Mercurial > repos > ufz > omero_get_value

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planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 233f0e70cb20a02ec8530dbcfd5c7e70eef74476
author ufz
date Mon, 26 Jan 2026 15:06:01 +0000
parents 7a94eb8c345d
children
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1ae349b83c08 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
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1 <tool id="omero_get_value" name="OMERO get Object" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
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2 <description> with ezomero </description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <token name="@VERSION_SUFFIX@">3</token>
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6 </macros>
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7 <xrefs>
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8 <xref type="bio.tools">omero</xref>
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9 </xrefs>
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10 <expand macro="ezomero_requirements"/>
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11 <required_files>
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12 <include path="connect_omero.py" />
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13 <include path="omero_get_value.py" />
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14 </required_files>
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15 <command detect_errors="exit_code"><![CDATA[
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16 #if $test_username != ""
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17 export OMERO_USER="$test_username" &&
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18 export OMERO_PASSWORD="$test_password" &&
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19 #end if
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20
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21 mkdir output;
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22 python '$__tool_directory__/omero_get_value.py'
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23 @HOST_PORT@
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24 --obj_type '$obj_type'
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25 #if $ids_input.ids_format == "values"
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26 --ids ${str($ids_input.ids).replace(',', ' ')}
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27 #else
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28 --ids_path '$ids_input.ids_path'
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29 #end if
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30 @SESSION_ID@
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31 --out_dir ./output/
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32 ]]></command>
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33 <inputs>
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34 <expand macro="host_port"/>
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35 <param argument="obj_type" type="select" optional="false" label="Type of object to fetch:">
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36 <option value="Annotation">Annotation</option>
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37 <option value="Tag">Tag</option>
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38 <option value="Table">Table</option>
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39 <option value="Attachment">Attachment</option>
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40 </param>
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41 <conditional name="ids_input">
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42 <param name="ids_format" type="select" label="How do you provide the ID(s) of the OMERO object?">
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43 <option value="values">Comma separated values</option>
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44 <option value="file">From a dataset (one per line)</option>
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45 </param>
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46 <when value="values">
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47 <param argument="--ids" type="text" value="" label="ID(s) of the object(s) to fetch on OMERO separated by comma">
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48 <validator type="regex" message="Enter a valid list of IDs (i.e. 2,45,56,67)">^(\d+)(,\d+)*$</validator>
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49 </param>
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50 </when>
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51 <when value="file">
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52 <param argument="--ids_path" type="data" format="txt,tabular" label="Dataset with ID(s) of the object(s) to fetch on OMERO (one per line)"/>
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53 </when>
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54 </conditional>
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55 </inputs>
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56 <outputs>
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57 <collection name="split_output" type="list">
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58 <discover_datasets pattern="__name_and_ext__" directory="output"/>
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59 <filter> not (obj_type=="Tag" or obj_type=="Annotation")</filter>
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60 </collection>
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61 <data name="tsv" from_work_dir="output.tsv" format="tabular">
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62 <filter> obj_type=="Tag" or obj_type=="Annotation"</filter>
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63 </data>
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64 </outputs>
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65 <tests>
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66 <test expect_num_outputs="1">
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67 <param name="omero_host" value="host.docker.internal"/>
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68 <param name="omero_port" value="6064"/>
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69 <param name="obj_type" value="Tag"/>
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70 <conditional name="ids_input">
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71 <param name="ids_format" value="values"/>
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72 <param name="ids" value="1"/>
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73 </conditional>
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74 <param name="test_username" value="root"/>
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75 <param name="test_password" value="omero"/>
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76 <output name="tsv" ftype="tabular">
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77 <assert_contents>
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78 <has_text text="test_tag"/>
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79 <has_n_lines n="2"/>
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80 </assert_contents>
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81 </output>
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82 </test>
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83 <test expect_num_outputs="1">
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84 <param name="omero_host" value="host.docker.internal"/>
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85 <param name="omero_port" value="6064"/>
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86 <param name="obj_type" value="Annotation"/>
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87 <conditional name="ids_input">
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88 <param name="ids_format" value="values"/>
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89 <param name="ids" value="7"/>
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90 </conditional>
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91 <param name="test_username" value="root"/>
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92 <param name="test_password" value="omero"/>
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93 <output name="tsv" ftype="tabular">
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94 <assert_contents>
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95 <has_n_lines n="4"/>
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96 </assert_contents>
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97 </output>
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98 </test>
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99 <test expect_num_outputs="1">
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100 <param name="omero_host" value="host.docker.internal"/>
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101 <param name="omero_port" value="6064"/>
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102 <param name="obj_type" value="Attachment"/>
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103 <conditional name="ids_input">
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104 <param name="ids_format" value="values"/>
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105 <param name="ids" value="2,3,4"/>
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106 </conditional>
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107 <param name="test_username" value="root"/>
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108 <param name="test_password" value="omero"/>
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109 <output_collection name="split_output" type="list" count="3">
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110 <element name="ID_2_attachment">
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111 <assert_contents>
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112 <has_text text="col1"/>
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113 </assert_contents>
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114 </element>
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115 <element name="ID_3_attachment">
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116 <assert_contents>
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117 <has_text text="col1"/>
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118 </assert_contents>
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119 </element>
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120 <element name="ID_4_attachment">
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121 <assert_contents>
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122 <has_text text="col1"/>
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123 </assert_contents>
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124 </element>
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125 </output_collection>
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126 </test>
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127 <test expect_num_outputs="1">
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128 <param name="omero_host" value="host.docker.internal"/>
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129 <param name="omero_port" value="6064"/>
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130 <param name="obj_type" value="Table"/>
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131 <conditional name="ids_input">
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132 <param name="ids_format" value="values"/>
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133 <param name="ids" value="5,6"/>
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134 </conditional>
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135 <param name="test_username" value="root"/>
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136 <param name="test_password" value="omero"/>
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137 <output_collection name="split_output" type="list" count="2">
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138 <element name="ID_5_table">
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139 <assert_contents>
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140 <has_n_lines n="5"/>
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141 </assert_contents>
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142 </element>
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143 <element name="ID_6_table">
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144 <assert_contents>
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145 <has_n_lines n="5"/>
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146 </assert_contents>
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147 </element>
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148 </output_collection>
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149 </test>
0
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150 </tests>
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151 <help>
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152 Description
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153 -----------
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154
4
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155 Tool to fetch Annotation, Tag, Tables and Attachments from IDs.
0
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156
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157 The IDs can be obtained with the tool OMERO get IDs with ezomero
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158
1
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159 @SECURITY_DISCLAIMER@
0
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160 </help>
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161 <citations>
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162 <citation type="doi">10.1038/nmeth.1896</citation>
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163 </citations>
6
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164 </tool>