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annotate starting_modules.xml @ 3:27396311a314 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
author bgruening
date Mon, 11 May 2020 07:45:07 -0400
parents 3c3cd68d6d5a
children 670975e92458
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1 <tool id="cp_common" name="Starting Modules" version="@CP_VERSION@">
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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 <import>starting_modules_images.xml</import>
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6 <import>starting_modules_metadata.xml</import>
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7 <import>starting_modules_nameandtypes.xml</import>
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8 <import>starting_modules_groups.xml</import>
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9 </macros>
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10
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11 <expand macro="py_requirements"/>
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13 <command detect_errors="aggressive"><![CDATA[
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14 python '$__tool_directory__/starting_modules.py' '$inputs'
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15 ]]></command>
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17 <configfiles>
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18 <inputs name="inputs"/>
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19 </configfiles>
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21 <inputs>
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22 <!-- Images module-->
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23 <expand macro="starting_modules_images" />
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24 <!-- Metadata module-->
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25 <expand macro="starting_modules_metadata" />
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26 <!-- NamesAndTypes-->
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27 <expand macro="starting_modules_nameandtypes" />
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28 <!-- Groups -->
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29 <expand macro="starting_modules_groups" />
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30 </inputs>
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31 <outputs>
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32 <expand macro="output_pipeline_param" />
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33 </outputs>
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34 <tests>
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35 <test>
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36 <!-- one big test case for various inputs scenarios -->
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37 <param name="filter_images" value="Images only"/>
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38 <conditional name="con_metadata_extraction">
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39 <param name="extract" value="Yes"/>
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40 <repeat name="extraction_method">
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41 <param name="metadata_extraction_method" value="Extract from file/folder names"/>
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42 <conditional name="con_metadata_extract_from">
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43 <param name="match_all_any" value="and" />
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44 <repeat name="r_match">
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45 <conditional name="con_match">
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46 <param name="operator" value="does"/>
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47 <param name="rule_type" value="file"/>
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48 <param name="match_value" value="im"/>
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49 <param name="contain" value="contain"/>
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50 </conditional>
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51 </repeat>
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52 <repeat name="r_match">
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53 <conditional name="con_match">
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54 <param name="operator" value="does"/>
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55 <param name="rule_type" value="extension"/>
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56 <param name="match_type" value="istif"/>
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57 </conditional>
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58 </repeat>
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59 <param name="extract_metadata_from" value="Images matching a rule" />
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60 </conditional>
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61 <conditional name="con_metadata_source">
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62 <param name="metadata_source" value="File name" />
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63 <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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64 </conditional>
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65 </repeat>
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66 <repeat name="extraction_method">
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67 <param name="metadata_extraction_method" value="Extract from file/folder names"/>
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68 <conditional name="con_metadata_extract_from">
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69 <param name="extract_metadata_from" value="All images" />
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70 </conditional>
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71 <conditional name="con_metadata_source">
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72 <param name="metadata_source" value="Folder name" />
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73 <param name="folder_name_regex" value="(?P&lt;folderField1>.*)_(?P&lt;folderField2>[a-zA-Z0-9]+)" />
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74 </conditional>
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75 </repeat>
2
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76 </conditional>
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77 <conditional name="pixel_space">
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78 <param name="process_3d" value="No"/>
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79 </conditional>
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80 <conditional name="con_assign_a_name_to">
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81 <param name="assign_a_name_to" value="Images matching rules"/>
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82 <repeat name="r_match_rule">
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83 <param name="match_all_any" value="and" />
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84 <repeat name="r_match">
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85 <conditional name="con_match">
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86 <param name="rule_type" value="file" />
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87 <param name="operator" value="does" />
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88 <param name="contain" value="contain" />
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89 <param name="match_value" value="im" />
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90 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
91 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
92 <repeat name="r_match">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
93 <conditional name="con_match">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
94 <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
95 <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
96 <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
97 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
98 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
99 <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
100 <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
101 <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
102 </conditional>
3
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
103 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
104
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
105 <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
106 <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
107 <repeat name="r_match" />
2
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
108 <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
109 <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
110 <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
111 </conditional>
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="or" />
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">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
117 <conditional name="con_match">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
118 <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
119 <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
120 <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
121 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
122 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
123 <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
124 <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
125 <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
126 <conditional name="con_set_intensity">
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
127 <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
128 </conditional>
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 </repeat>
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
131 <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
132 </conditional>
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
133 <conditional name="con_groups">
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
134 <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
135 <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
136 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
137 <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
138 </test>
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 <!-- 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
141 <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
142 <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
143 <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
144 <repeat name="extraction_method">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
145 <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
146 <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
147 <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
148 <repeat name="r_match">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
149 <conditional name="con_match">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
150 <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
151 <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
152 <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
153 <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
154 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
155 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
156 <repeat name="r_match">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
157 <conditional name="con_match">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
158 <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
159 <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
160 <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
161 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
162 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
163 <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
164 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
165 <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
166 <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
167 <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
168 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
169 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
170 <repeat name="extraction_method">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
171 <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
172 <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
173 <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
174 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
175 <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
176 <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
177 <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
178 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
179 </repeat>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
180 </conditional>
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
181 <conditional name="pixel_space">
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
182 <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
183 </conditional>
3
27396311a314 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
184 <conditional name="con_assign_a_name_to">
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185 <param name="assign_a_name_to" value="Images matching rules"/>
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186 <repeat name="r_match_rule">
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187 <param name="match_all_any" value="and" />
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188 <repeat name="r_match">
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189 <conditional name="con_match">
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190 <param name="rule_type" value="file" />
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191 <param name="operator" value="does" />
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192 <param name="contain" value="contain" />
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193 <param name="match_value" value="im" />
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194 </conditional>
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195 </repeat>
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196 <repeat name="r_match">
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197 <conditional name="con_match">
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198 <param name="rule_type" value="image" />
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199 <param name="operator" value="doesnot" />
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200 <param name="match_type" value="ismonochrome" />
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201 </conditional>
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202 </repeat>
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203 <conditional name="con_select_image_type">
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204 <param name="name_to_assign" value="Cell" />
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205 <param name="select_image_type" value="Objects" />
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206 </conditional>
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207 </repeat>
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208
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209 <repeat name="r_match_rule">
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210 <param name="match_all_any" value="and" />
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211 <repeat name="r_match" />
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212 <conditional name="con_select_image_type">
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213 <param name="name_to_assign" value="GFP" />
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214 <param name="select_image_type" value="Illumination function" />
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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="or" />
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220 <repeat name="r_match">
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221 <conditional name="con_match">
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222 <param name="rule_type" value="extension" />
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223 <param name="operator" value="does" />
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224 <param name="match_type" value="istif" />
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225 </conditional>
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226 </repeat>
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227 <conditional name="con_select_image_type">
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228 <param name="name_to_assign" value="Actin" />
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229 <param name="select_image_type" value="Grayscale image" />
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230 <conditional name="con_set_intensity">
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231 <param name="set_intensity_range_from" value="Image metadata" />
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232 </conditional>
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233 </conditional>
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234 </repeat>
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235 <param name="matching_method" value="Order" />
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236 </conditional>
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237 <conditional name="con_groups">
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238 <param name="group_images" value="No" />
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239 </conditional>
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240 <expand macro="test_out_file" file="common-nogroup.cppipe" />
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241 </test>
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242 </tests>
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243
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244 <help>
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245 <![CDATA[
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246
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247 .. class:: infomark
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248
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249 **What it does**
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250
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251 This tool is the first in a CellProfiler pipeline and includes the first four modules:
2
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252
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253 *Images*: use the Images module to compile a list of files that you want to analyze.
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254
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255 *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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256
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257 *NamesAndTypes*: allows you to assign a meaningful name to each image by which other modules will refer to it.
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258
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259 *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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260
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261 .. class:: infomark
2
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262
3
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263 **Input**
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264
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265 No input parameters are needed for this tool.
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266
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267 .. class:: infomark
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268
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269 **Output**
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270
3
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271 A CellProfiler pipeline file *(.cppipe)* with the settings of the 4 modules.
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272
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273 .. class:: warningmark
2
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274
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275 **IMPORTANT**
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276
3
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277 This tool has to be the first one in a CellProfiler workflow and the last one **CellProfiler**.
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278
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279 ]]>
2
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280 </help>
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parents:
diff changeset
281 <expand macro="citations" />
3c3cd68d6d5a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
bgruening
parents:
diff changeset
282 </tool>