Mercurial > repos > iuc > anndata_manipulate

annotate manipulate.xml @ 12:461db9d6cf00 draft

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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 19:55:55 +0000
parents 9ac67979e25e
children 3aa539e5b254
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12
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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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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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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
12
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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
12
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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>
12
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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>
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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>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
261 <option value="boolean">Boolean</option>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
262 </param>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
263 <when value="number">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
264 <param name="filter" type="select" label="Filter">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
265 <option value="equal">equal to</option>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
266 <option value="not_equal">not equal to</option>
1a9848100b1e "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>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
268 <option value="less_or_equal">less than or equal to</option>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
269 <option value="greater">greater than</option>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
270 <option value="greater_or_equal">greater than or equal to</option>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
271 </param>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
272 <param name="value" type="float" value="2500" label="Value"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
273 </when>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
274 <when value="text">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
275 <param name="filter" type="select" label="Filter">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
276 <option value="equal">equal to</option>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
277 <option value="not_equal">not equal to</option></param>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
278 <param name="value" type="text" value="2500" label="Value"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
279 </when>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
280 <when value="boolean">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
281 <param name="value" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Value to keep"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
282 </when>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
283 </conditional>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
284 </when>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
285 <when value="index">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
286 <conditional name="index">
1a9848100b1e "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">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
288 <option value="file">File</option>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
289 <option value="text" selected="true">Text</option>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
290 </param>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
291 <when value="text">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
292 <param name="text" type="text" value="" label="List of index to keep" help="Indexes separated by a comma"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
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293 </when>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
294 <when value="file">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
295 <param name="file" type="data" format="txt" label="File with the list of index to keep" help="One index per line"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
296 </when>
1a9848100b1e "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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297 </conditional>
1a9848100b1e "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>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
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299 </conditional>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
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300 </when>
7
1cd7d1a94481 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 033c2d20a0c73cd84c5c3aee73ae224183a9c1c2"
iuc
parents: 6
diff changeset
301 <when value="save_raw"></when>
0
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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302 </conditional>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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303 </inputs>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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304 <outputs>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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305 <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${manipulate.function}) on ${on_string}">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
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diff changeset
306 <filter>manipulate['function'] != 'split_on_obs'</filter>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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parents: 11
diff changeset
307 </data>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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308 <collection name="output_h5ad_split" type="list" label="${tool.name} (${manipulate.function}) on ${on_string} Collection">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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309 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.h5" directory="output_split" format="h5ad" visible="true"/>
461db9d6cf00 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>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
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311 </collection>
0
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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312 </outputs>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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313 <tests>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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314 <test expect_num_outputs="1">
1
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
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315 <!-- test 1 -->
8
f1b4b1591958 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6497f5415b57bedd849b876883574b3f0050741a"
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parents: 7
diff changeset
316 <param name="input" value="import.csv.h5ad"/>
0
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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317 <conditional name="manipulate">
c2043062cbc0 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"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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319 <param name="other_adatas" value="import.csv.h5ad"/>
c2043062cbc0 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"/>
c2043062cbc0 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"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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322 <param name="index_unique" value="-"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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323 </conditional>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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324 <assert_stdout>
c2043062cbc0 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"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
326 <has_text_matching expression="adata.concatenate"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
327 <has_text_matching expression="join='inner'"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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328 <has_text_matching expression="index_unique='-'"/>
c2043062cbc0 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'"/>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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diff changeset
330 <has_text_matching expression="6 × 2"/>
0
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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331 </assert_stdout>
12
461db9d6cf00 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">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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diff changeset
333 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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diff changeset
334 <has_h5_keys keys="obs/batch"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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parents: 11
diff changeset
335 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
336 </output>
0
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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337 </test>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
338 <test expect_num_outputs="1">
1
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
339 <!-- test 2 -->
0
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
340 <param name="input" value="krumsiek11.h5ad"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
341 <conditional name="manipulate">
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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342 <param name="function" value="obs_names_make_unique"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
343 <param name="join" value="-"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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parents:
diff changeset
344 </conditional>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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345 <assert_stdout>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
346 <has_text_matching expression="adata.obs_names_make_unique\(join='-'\)"/>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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parents: 11
diff changeset
347 <has_text_matching expression="500 × 11"/>
0
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
348 </assert_stdout>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
349 <output name="anndata" ftype="h5ad">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
350 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
351 <has_h5_keys keys="obs/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
352 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
353 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
354 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
355 </output>
0
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
356 </test>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
357 <test expect_num_outputs="1">
1
1a9848100b1e "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
c2043062cbc0 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"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
360 <conditional name="manipulate">
c2043062cbc0 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"/>
c2043062cbc0 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="-"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
363 </conditional>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
364 <assert_stdout>
c2043062cbc0 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\(join='-'\)"/>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
366 <has_text_matching expression="500 × 11"/>
0
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
367 </assert_stdout>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
368 <output name="anndata" ftype="h5ad">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
369 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
370 <has_h5_keys keys="obs/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
371 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
372 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
373 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
374 </output>
0
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
375 </test>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
376 <test expect_num_outputs="1">
1
1a9848100b1e "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
c2043062cbc0 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"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
379 <conditional name="manipulate">
c2043062cbc0 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"/>
c2043062cbc0 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"/>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
382 <param name="categories" value="ery, mk, mo, progenitor"/>
0
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
383 </conditional>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
384 <assert_stdout>
c2043062cbc0 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"/>
c2043062cbc0 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'"/>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
387 <has_text_matching expression="categories=\['ery', 'mk', 'mo', 'progenitor'\]"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
388 <has_text_matching expression="500 × 11"/>
0
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
389 </assert_stdout>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
390 <output name="anndata" ftype="h5ad">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
391 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
392 <has_h5_keys keys="obs/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
393 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
394 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
395 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
396 </output>
0
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
397 </test>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
398 <test expect_num_outputs="1">
1
1a9848100b1e "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
c2043062cbc0 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"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
401 <conditional name="manipulate">
c2043062cbc0 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"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
403 </conditional>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
404 <assert_stdout>
c2043062cbc0 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"/>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
406 <has_text_matching expression="500 × 11"/>
0
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
407 </assert_stdout>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
408 <output name="anndata" ftype="h5ad">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
409 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
410 <has_h5_keys keys="obs/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
411 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
412 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
413 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
414 </output>
0
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
415 </test>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
416 <test expect_num_outputs="1">
1
1a9848100b1e "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
c2043062cbc0 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"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
419 <conditional name="manipulate">
c2043062cbc0 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"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
421 </conditional>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
422 <assert_stdout>
c2043062cbc0 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"/>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
424 <has_text_matching expression="11 × 500"/>
0
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
425 </assert_stdout>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
426 <output name="anndata" ftype="h5ad">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
427 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
428 <has_h5_keys keys="var/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
429 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
430 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
431 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
432 </output>
0
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
433 </test>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
434 <test expect_num_outputs="1">
1
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
435 <!-- test 7 -->
1a9848100b1e "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"/>
1a9848100b1e "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">
1a9848100b1e "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"/>
1a9848100b1e "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"/>
1a9848100b1e "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"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
441 </conditional>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
442 <assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
443 <has_text_matching expression="500 × 11"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
444 </assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
445 <output name="anndata" ftype="h5ad">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
446 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
447 <has_h5_keys keys="obs/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
448 <has_h5_keys keys="var/annot1"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
449 <has_h5_keys keys="var/annot2"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
450 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
451 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
452 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
453 </output>
1
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
454 </test>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
455 <test expect_num_outputs="1">
1
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
456 <!-- test 8 -->
1a9848100b1e "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"/>
1a9848100b1e "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">
1a9848100b1e "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"/>
1a9848100b1e "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"/>
1a9848100b1e "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"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
462 </conditional>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
463 <assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
464 <has_text_matching expression="500 × 11"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
465 </assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
466 <output name="anndata" ftype="h5ad">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
467 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
468 <has_h5_keys keys="obs/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
469 <has_h5_keys keys="obs/annot1"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
470 <has_h5_keys keys="obs/annot2"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
471 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
472 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
473 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
474 </output>
1
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
475 </test>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
476 <test expect_num_outputs="1">
1
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
477 <!-- test 9 -->
1a9848100b1e "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"/>
1a9848100b1e "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">
1a9848100b1e "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"/>
1a9848100b1e "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"/>
1a9848100b1e "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">
1a9848100b1e "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"/>
1a9848100b1e "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">
1a9848100b1e "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"/>
1a9848100b1e "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"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
487 </conditional>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
488 </conditional>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
489 </conditional>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
490 <assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
491 <has_text_matching expression="500 × 2"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
492 </assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
493 <output name="anndata" ftype="h5ad">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
494 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
495 <has_h5_keys keys="obs/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
496 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
497 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
498 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
499 </output>
1
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
500 </test>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
501 <test expect_num_outputs="1">
1
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
502 <!-- test 10 -->
1a9848100b1e "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"/>
1a9848100b1e "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">
1a9848100b1e "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"/>
1a9848100b1e "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"/>
1a9848100b1e "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">
1a9848100b1e "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"/>
1a9848100b1e "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"/>
1a9848100b1e "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">
1a9848100b1e "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"/>
1a9848100b1e "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"/>
1a9848100b1e "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"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
514 </conditional>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
515 </conditional>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
516 </conditional>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
517 <assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
518 <has_text_matching expression="260 × 11"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
519 </assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
520 <output name="anndata" ftype="h5ad">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
521 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
522 <has_h5_keys keys="obs/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
523 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
524 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
525 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
526 </output>
1
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents: 0
diff changeset
527 </test>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
528 <test expect_num_outputs="1">
2
a28cc202e9f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 1
diff changeset
529 <!-- test 11 -->
a28cc202e9f5 "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"/>
a28cc202e9f5 "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">
a28cc202e9f5 "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"/>
a28cc202e9f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents: 1
diff changeset
533 </conditional>
12
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
534 <assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
535 <has_text_matching expression="500 × 11"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
536 </assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
537 <output name="anndata" ftype="h5ad">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
538 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
539 <has_h5_keys keys="obs/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
540 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
541 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
542 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
543 </output>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
544 </test>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
545 <test expect_num_outputs="1">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
546 <!-- test 12 remove_keys -->
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
547 <param name="input" value="krumsiek11.h5ad"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
548 <conditional name="manipulate">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
549 <param name="function" value="remove_keys"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
550 <param name="obs_keys" value="cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
551 </conditional>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
552 <assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
553 <has_text_matching expression="500 × 11"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
554 </assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
555 <output name="anndata" ftype="h5ad">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
556 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
557 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
558 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
559 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
560 </output>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
561 </test>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
562 <test expect_num_outputs="1">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
563 <!-- test 13 flag_genes -->
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
564 <param name="input" value="krumsiek11.h5ad"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
565 <conditional name="manipulate">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
566 <param name="function" value="flag_genes"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
567 <repeat name="gene_flags">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
568 <param name="startswith" value="Gata"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
569 <param name="col_name" value="Gata_TF"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
570 </repeat>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
571 <repeat name="gene_flags">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
572 <param name="startswith" value="Gf"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
573 <param name="col_name" value="GF"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
574 </repeat>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
575 </conditional>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
576 <assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
577 <has_text_matching expression="500 × 11"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
578 </assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
579 <output name="anndata" ftype="h5ad">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
580 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
581 <has_h5_keys keys="var/Gata_TF"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
582 <has_h5_keys keys="var/GF"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
583 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
584 </output>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
585 </test>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
586 <test expect_num_outputs="1">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
587 <!-- test 14 split_on_obs -->
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
588 <param name="input" value="krumsiek11.h5ad"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
589 <conditional name="manipulate">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
590 <param name="function" value="split_on_obs"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
591 <param name="key" value="cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
592 </conditional>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
593 <output_collection name="output_h5ad_split" type="list">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
594 <element name="cell_type_0">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
595 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
596 <has_h5_keys keys="obs/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
597 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
598 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
599 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
600 </element>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
601 <element name="cell_type_1">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
602 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
603 <has_h5_keys keys="obs/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
604 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
605 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
606 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
607 </element>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
608 <element name="cell_type_2">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
609 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
610 <has_h5_keys keys="obs/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
611 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
612 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
613 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
614 </element>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
615 <element name="cell_type_3">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
616 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
617 <has_h5_keys keys="obs/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
618 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 11
diff changeset
619 <has_h5_keys keys="uns/iroot"/>
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620 </assert_contents>
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621 </element>
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622 </output_collection>
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623 </test>
0
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624 </tests>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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625 <help><![CDATA[
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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626 **What it does**
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627
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628 This tool takes a AnnData dataset, manipulates it and returns it.
0
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629
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630 The possible manipulations are:
0
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631
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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
c2043062cbc0 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
c2043062cbc0 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`
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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
c2043062cbc0 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.
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641
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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
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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643
c2043062cbc0 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.
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645
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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
c2043062cbc0 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`
c2043062cbc0 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
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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.
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653
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654 - Flag genes start with a pattern
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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>`__)
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659
c2043062cbc0 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>`__)
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663
c2043062cbc0 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.
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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
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672 - Filter data variables or observations, by index or key
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673
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674 - Freeze the current state into the 'raw' attribute
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675
0
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676 @HELP@
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677 ]]></help>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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678 <expand macro="citations"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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679 </tool>