Mercurial > repos > ufz > omero_filter

annotate omero_filter.xml @ 5:e6b2a026843d draft default tip

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planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 3a3a04c0b20310f8d4fbc5be27559353c7e2cc61
author ufz
date Tue, 10 Feb 2026 16:47:59 +0000
parents 25d2036b9b8b
children
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063ce7148f7d planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 54b50795912de3f2508cfcfc6911d71a94b34c56
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1 <tool id="omero_filter" name="OMERO IDs" 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_filter.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="$test_password" &&
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19 #end if
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20
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21 python '$__tool_directory__'/omero_filter.py
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22 @HOST_PORT@
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23 --filter $filter_type.filter
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24 --value1 '$filter_type.value1'
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25 --id '$filter_type.did'
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26 --tsv_file '$tsv'
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27 #if $filter == "KP"
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28 --value2 '$filter_type.value2'
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29 #end if
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30 @SESSION_ID@
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31 ]]></command>
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32 <inputs>
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33 <expand macro="host_port"/>
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34 <conditional name = "filter_type">
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35 <param name="filter" type="select" optional="false" label="Filter type to apply:">
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36 <option value="filename">Filename</option>
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37 <option value="KP">Key-Value</option>
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38 <option value="tag">Tag</option>
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39 </param>
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40 <when value="filename">
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41 <param name="value1" type="text" label="Filename to search among the image IDs">
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42 <validator type="regex" message="Enter a valid filename to search in the OMERO server">^[\w\-. ]+$</validator>
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43 </param>
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44 <param name="value2" value="" type="hidden" label="Not necessary filter"/>
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45 <param name="did" type="text" label="List of images IDs">
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46 <validator type="regex" message="Enter a valid list of IDs (i.e. 2,45,56,67)">^\d+(,\d+)*$</validator>
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47 </param>
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48 </when>
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49 <when value="KP">
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50 <param name="value1" type="text" label="Key to search among the image IDs">
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51 <validator type="regex" message="Enter a valid Key to search in the OMERO server">^[\w\-. ]+$</validator>
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52 </param>
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53 <param name="value2" type="text" label="Value to search among the image IDs">
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54 <validator type="regex" message="Enter a valid Value to search in the OMERO server">^[\w\-. ]+$</validator>
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55 </param>
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56 <param name="did" type="text" label="List of images IDs">
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57 <validator type="regex" message="Enter a valid list of IDs (i.e. 2,45,56,67)">^\d+(,\d+)*$</validator>
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58 </param>
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59 </when>
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60 <when value="tag">
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61 <param name="value1" type="text" label="Tag to search among the images IDs">
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62 <validator type="regex" message="Enter a valid Key to search in the OMERO server">^[\w\-. ]+$</validator>
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63 </param>
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64 <param name="value2" value="" optional="true" type="hidden" label="Not necessary filter"/>
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65 <param name="did" type="text" label="List of images IDs">
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66 <validator type="regex" message="Enter a valid list of IDs (i.e. 2,45,56,67)">^(\d+)(,\d+)*$</validator>
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67 </param>
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68 </when>
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69 </conditional>
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70 </inputs>
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71 <outputs>
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72 <data name="tsv" format="tabular"/>
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73 </outputs>
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74 <tests>
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75 <test>
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76 <param name="omero_host" value="host.docker.internal"/>
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77 <param name="omero_port" value="6064"/>
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78 <conditional name="filter_type">
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79 <param name="filter" value="filename"/>
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80 <param name="value1" value="sample_image.jpg"/>
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81 <param name="did" value="1,2"/>
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82 </conditional>
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83 <param name="test_username" value="root"/>
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84 <param name="test_password" value="omero"/>
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85 <output name="tsv" value="output_filter_filename.tsv" ftype="tabular">
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86 <assert_contents>
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87 <has_text text="1"/>
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88 <has_n_columns n="1"/>
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89 </assert_contents>
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90 </output>
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91 </test>
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92 <test>
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93 <param name="omero_host" value="host.docker.internal"/>
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94 <param name="omero_port" value="6064"/>
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95 <conditional name="filter_type">
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96 <param name="filter" value="tag"/>
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97 <param name="value1" value="test_tag"/>
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98 <param name="did" value="1,2"/>
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99 </conditional>
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100 <param name="test_username" value="root"/>
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101 <param name="test_password" value="omero"/>
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102 <output name="tsv" value="output_filter_tag.tsv" ftype="tabular">
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103 <assert_contents>
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104 <has_text text="1"/>
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105 <has_n_columns n="1"/>
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106 </assert_contents>
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107 </output>
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108 </test>
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109 </tests>
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110 <help>
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111 Description
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112 -----------
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113
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114 - Tool to filter images IDs by filename, Key-Value Pairs and Tag value.
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115 - For Key-Value Pairs search, two values are required (Value1 = Key, Value2 = Pair).
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116 - IDs are a list of image IDs which can be fetched using the omero_get tool.
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117
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118 @SECURITY_DISCLAIMER@
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119
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120 </help>
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121 <citations>
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122 <citation type="doi">10.1038/nmeth.1896</citation>
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123 </citations>
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124 </tool>