Repository revision
5:670975e92458

Repository 'cp_common'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/cp_common

Starting Modules tool metadata
Miscellaneous
load images and metadata into CellProfiler (Images, Metadata, NamesAndTypes, Groups)
cp_common
toolshed.g2.bx.psu.edu/repos/bgruening/cp_common/cp_common/3.1.9+galaxy1
3.1.9+galaxy1
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/cp_common/cp_common/3.1.9+galaxy2
toolshed.g2.bx.psu.edu/repos/bgruening/cp_common/cp_common/3.1.9+galaxy1 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/cp_common/cp_common/3.1.9
cp_common
Requirements (dependencies defined in the <requirements> tag set)
name version type
python 3.7 package
Functional tests
name inputs outputs required files
Test-1 images|filter_images: Images only
metadata|con_metadata_extraction|extraction_method_0|metadata_extraction_method: Extract from file/folder names
metadata|con_metadata_extraction|extraction_method_0|con_metadata_source|file_name_regex: (?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
metadata|con_metadata_extraction|extraction_method_0|con_metadata_source|metadata_source: File name
metadata|con_metadata_extraction|extraction_method_0|con_metadata_extract_from|match_all_any: and
metadata|con_metadata_extraction|extraction_method_0|con_metadata_extract_from|r_match_0|con_match|operator: does
metadata|con_metadata_extraction|extraction_method_0|con_metadata_extract_from|r_match_0|con_match|contain: contain
metadata|con_metadata_extraction|extraction_method_0|con_metadata_extract_from|r_match_0|con_match|match_value: im
metadata|con_metadata_extraction|extraction_method_0|con_metadata_extract_from|r_match_0|con_match|rule_type: file
metadata|con_metadata_extraction|extraction_method_0|con_metadata_extract_from|r_match_1|con_match|operator: does
metadata|con_metadata_extraction|extraction_method_0|con_metadata_extract_from|r_match_1|con_match|match_type: istif
metadata|con_metadata_extraction|extraction_method_0|con_metadata_extract_from|r_match_1|con_match|rule_type: extension
metadata|con_metadata_extraction|extraction_method_0|con_metadata_extract_from|extract_metadata_from: Images matching a rule
metadata|con_metadata_extraction|extraction_method_1|metadata_extraction_method: Extract from file/folder names
metadata|con_metadata_extraction|extraction_method_1|con_metadata_source|folder_name_regex: (?P<folderField1>.*)_(?P<folderField2>[a-zA-Z0-9]+)
metadata|con_metadata_extraction|extraction_method_1|con_metadata_source|metadata_source: Folder name
metadata|con_metadata_extraction|extraction_method_1|con_metadata_extract_from|extract_metadata_from: All images
metadata|con_metadata_extraction|extract: Yes
nameandtypes|pixel_space|process_3d: No
nameandtypes|con_assign_a_name_to|r_match_rule_0|match_all_any: and
nameandtypes|con_assign_a_name_to|r_match_rule_0|r_match_0|con_match|operator: does
nameandtypes|con_assign_a_name_to|r_match_rule_0|r_match_0|con_match|contain: contain
nameandtypes|con_assign_a_name_to|r_match_rule_0|r_match_0|con_match|match_value: im
nameandtypes|con_assign_a_name_to|r_match_rule_0|r_match_0|con_match|rule_type: file
nameandtypes|con_assign_a_name_to|r_match_rule_0|r_match_1|con_match|operator: doesnot
nameandtypes|con_assign_a_name_to|r_match_rule_0|r_match_1|con_match|match_type: ismonochrome
nameandtypes|con_assign_a_name_to|r_match_rule_0|r_match_1|con_match|rule_type: image
nameandtypes|con_assign_a_name_to|r_match_rule_0|con_select_image_type|name_to_assign: Cell
nameandtypes|con_assign_a_name_to|r_match_rule_0|con_select_image_type|select_image_type: Objects
nameandtypes|con_assign_a_name_to|r_match_rule_1|match_all_any: and
nameandtypes|con_assign_a_name_to|r_match_rule_1|con_select_image_type|name_to_assign: GFP
nameandtypes|con_assign_a_name_to|r_match_rule_1|con_select_image_type|select_image_type: Illumination function
nameandtypes|con_assign_a_name_to|r_match_rule_2|match_all_any: or
nameandtypes|con_assign_a_name_to|r_match_rule_2|r_match_0|con_match|operator: does
nameandtypes|con_assign_a_name_to|r_match_rule_2|r_match_0|con_match|match_type: istif
nameandtypes|con_assign_a_name_to|r_match_rule_2|r_match_0|con_match|rule_type: extension
nameandtypes|con_assign_a_name_to|r_match_rule_2|con_select_image_type|name_to_assign: Actin
nameandtypes|con_assign_a_name_to|r_match_rule_2|con_select_image_type|con_set_intensity|set_intensity_range_from: Image metadata
nameandtypes|con_assign_a_name_to|r_match_rule_2|con_select_image_type|select_image_type: Grayscale image
nameandtypes|con_assign_a_name_to|matching_method: Order
nameandtypes|con_assign_a_name_to|assign_a_name_to: Images matching rules
groups|con_groups|group_category: field1
groups|con_groups|group_images: Yes
name: value
value
Test-2 images|filter_images: Images only
metadata|con_metadata_extraction|extraction_method_0|metadata_extraction_method: Extract from file/folder names
metadata|con_metadata_extraction|extraction_method_0|con_metadata_source|file_name_regex: (?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
metadata|con_metadata_extraction|extraction_method_0|con_metadata_source|metadata_source: File name
metadata|con_metadata_extraction|extraction_method_0|con_metadata_extract_from|match_all_any: and
metadata|con_metadata_extraction|extraction_method_0|con_metadata_extract_from|r_match_0|con_match|operator: does
metadata|con_metadata_extraction|extraction_method_0|con_metadata_extract_from|r_match_0|con_match|contain: contain
metadata|con_metadata_extraction|extraction_method_0|con_metadata_extract_from|r_match_0|con_match|match_value: im
metadata|con_metadata_extraction|extraction_method_0|con_metadata_extract_from|r_match_0|con_match|rule_type: file
metadata|con_metadata_extraction|extraction_method_0|con_metadata_extract_from|r_match_1|con_match|operator: does
metadata|con_metadata_extraction|extraction_method_0|con_metadata_extract_from|r_match_1|con_match|match_type: istif
metadata|con_metadata_extraction|extraction_method_0|con_metadata_extract_from|r_match_1|con_match|rule_type: extension
metadata|con_metadata_extraction|extraction_method_0|con_metadata_extract_from|extract_metadata_from: Images matching a rule
metadata|con_metadata_extraction|extraction_method_1|metadata_extraction_method: Extract from file/folder names
metadata|con_metadata_extraction|extraction_method_1|con_metadata_source|folder_name_regex: (?P<folderField1>.*)_(?P<folderField2>[a-zA-Z0-9]+)
metadata|con_metadata_extraction|extraction_method_1|con_metadata_source|metadata_source: Folder name
metadata|con_metadata_extraction|extraction_method_1|con_metadata_extract_from|extract_metadata_from: All images
metadata|con_metadata_extraction|extract: Yes
nameandtypes|pixel_space|process_3d: No
nameandtypes|con_assign_a_name_to|r_match_rule_0|match_all_any: and
nameandtypes|con_assign_a_name_to|r_match_rule_0|r_match_0|con_match|operator: does
nameandtypes|con_assign_a_name_to|r_match_rule_0|r_match_0|con_match|contain: contain
nameandtypes|con_assign_a_name_to|r_match_rule_0|r_match_0|con_match|match_value: im
nameandtypes|con_assign_a_name_to|r_match_rule_0|r_match_0|con_match|rule_type: file
nameandtypes|con_assign_a_name_to|r_match_rule_0|r_match_1|con_match|operator: doesnot
nameandtypes|con_assign_a_name_to|r_match_rule_0|r_match_1|con_match|match_type: ismonochrome
nameandtypes|con_assign_a_name_to|r_match_rule_0|r_match_1|con_match|rule_type: image
nameandtypes|con_assign_a_name_to|r_match_rule_0|con_select_image_type|name_to_assign: Cell
nameandtypes|con_assign_a_name_to|r_match_rule_0|con_select_image_type|select_image_type: Objects
nameandtypes|con_assign_a_name_to|r_match_rule_1|match_all_any: and
nameandtypes|con_assign_a_name_to|r_match_rule_1|con_select_image_type|name_to_assign: GFP
nameandtypes|con_assign_a_name_to|r_match_rule_1|con_select_image_type|select_image_type: Illumination function
nameandtypes|con_assign_a_name_to|r_match_rule_2|match_all_any: or
nameandtypes|con_assign_a_name_to|r_match_rule_2|r_match_0|con_match|operator: does
nameandtypes|con_assign_a_name_to|r_match_rule_2|r_match_0|con_match|match_type: istif
nameandtypes|con_assign_a_name_to|r_match_rule_2|r_match_0|con_match|rule_type: extension
nameandtypes|con_assign_a_name_to|r_match_rule_2|con_select_image_type|name_to_assign: Actin
nameandtypes|con_assign_a_name_to|r_match_rule_2|con_select_image_type|con_set_intensity|set_intensity_range_from: Image metadata
nameandtypes|con_assign_a_name_to|r_match_rule_2|con_select_image_type|select_image_type: Grayscale image
nameandtypes|con_assign_a_name_to|matching_method: Order
nameandtypes|con_assign_a_name_to|assign_a_name_to: Images matching rules
groups|con_groups|group_images: No
name: value
value