Mercurial > repos > bgruening > cp_cellprofiler

comparison test-data/common-nogroup.cppipe @ 3:a98608f3abc5 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 07:50:04 -0400
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children 0e4dccaafef5
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2:78a16d8c8d5e 3:a98608f3abc5
1 CellProfiler Pipeline: http://www.cellprofiler.org
2 Version:3
3 DateRevision:319
4 GitHash:
5 ModuleCount:4
6 HasImagePlaneDetails:False
7
8 Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
9 :
10 Filter images?:Images only
11 Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
12
13 Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
14 Extract metadata?:Yes
15 Metadata data type:Text
16 Metadata types:{}
17 Extraction method count:2
18 Metadata extraction method:Extract from file/folder names
19 Metadata source:File name
20 Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
21 Regular expression to extract from folder name:(?P<folderField1>.*)
22 Extract metadata from:Images matching a rule
23 Select the filtering criteria:and (file does contain "im") (extension does istif)
24 Metadata file location:
25 Match file and image metadata:[]
26 Use case insensitive matching?:No
27 Metadata extraction method:Extract from file/folder names
28 Metadata source:Folder name
29 Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)
30 Regular expression to extract from folder name:(?P<folderField1>.*)_(?P<folderField2>[a-zA-Z0-9]+)
31 Extract metadata from:All images
32 Select the filtering criteria:and (file does contain "")
33 Metadata file location:
34 Match file and image metadata:[]
35 Use case insensitive matching?:No
36
37 NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
38 Assign a name to:Images matching rules
39 Select the image type:Grayscale image
40 Name to assign these images:DNA
41 Match metadata:[]
42 Image set matching method:Order
43 Set intensity range from:Image metadata
44 Assignments count:3
45 Single images count:0
46 Maximum intensity:255.0
47 Process as 3D?:No
48 Relative pixel spacing in X:1.0
49 Relative pixel spacing in Y:1.0
50 Relative pixel spacing in Z:1.0
51 Select the rule criteria:and (file does contain "im") (image doesnot ismonochrome)
52 Name to assign these images:DNA
53 Name to assign these objects:Cell
54 Select the image type:Objects
55 Set intensity range from:Image metadata
56 Maximum intensity:255.0
57 Select the rule criteria:and (file does contain "")
58 Name to assign these images:GFP
59 Name to assign these objects:Cell
60 Select the image type:Illumination function
61 Set intensity range from:Image metadata
62 Maximum intensity:255.0
63 Select the rule criteria:or (extension does istif)
64 Name to assign these images:Actin
65 Name to assign these objects:Cell
66 Select the image type:Grayscale image
67 Set intensity range from:Image metadata
68 Maximum intensity:255.0
69
70 Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module 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.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
71 Do you want to group your images?:No
72 grouping metadata count:1
73 Metadata category:None