Mercurial > repos > iuc > anndata_inspect

annotate inspect.xml @ 0:b2a6ce371781 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
author iuc
date Wed, 10 Apr 2019 03:25:39 -0400
parents
children 05304c5c195d
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0
b2a6ce371781 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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1 <tool id="anndata_inspect" name="Inspect AnnData" version="@VERSION@+@GALAXY_VERSION@">
b2a6ce371781 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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2 <description>object</description>
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3 <macros>
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iuc
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4 <import>macros.xml</import>
b2a6ce371781 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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5 </macros>
b2a6ce371781 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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6 <expand macro="requirements"/>
b2a6ce371781 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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7 <expand macro="version_command"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 @CMD@
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10 ]]></command>
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11 <configfiles>
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12 <configfile name="script_file"><![CDATA[
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13 @CMD_imports@
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14
b2a6ce371781 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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15 adata = ad.read('$input')
b2a6ce371781 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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16
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17 #if $inspect.info == 'general'
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18 with open('$general', 'w') as f:
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19 print(adata, file=f)
b2a6ce371781 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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20 #else if $inspect.info == 'X'
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21 adata.to_df().to_csv('$X', sep='\t')
b2a6ce371781 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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22 #else if $inspect.info == 'obs'
b2a6ce371781 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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23 adata.obs.to_csv('$obs', sep='\t')
b2a6ce371781 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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24 #else if $inspect.info == 'var'
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25 adata.var.to_csv('$var', sep='\t')
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26 #else if $inspect.info == 'chunk_X'
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27 import pandas as pd
b2a6ce371781 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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28 #if $inspect.chunk.info == 'random'
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29 X = adata.chunk_X(select=$inspect.chunk.size, replace=$inspect.chunk.replace)
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30 #else
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31 #set $select = [int(x.strip()) for x in str($inspect.chunk.list).split(',')]
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32 X = adata.chunk_X(select=$select)
b2a6ce371781 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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33 #end if
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34 pd.DataFrame(X).to_csv('$chunk_X', sep='\t')
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35 #end if
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36 ]]></configfile>
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37 </configfiles>
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38 <inputs>
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39 <param name="input" type="data" format="h5ad" label="Annotated data matrix"/>
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40 <conditional name="inspect">
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41 <param name="info" type="select" label="What to inspect?">
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42 <option value="general">General information about the object</option>
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43 <option value="X">The full data matrix</option>
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44 <option value="chunk_X">A chunk of the data matrix</option>
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45 <option value="obs">Key-indexed observations annotation</option>
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46 <option value="var">Key-indexed annotation of variables/features</option>
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47 <!--<option value="uns">Unstructured annotation</option>!-->
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48 </param>
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49 <when value="general"/>
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50 <when value="X"/>
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51 <when value="obs"/>
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52 <when value="var"/>
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53 <when value="chunk_X">
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54 <expand macro="params_chunk_X"/>
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55 </when>
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56 </conditional>
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57 </inputs>
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58 <outputs>
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59 <data name="general" format="txt" label="${tool.name} on ${on_string}: General information">
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60 <filter>inspect['info'] == 'general'</filter>
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61 </data>
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62 <data name="X" format="tabular" label="${tool.name} on ${on_string}: Key-indexed observations annotation (X)">
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63 <filter>inspect['info'] == 'X'</filter>
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64 </data>
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65 <data name="obs" format="tabular" label="${tool.name} on ${on_string}: Key-indexed observations annotation (obs)">
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66 <filter>inspect['info'] == 'obs'</filter>
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67 </data>
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68 <data name="var" format="tabular" label="${tool.name} on ${on_string}: Key-indexed annotation of variables/features (var)">
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69 <filter>inspect['info'] == 'var'</filter>
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70 </data>
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71 <data name="chunk_X" format="tabular" label="${tool.name} on ${on_string}: Observations annotation">
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72 <filter>inspect['info'] == 'chunk_X'</filter>
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73 </data>
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74 </outputs>
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75 <tests>
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76 <test>
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77 <param name="input" value="krumsiek11.h5ad"/>
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78 <conditional name="inspect">
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79 <param name="info" value="general"/>
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80 </conditional>
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81 <output name="general" value="inspect.general.txt"/>
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82 </test>
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83 <test>
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84 <param name="input" value="krumsiek11.h5ad"/>
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85 <conditional name="inspect">
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86 <param name="info" value="X"/>
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87 </conditional>
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88 <assert_stdout>
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89 <has_text_matching expression="adata.to_df\(\).to_csv"/>
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90 </assert_stdout>
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91 <output name="X" value="inspect.X.tabular" ftype="tabular"/>
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92 </test>
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93 <test>
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94 <param name="input" value="krumsiek11.h5ad"/>
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95 <conditional name="inspect">
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96 <param name="info" value="obs"/>
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97 </conditional>
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98 <assert_stdout>
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99 <has_text_matching expression="adata.obs.to_csv"/>
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100 </assert_stdout>
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101 <output name="obs" value="inspect.obs.tabular" ftype="tabular"/>
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102 </test>
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103 <test>
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104 <param name="input" value="krumsiek11.h5ad"/>
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105 <conditional name="inspect">
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106 <param name="info" value="var"/>
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107 </conditional>
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108 <assert_stdout>
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109 <has_text_matching expression="adata.var.to_csv"/>
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110 </assert_stdout>
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111 <output name="var" value="inspect.var.tabular" ftype="tabular"/>
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112 </test>
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113 <test>
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114 <param name="input" value="krumsiek11.h5ad"/>
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115 <conditional name="inspect">
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116 <param name="info" value="chunk_X"/>
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117 <conditional name="chunk">
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118 <param name="info" value="specified"/>
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119 <param name="list" value="3,5,8"/>
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120 </conditional>
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121 </conditional>
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122 <assert_stdout>
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123 <has_text_matching expression="adata.chunk_X"/>
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124 <has_text_matching expression="select=\[3, 5, 8\]"/>
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125 </assert_stdout>
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126 <output name="chunk_X" value="inspect.chunk_X.specified.tabular" ftype="tabular"/>
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127 </test>
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128 <test>
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129 <param name="input" value="krumsiek11.h5ad"/>
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130 <conditional name="inspect">
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131 <param name="info" value="chunk_X"/>
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132 <conditional name="chunk">
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133 <param name="info" value="random"/>
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134 <param name="list" value="10"/>
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135 <param name="replace" value="true"/>
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136 </conditional>
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137 </conditional>
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138 <assert_stdout>
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139 <has_text_matching expression="adata.chunk_X"/>
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140 <has_text_matching expression="select=10"/>
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141 <has_text_matching expression="replace=True"/>
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142 </assert_stdout>
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143 <output name="chunk_X">
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144 <assert_contents>
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145 <has_text_matching expression="0\t1\t2\t3\t4\t5\t6\t7\t8\t9\t10"/>
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146 </assert_contents>
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147 </output>
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148 </test>
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149 </tests>
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150 <help><![CDATA[
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151 **What it does**
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152
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153 This tool inspects a AnnData dataset and returns:
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154
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155 - General information about the object as text
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156 - The full data matrix (`X`) as a Tabular
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157 - A chunk of the data matrix as a Tabular, using the `chunk_X method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.chunk_X.html>`__
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158 - Key-indexed observations annotation (`obs`) as a Tabular
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159 - Key-indexed annotation of variables/features (`var`) as a Tabular
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160
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161 @HELP@
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162 ]]></help>
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163 <expand macro="citations"/>
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164 </tool>