Mercurial > repos > bgruening > cp_common

annotate starting_modules.xml @ 5:670975e92458 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
author bgruening
date Fri, 26 Feb 2021 14:09:20 +0000
parents 27396311a314
children 6070780813d9
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5
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1 <tool id="cp_common" name="Starting Modules" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>load images and metadata into CellProfiler (Images, Metadata, NamesAndTypes, Groups)</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@">1</token>
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6 <import>starting_modules_images.xml</import>
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7 <import>starting_modules_metadata.xml</import>
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8 <import>starting_modules_nameandtypes.xml</import>
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9 <import>starting_modules_groups.xml</import>
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10 </macros>
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11
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12 <expand macro="py_requirements"/>
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14 <command detect_errors="aggressive"><![CDATA[
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15 python '$__tool_directory__/starting_modules.py' '$inputs'
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16 ]]></command>
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18 <configfiles>
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19 <inputs name="inputs"/>
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20 </configfiles>
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21
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22 <inputs>
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23 <!-- Images module-->
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24 <expand macro="starting_modules_images" />
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25 <!-- Metadata module-->
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26 <expand macro="starting_modules_metadata" />
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27 <!-- NamesAndTypes-->
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28 <expand macro="starting_modules_nameandtypes" />
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29 <!-- Groups -->
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30 <expand macro="starting_modules_groups" />
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31 </inputs>
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32 <outputs>
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33 <expand macro="output_pipeline_param" />
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34 </outputs>
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35 <tests>
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36 <test>
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37 <!-- one big test case for various inputs scenarios -->
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38 <param name="filter_images" value="Images only"/>
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39 <conditional name="con_metadata_extraction">
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40 <param name="extract" value="Yes"/>
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41 <repeat name="extraction_method">
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42 <param name="metadata_extraction_method" value="Extract from file/folder names"/>
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43 <conditional name="con_metadata_extract_from">
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44 <param name="match_all_any" value="and" />
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45 <repeat name="r_match">
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46 <conditional name="con_match">
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47 <param name="operator" value="does"/>
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48 <param name="rule_type" value="file"/>
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49 <param name="match_value" value="im"/>
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50 <param name="contain" value="contain"/>
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51 </conditional>
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52 </repeat>
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53 <repeat name="r_match">
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54 <conditional name="con_match">
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55 <param name="operator" value="does"/>
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56 <param name="rule_type" value="extension"/>
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57 <param name="match_type" value="istif"/>
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58 </conditional>
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59 </repeat>
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60 <param name="extract_metadata_from" value="Images matching a rule" />
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61 </conditional>
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62 <conditional name="con_metadata_source">
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63 <param name="metadata_source" value="File name" />
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64 <param name="file_name_regex" value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)" />
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65 </conditional>
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66 </repeat>
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67 <repeat name="extraction_method">
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68 <param name="metadata_extraction_method" value="Extract from file/folder names"/>
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69 <conditional name="con_metadata_extract_from">
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70 <param name="extract_metadata_from" value="All images" />
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71 </conditional>
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72 <conditional name="con_metadata_source">
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73 <param name="metadata_source" value="Folder name" />
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74 <param name="folder_name_regex" value="(?P&lt;folderField1>.*)_(?P&lt;folderField2>[a-zA-Z0-9]+)" />
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75 </conditional>
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76 </repeat>
2
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77 </conditional>
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78 <conditional name="pixel_space">
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79 <param name="process_3d" value="No"/>
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80 </conditional>
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81 <conditional name="con_assign_a_name_to">
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82 <param name="assign_a_name_to" value="Images matching rules"/>
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83 <repeat name="r_match_rule">
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84 <param name="match_all_any" value="and" />
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85 <repeat name="r_match">
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86 <conditional name="con_match">
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87 <param name="rule_type" value="file" />
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88 <param name="operator" value="does" />
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89 <param name="contain" value="contain" />
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90 <param name="match_value" value="im" />
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
91 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
92 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
93 <repeat name="r_match">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
94 <conditional name="con_match">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
95 <param name="rule_type" value="image" />
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
96 <param name="operator" value="doesnot" />
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
97 <param name="match_type" value="ismonochrome" />
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
98 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
99 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
100 <conditional name="con_select_image_type">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
101 <param name="name_to_assign" value="Cell" />
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
102 <param name="select_image_type" value="Objects" />
2
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
103 </conditional>
3
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
104 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
105
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
106 <repeat name="r_match_rule">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
107 <param name="match_all_any" value="and" />
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
108 <repeat name="r_match" />
2
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
109 <conditional name="con_select_image_type">
3
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
110 <param name="name_to_assign" value="GFP" />
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
111 <param name="select_image_type" value="Illumination function" />
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
112 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
113 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
114
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
115 <repeat name="r_match_rule">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
116 <param name="match_all_any" value="or" />
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
117 <repeat name="r_match">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
118 <conditional name="con_match">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
119 <param name="rule_type" value="extension" />
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
120 <param name="operator" value="does" />
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
121 <param name="match_type" value="istif" />
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
122 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
123 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
124 <conditional name="con_select_image_type">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
125 <param name="name_to_assign" value="Actin" />
2
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
126 <param name="select_image_type" value="Grayscale image" />
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
127 <conditional name="con_set_intensity">
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
128 <param name="set_intensity_range_from" value="Image metadata" />
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
129 </conditional>
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
130 </conditional>
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
131 </repeat>
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
132 <param name="matching_method" value="Order" />
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
133 </conditional>
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
134 <conditional name="con_groups">
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
135 <param name="group_images" value="Yes" />
3
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
136 <param name="group_category" value="field1" />
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
137 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
138 <expand macro="test_out_file" file="common-complicated.cppipe"/>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
139 </test>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
140 <test>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
141 <!-- Repeat test for no grouping -->
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
142 <param name="filter_images" value="Images only"/>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
143 <conditional name="con_metadata_extraction">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
144 <param name="extract" value="Yes"/>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
145 <repeat name="extraction_method">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
146 <param name="metadata_extraction_method" value="Extract from file/folder names"/>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
147 <conditional name="con_metadata_extract_from">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
148 <param name="match_all_any" value="and" />
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
149 <repeat name="r_match">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
150 <conditional name="con_match">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
151 <param name="operator" value="does"/>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
152 <param name="rule_type" value="file"/>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
153 <param name="match_value" value="im"/>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
154 <param name="contain" value="contain"/>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
155 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
156 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
157 <repeat name="r_match">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
158 <conditional name="con_match">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
159 <param name="operator" value="does"/>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
160 <param name="rule_type" value="extension"/>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
161 <param name="match_type" value="istif"/>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
162 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
163 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
164 <param name="extract_metadata_from" value="Images matching a rule" />
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
165 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
166 <conditional name="con_metadata_source">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
167 <param name="metadata_source" value="File name" />
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
168 <param name="file_name_regex" value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)" />
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
169 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
170 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
171 <repeat name="extraction_method">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
172 <param name="metadata_extraction_method" value="Extract from file/folder names"/>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
173 <conditional name="con_metadata_extract_from">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
174 <param name="extract_metadata_from" value="All images" />
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
175 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
176 <conditional name="con_metadata_source">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
177 <param name="metadata_source" value="Folder name" />
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
178 <param name="folder_name_regex" value="(?P&lt;folderField1>.*)_(?P&lt;folderField2>[a-zA-Z0-9]+)" />
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
179 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
180 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
181 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
182 <conditional name="pixel_space">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
183 <param name="process_3d" value="No"/>
2
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
184 </conditional>
3
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185 <conditional name="con_assign_a_name_to">
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186 <param name="assign_a_name_to" value="Images matching rules"/>
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187 <repeat name="r_match_rule">
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188 <param name="match_all_any" value="and" />
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189 <repeat name="r_match">
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190 <conditional name="con_match">
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191 <param name="rule_type" value="file" />
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192 <param name="operator" value="does" />
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193 <param name="contain" value="contain" />
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194 <param name="match_value" value="im" />
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195 </conditional>
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196 </repeat>
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197 <repeat name="r_match">
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198 <conditional name="con_match">
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199 <param name="rule_type" value="image" />
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200 <param name="operator" value="doesnot" />
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201 <param name="match_type" value="ismonochrome" />
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202 </conditional>
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203 </repeat>
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204 <conditional name="con_select_image_type">
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205 <param name="name_to_assign" value="Cell" />
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206 <param name="select_image_type" value="Objects" />
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207 </conditional>
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208 </repeat>
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209
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210 <repeat name="r_match_rule">
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211 <param name="match_all_any" value="and" />
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212 <repeat name="r_match" />
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213 <conditional name="con_select_image_type">
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214 <param name="name_to_assign" value="GFP" />
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215 <param name="select_image_type" value="Illumination function" />
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216 </conditional>
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217 </repeat>
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218
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219 <repeat name="r_match_rule">
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220 <param name="match_all_any" value="or" />
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221 <repeat name="r_match">
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222 <conditional name="con_match">
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223 <param name="rule_type" value="extension" />
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224 <param name="operator" value="does" />
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225 <param name="match_type" value="istif" />
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226 </conditional>
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227 </repeat>
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228 <conditional name="con_select_image_type">
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229 <param name="name_to_assign" value="Actin" />
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230 <param name="select_image_type" value="Grayscale image" />
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231 <conditional name="con_set_intensity">
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232 <param name="set_intensity_range_from" value="Image metadata" />
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233 </conditional>
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234 </conditional>
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235 </repeat>
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236 <param name="matching_method" value="Order" />
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237 </conditional>
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238 <conditional name="con_groups">
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239 <param name="group_images" value="No" />
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240 </conditional>
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241 <expand macro="test_out_file" file="common-nogroup.cppipe" />
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242 </test>
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243 </tests>
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244
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245 <help>
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246 <![CDATA[
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247
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248 .. class:: infomark
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249
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250 **What it does**
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251
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252 This tool is the first in a CellProfiler pipeline and includes the first four modules:
2
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253
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254 *Images*: use the Images module to compile a list of files that you want to analyze.
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255
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256 *Metadata*: optionally allows you to extract information describing your images (i.e., metadata) which will be stored along with your measurements.
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257
3
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258 *NamesAndTypes*: allows you to assign a meaningful name to each image by which other modules will refer to it.
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259
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260 *Groups*: optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.
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261
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262 .. class:: infomark
2
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263
3
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264 **Input**
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265
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266 No input parameters are needed for this tool.
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267
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268 .. class:: infomark
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269
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270 **Output**
2
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271
3
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272 A CellProfiler pipeline file *(.cppipe)* with the settings of the 4 modules.
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273
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274 .. class:: warningmark
2
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275
3
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276 **IMPORTANT**
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277
3
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278 This tool has to be the first one in a CellProfiler workflow and the last one **CellProfiler**.
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279
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280 ]]>
2
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281 </help>
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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282 <expand macro="citations" />
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
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283 </tool>