" label="Filter">
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200 <option value="equal">equal to</option>
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201 <option value="not_equal">not equal to</option>
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202 <option value="less">less than</option>
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203 <option value="less_or_equal">less than or equal to</option>
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204 <option value="greater">greater than</option>
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205 <option value="greater_or_equal">greater than or equal to</option>
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206 </param>
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207 <param name="value" type="float" value="2500" label="Value"/>
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208 </when>
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209 <when value="text">
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210 <param name="filter" type="select" label="Filter">
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211 <option value="equal">equal to</option>
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212 <option value="not_equal">not equal to</option></param>
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213 <param name="value" type="text" value="2500" label="Value"/>
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214 </when>
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215 <when value="boolean">
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216 <param name="value" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Value to keep"/>
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217 </when>
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218 </conditional>
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219 </when>
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220 <when value="index">
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221 <conditional name="index">
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222 <param name="format" type="select" label="Format for the filter by index">
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223 <option value="file">File</option>
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224 <option value="text" selected="true">Text</option>
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225 </param>
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226 <when value="text">
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227 <param name="text" type="text" value="" label="List of index to keep" help="Indexes separated by a comma"/>
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228 </when>
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229 <when value="file">
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230 <param name="file" type="data" format="txt" label="File with the list of index to keep" help="One index per line"/>
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231 </when>
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232 </conditional>
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233 </when>
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234 </conditional>
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235 </when>
0
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236 </conditional>
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237 </inputs>
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238 <outputs>
1
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239 <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${manipulate.function}) on ${on_string}"/>
0
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240 </outputs>
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241 <tests>
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242 <test>
1
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243 <!-- test 1 -->
0
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244 <param name="input" value="krumsiek11.h5ad"/>
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245 <conditional name="manipulate">
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246 <param name="function" value="concatenate"/>
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247 <param name="other_adatas" value="import.csv.h5ad"/>
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248 <param name="join" value="inner"/>
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249 <param name="batch_key" value="batch"/>
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250 <param name="index_unique" value="-"/>
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251 </conditional>
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252 <assert_stdout>
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253 <has_text_matching expression="adata_0"/>
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254 <has_text_matching expression="adata.concatenate"/>
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255 <has_text_matching expression="join='inner'"/>
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256 <has_text_matching expression="index_unique='-'"/>
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257 <has_text_matching expression="batch_key='batch'"/>
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258 </assert_stdout>
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259 <output name="anndata" value="manipulate.concatenate.h5ad" ftype="h5ad" compare="sim_size"/>
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260 </test>
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261 <test>
1
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262 <!-- test 2 -->
0
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diff changeset
263 <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
264 <conditional name="manipulate">
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
265 <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
iuc
parents:
diff changeset
266 <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
267 </conditional>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
268 <assert_stdout>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
269 <has_text_matching expression="adata.obs_names_make_unique\(join='-'\)"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
270 </assert_stdout>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
271 <output name="anndata" value="manipulate.obs_names_make_unique.h5ad" ftype="h5ad" compare="sim_size"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
272 </test>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
273 <test>
1
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
274 <!-- test 3 -->
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
275 <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
276 <conditional name="manipulate">
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
277 <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
278 <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
279 </conditional>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
280 <assert_stdout>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
281 <has_text_matching expression="adata.var_names_make_unique\(join='-'\)"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
282 </assert_stdout>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
283 <output name="anndata" value="manipulate.var_names_make_unique.h5ad" ftype="h5ad" compare="sim_size"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
284 </test>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
285 <test>
1
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
286 <!-- test 4 -->
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
287 <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
288 <conditional name="manipulate">
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
289 <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
290 <param name="key" value="cell_type"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
291 <param name="categories" value="Er,Ml,Mt, Ne, pr"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
292 </conditional>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
293 <assert_stdout>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
294 <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
295 <has_text_matching expression="key='cell_type'"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
296 <has_text_matching expression="categories=\['Er', 'Ml', 'Mt', 'Ne', 'pr'\]"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
297 </assert_stdout>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
298 <output name="anndata" value="manipulate.rename_categories.h5ad" ftype="h5ad" compare="sim_size"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
299 </test>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
300 <test>
1
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
301 <!-- test 5 -->
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
302 <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
303 <conditional name="manipulate">
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
304 <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
305 </conditional>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
306 <assert_stdout>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
307 <has_text_matching expression="adata.strings_to_categoricals"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
308 </assert_stdout>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
309 <output name="anndata" value="manipulate.strings_to_categoricals.h5ad" ftype="h5ad" compare="sim_size"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
310 </test>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
311 <test>
1
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
312 <!-- test 6 -->
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
313 <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
314 <conditional name="manipulate">
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
315 <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
316 </conditional>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
317 <assert_stdout>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
318 <has_text_matching expression="adata.transpose"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
319 </assert_stdout>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
320 <output name="anndata" value="manipulate.transpose.h5ad" ftype="h5ad" compare="sim_size"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
321 </test>
1
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
322 <test>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
323 <!-- test 7 -->
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
324 <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
325 <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
326 <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
327 <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
328 <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
329 </conditional>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
330 <output name="anndata" value="manipulate.add_annotation_var.h5ad" ftype="h5ad" compare="sim_size"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
331 </test>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
332 <test>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
333 <!-- test 8 -->
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
334 <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
335 <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
336 <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
337 <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
338 <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
339 </conditional>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
340 <output name="anndata" value="manipulate.add_annotation_obs.h5ad" ftype="h5ad" compare="sim_size"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
341 </test>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
342 <test>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
343 <!-- test 9 -->
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
344 <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
345 <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
346 <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
347 <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
348 <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
349 <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
350 <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
351 <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
352 <param name="text" value="Gata2,EKLF"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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353 </conditional>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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354 </conditional>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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355 </conditional>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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356 <output name="anndata" value="manipulate.filter_var_index.h5ad" ftype="h5ad" compare="sim_size"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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357 </test>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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358 <test>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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359 <!-- test 10 -->
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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360 <param name="input" value="krumsiek11.h5ad"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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361 <conditional name="manipulate">
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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362 <param name="function" value="filter"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
363 <param name="var_obs" value="obs"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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364 <conditional name="filter">
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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365 <param name="filter" value="key"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
366 <param name="key" value="cell_type"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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367 <conditional name="filter_key">
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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368 <param name="type" value="text"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
369 <param name="filter" value="equal"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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diff changeset
370 <param name="value" value="progenitor"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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371 </conditional>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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372 </conditional>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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373 </conditional>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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374 <output name="anndata" value="manipulate.filter_obs_key.h5ad" ftype="h5ad" compare="sim_size"/>
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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375 </test>
2
a56baceb1900 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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376 <test>
a56baceb1900 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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377 <!-- test 11 -->
a56baceb1900 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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378 <param name="input" value="krumsiek11.h5ad"/>
a56baceb1900 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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379 <conditional name="manipulate">
a56baceb1900 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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380 <param name="function" value="save_raw"/>
a56baceb1900 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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381 </conditional>
a56baceb1900 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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382 <output name="anndata" value="manipulate.save_raw.h5ad" ftype="h5ad" compare="sim_size"/>
a56baceb1900 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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383 </test>
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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384 </tests>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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385 <help><![CDATA[
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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386 **What it does**
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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387
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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388 This tool takes a AnnData dataset, manipulates it and returns it.
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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389
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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390 The possible manipulations are:
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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391
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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392 - Concatenate along the observations axis (`concatenate method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.concatenate.html>`__)
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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diff changeset
393
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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394 The `uns`, `varm` and `obsm` attributes are ignored.
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395
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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396 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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397
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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398 - Makes the obs index unique by appending '1', '2', etc (`obs_names_make_unique method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.obs_names_make_unique.html>`__)
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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399
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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400 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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401
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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402 - Makes the var index unique by appending '1', '2', etc (`var_names_make_unique method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.var_names_make_unique.html>`__)
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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403
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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404 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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diff changeset
405
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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406 - Rename categories of annotation `key` in `obs`, `var` and `uns` (`rename_categories method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.rename_categories.html>`__)
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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407
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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408 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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409
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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410 - Transform string annotations to categoricals (`strings_to_categoricals method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.strings_to_categoricals.html>`__)
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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411
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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412 Only affects string annotations that lead to less categories than the total number of observations.
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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413
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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414 - Transpose the data matrix, leaving observations and variables interchanged (`transpose method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.transpose.html>`__)
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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415
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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416 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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417
1
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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418 - Add annotation for variables or observations
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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419
19592ec717ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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420 - 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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421
2
a56baceb1900 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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422 - 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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423
0
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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424 @HELP@
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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425 ]]></help>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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426 <expand macro="citations"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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427 </tool>