annotate omero_metadata_import.xml @ 3:eba4011643dd draft

planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
author ufz
date Tue, 22 Oct 2024 11:52:32 +0000
parents e41f70e69349
children 351c6b43e16c
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1 <tool id="omero_metadata_import" name="OMERO Metadata Import" 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 <command detect_errors="exit_code"><![CDATA[
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12 python $__tool_directory__/omero_metadata_upload.py
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13 --credential-file '$credentials'
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14 @HOST_PORT@
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15 --obj_type $obj_type
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16 --ann_type $ann_type
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17 --ann_file $ann_file
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18 --an_name $an_name
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19 --log_file $log
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20 #if $object_id_selection == "existing_object"
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21 --did "$did"
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22 #end if
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23 ]]></command>
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24 <configfiles>
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25 <expand macro="credentials"/>
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26 </configfiles>
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27 <inputs>
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28 <expand macro="host_port"/>
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29 <param argument="obj_type" type="select" optional="true" label="Target Object Type">
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30 <option value="project">Project</option>
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31 <option value="screen">Screen</option>
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32 <option value="dataset">Dataset</option>
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33 <option value="image">Image</option>
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34 </param>
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35 <conditional name="object_id">
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36 <param name="object_id_selection" type="select" label="Selection" help="Create a new OMERO object or target an existing one">
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37 <option value="new_object">Create new object</option>
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38 <option value="existing_object">Target an existing object</option>
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39 </param>
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40 <when value="new_object"/>
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41 <when value="existing_object">
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42 <param name="did" type="integer" value="" optional="false" label="Object ID"/>
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43 </when>
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44 </conditional>
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45 <param argument="ann_type" type="select" optional="false" label="Annotation type" help="Select annotation format">
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46 <option value="table">Table</option>
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47 <option value="KV">Key-Value Pairs</option>
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48 </param>
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49 <param argument="ann_file" type="data" format="tabular" optional="false" label="Annotation file" help="Select annotation file"/>
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50 <param argument="an_name" type="text" optional="false" label="Annotation Name"/>
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51 </inputs>
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52 <outputs>
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53 <data name="log" format="txt"/>
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54 </outputs>
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55 <tests>
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56 <test>
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57 <param name="omero_host" value="host.docker.internal"/>
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58 <param name="omero_port" value="6064"/>
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59 <param name="obj_type" value="project"/>
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60 <param name="ann_type" value="table"/>
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61 <param name="object_id_selection" value="new_object"/>
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62 <param name="ann_file" value="metadata.tsv"/>
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63 <param name="an_name" value="Table_Test"/>
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64 <param name="test_username" value="root"/>
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65 <param name="test_password" value="omero"/>
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66 <output name="log" value="output_table_import.txt" ftype="txt">
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67 <assert_contents>
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68 <has_text text="SUCCESS: Successfully uploaded metadata for project"/>
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69 </assert_contents>
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70 </output>
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71 </test>
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72 <test>
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73 <param name="omero_host" value="host.docker.internal"/>
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74 <param name="omero_port" value="6064"/>
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75 <param name="obj_type" value="dataset"/>
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76 <param name="ann_type" value="KV"/>
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77 <param name="object_id_selection" value="new_object"/>
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78 <param name="ann_file" value="metadata.tsv"/>
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79 <param name="an_name" value="KV_Test"/>
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80 <param name="test_username" value="root"/>
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81 <param name="test_password" value="omero"/>
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82 <output name="log" value="output_KV_import.txt" ftype="txt">
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83 <assert_contents>
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84 <has_text text="SUCCESS: Successfully uploaded metadata for dataset"/>
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85 </assert_contents>
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86 </output>
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87 </test>
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88 <test>
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89 <param name="omero_host" value="host.docker.internal"/>
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90 <param name="omero_port" value="6064"/>
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91 <param name="obj_type" value="dataset"/>
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92 <param name="ann_type" value="KV"/>
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93 <param name="object_id_selection" value="existing_object"/>
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94 <param name="did" value="1"/>
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95 <param name="ann_file" value="metadata.tsv"/>
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96 <param name="an_name" value="Additional_KV_Values"/>
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97 <param name="test_username" value="root"/>
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98 <param name="test_password" value="omero"/>
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99 <output name="log" value="output_target_import.txt" ftype="txt">
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100 <assert_contents>
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101 <has_text text="SUCCESS: Successfully uploaded metadata for dataset"/>
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102 </assert_contents>
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103 </output>
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104 </test>
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105 </tests>
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106 <help>
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107 Description
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108 -----------
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109
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110 Tool to import metadata (Table and K/V pairs) into user defined OMERO.server.
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111 Metadata can be attached to an existing OMERO object (Project, Dataset, Screen, or Image).
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112 Optionally, a new OMERO object can be created before uploading the metadata.
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113 If the object does not exist, a new one will be created.
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114
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115 **Tabular metadata file example**
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116
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117 - Table
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118
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119 +------------+---------------+---------------+
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120 | image_id | attribute_1 | attribute_2 |
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121 +============+===============+===============+
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122 | 235 | 0 | 1 |
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123 +------------+---------------+---------------+
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124 | 564 | 1 | 1 |
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125 +------------+---------------+---------------+
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126 | 120 | 0 | 1 |
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127 +------------+---------------+---------------+
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128
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129 - Key-Value Pairs
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130
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131 +--------+---------+----------+
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132 | Key1 | Key2 | Key3 |
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133 +========+=========+==========+
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134 | Value1 | Value2 | Value3 |
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135 +--------+---------+----------+
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136 </help>
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137 <citations>
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138 <citation type="doi">10.1038/nmeth.1896</citation>
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139 </citations>
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140 </tool>