view test-data/save_images.cppipe @ 3:08a2cf887a44 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"

CellProfiler Pipeline: http://www.cellprofiler.org
Version:3
DateRevision:319
GitHash:
ModuleCount:5
HasImagePlaneDetails:False

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]
    :
    Filter images?:Images only
    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")

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]
    Extract metadata?:Yes
    Metadata data type:Text
    Metadata types:{}
    Extraction method count:1
    Metadata extraction method:Extract from file/folder names
    Metadata source:File name
    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]+)
    Regular expression to extract from folder name:(?P<folderField1>.*)
    Extract metadata from:All images
    Select the filtering criteria:and (file does contain "")
    Metadata file location:
    Match file and image metadata:[]
    Use case insensitive matching?:No

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]
    Assign a name to:Images matching rules
    Select the image type:Grayscale image
    Name to assign these images:DNA
    Match metadata:[]
    Image set matching method:Order
    Set intensity range from:Image metadata
    Assignments count:1
    Single images count:0
    Maximum intensity:255.0
    Process as 3D?:No
    Relative pixel spacing in X:1.0
    Relative pixel spacing in Y:1.0
    Relative pixel spacing in Z:1.0
    Select the rule criteria:and (file does startwith "im")
    Name to assign these images:DNA
    Name to assign these objects:Cell
    Select the image type:Grayscale image
    Set intensity range from:Image metadata
    Select the image type:Grayscale image
    Maximum intensity:255.0

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]
    Do you want to group your images?:Yes
    grouping metadata count:1
    Metadata category:field1

SaveImages:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
    Select the type of image to save:Image
    Select the image to save:ImageDisplay
    Select method for constructing file names:From image filename
    Select image name for file prefix:DNA
    Enter single file name:OrigBlue
    Number of digits:4
    Append a suffix to the image file name?:Yes
    Text to append to the image name:_nucleiNumbers
    Saved file format:tiff
    Output file location:Default Output Folder\x7Coutput
    Image bit depth:8-bit integer
    Overwrite existing files without warning?:Yes
    When to save:Every cycle
    Record the file and path information to the saved image?:No
    Create subfolders in the output folder?:No
    Base image folder:Elsewhere...