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annotate starting_modules.xml @ 6:6070780813d9 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author bgruening
date Sun, 05 Nov 2023 09:36:34 +0000
parents 670975e92458
children
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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</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@">2</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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12 <edam_operations>
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13 <edam_operation>operation_3443</edam_operation>
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14 </edam_operations>
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15 <xrefs>
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16 <xref type="bio.tools">CellProfiler</xref>
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17 <xref type="biii">cellprofiler</xref>
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18 </xrefs>
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20 <expand macro="py_requirements"/>
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22 <command detect_errors="aggressive"><![CDATA[
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23 python '$__tool_directory__/starting_modules.py' '$inputs'
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24 ]]></command>
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26 <configfiles>
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27 <inputs name="inputs"/>
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28 </configfiles>
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30 <inputs>
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31 <!-- Images module-->
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32 <expand macro="starting_modules_images" />
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33 <!-- Metadata module-->
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34 <expand macro="starting_modules_metadata" />
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35 <!-- NamesAndTypes-->
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36 <expand macro="starting_modules_nameandtypes" />
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37 <!-- Groups -->
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38 <expand macro="starting_modules_groups" />
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39 </inputs>
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40 <outputs>
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41 <expand macro="output_pipeline_param" />
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42 </outputs>
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43 <tests>
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44 <test>
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45 <!-- one big test case for various inputs scenarios -->
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46 <param name="filter_images" value="Images only"/>
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47 <conditional name="con_metadata_extraction">
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48 <param name="extract" value="Yes"/>
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49 <repeat name="extraction_method">
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50 <param name="metadata_extraction_method" value="Extract from file/folder names"/>
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51 <conditional name="con_metadata_extract_from">
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52 <param name="match_all_any" value="and" />
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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="file"/>
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57 <param name="match_value" value="im"/>
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58 <param name="contain" value="contain"/>
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59 </conditional>
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60 </repeat>
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61 <repeat name="r_match">
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62 <conditional name="con_match">
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63 <param name="operator" value="does"/>
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64 <param name="rule_type" value="extension"/>
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65 <param name="match_type" value="istif"/>
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66 </conditional>
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67 </repeat>
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68 <param name="extract_metadata_from" value="Images matching a rule" />
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69 </conditional>
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70 <conditional name="con_metadata_source">
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71 <param name="metadata_source" value="File name" />
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72 <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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73 </conditional>
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74 </repeat>
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75 <repeat name="extraction_method">
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76 <param name="metadata_extraction_method" value="Extract from file/folder names"/>
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77 <conditional name="con_metadata_extract_from">
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78 <param name="extract_metadata_from" value="All images" />
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79 </conditional>
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80 <conditional name="con_metadata_source">
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81 <param name="metadata_source" value="Folder name" />
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82 <param name="folder_name_regex" value="(?P&lt;folderField1>.*)_(?P&lt;folderField2>[a-zA-Z0-9]+)" />
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83 </conditional>
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84 </repeat>
2
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85 </conditional>
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86 <conditional name="pixel_space">
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87 <param name="process_3d" value="No"/>
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88 </conditional>
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89 <conditional name="con_assign_a_name_to">
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90 <param name="assign_a_name_to" value="Images matching rules"/>
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91 <repeat name="r_match_rule">
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
92 <param name="match_all_any" value="and" />
3
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="file" />
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="does" />
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
97 <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
98 <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
99 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
100 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
101 <repeat name="r_match">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
102 <conditional name="con_match">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
103 <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
104 <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
105 <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
106 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
107 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
108 <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
109 <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
110 <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
111 </conditional>
3
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
112 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
113
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
114 <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
115 <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
116 <repeat name="r_match" />
2
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
117 <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
118 <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
119 <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
120 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
121 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
122
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
123 <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
124 <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
125 <repeat name="r_match">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
126 <conditional name="con_match">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
127 <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
128 <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
129 <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
130 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
131 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
132 <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
133 <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
134 <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
135 <conditional name="con_set_intensity">
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
136 <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
137 </conditional>
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
138 </conditional>
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
139 </repeat>
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
140 <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
141 </conditional>
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
142 <conditional name="con_groups">
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
143 <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
144 <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
145 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
146 <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
147 </test>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
148 <test>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
149 <!-- 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
150 <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
151 <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
152 <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
153 <repeat name="extraction_method">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
154 <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
155 <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
156 <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
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="file"/>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
161 <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
162 <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
163 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
164 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
165 <repeat name="r_match">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
166 <conditional name="con_match">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
167 <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
168 <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
169 <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
170 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
171 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
172 <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
173 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
174 <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
175 <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
176 <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
177 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
178 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
179 <repeat name="extraction_method">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
180 <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
181 <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
182 <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
183 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
184 <conditional name="con_metadata_source">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
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185 <param name="metadata_source" value="Folder name" />
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186 <param name="folder_name_regex" value="(?P&lt;folderField1>.*)_(?P&lt;folderField2>[a-zA-Z0-9]+)" />
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187 </conditional>
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188 </repeat>
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189 </conditional>
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190 <conditional name="pixel_space">
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191 <param name="process_3d" value="No"/>
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192 </conditional>
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193 <conditional name="con_assign_a_name_to">
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194 <param name="assign_a_name_to" value="Images matching rules"/>
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195 <repeat name="r_match_rule">
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196 <param name="match_all_any" value="and" />
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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="file" />
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200 <param name="operator" value="does" />
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201 <param name="contain" value="contain" />
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202 <param name="match_value" value="im" />
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203 </conditional>
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204 </repeat>
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205 <repeat name="r_match">
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206 <conditional name="con_match">
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207 <param name="rule_type" value="image" />
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208 <param name="operator" value="doesnot" />
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209 <param name="match_type" value="ismonochrome" />
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210 </conditional>
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211 </repeat>
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212 <conditional name="con_select_image_type">
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213 <param name="name_to_assign" value="Cell" />
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214 <param name="select_image_type" value="Objects" />
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215 </conditional>
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216 </repeat>
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217
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218 <repeat name="r_match_rule">
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219 <param name="match_all_any" value="and" />
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220 <repeat name="r_match" />
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221 <conditional name="con_select_image_type">
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222 <param name="name_to_assign" value="GFP" />
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223 <param name="select_image_type" value="Illumination function" />
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224 </conditional>
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225 </repeat>
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226
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227 <repeat name="r_match_rule">
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228 <param name="match_all_any" value="or" />
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229 <repeat name="r_match">
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230 <conditional name="con_match">
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231 <param name="rule_type" value="extension" />
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232 <param name="operator" value="does" />
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233 <param name="match_type" value="istif" />
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234 </conditional>
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235 </repeat>
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236 <conditional name="con_select_image_type">
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237 <param name="name_to_assign" value="Actin" />
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238 <param name="select_image_type" value="Grayscale image" />
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239 <conditional name="con_set_intensity">
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240 <param name="set_intensity_range_from" value="Image metadata" />
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241 </conditional>
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242 </conditional>
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243 </repeat>
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244 <param name="matching_method" value="Order" />
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245 </conditional>
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246 <conditional name="con_groups">
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247 <param name="group_images" value="No" />
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248 </conditional>
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249 <expand macro="test_out_file" file="common-nogroup.cppipe" />
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250 </test>
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251 </tests>
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252
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253 <help>
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254 <![CDATA[
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255
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256 .. class:: infomark
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257
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258 **What it does**
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259
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260 This tool is the first in a CellProfiler pipeline and includes the first four modules:
2
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261
3
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262 *Images*: use the Images module to compile a list of files that you want to analyze.
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263
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264 *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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265
3
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266 *NamesAndTypes*: allows you to assign a meaningful name to each image by which other modules will refer to it.
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267
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268 *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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269
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270 .. class:: infomark
2
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271
3
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272 **Input**
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273
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274 No input parameters are needed for this tool.
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275
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276 .. class:: infomark
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277
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278 **Output**
2
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279
3
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280 A CellProfiler pipeline file *(.cppipe)* with the settings of the 4 modules.
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281
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282 .. class:: warningmark
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283
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284 **IMPORTANT**
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285
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286 This tool has to be the first one in a CellProfiler workflow and the last one **CellProfiler**.
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287
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288 ]]>
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289 </help>
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290 <expand macro="citations" />
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291 </tool>