| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9 |
| cp_identify_primary_objects |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| python | 3.7 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_pipeline: common.cppipe con_advanced|input_from_nat: DNA con_advanced|name_to_be_identified: Nuclei con_advanced|min_diameter: 15 con_advanced|max_diameter: 200 con_advanced|discard_outside_border: Yes con_advanced|discard_touching_border: Yes con_advanced|advanced: No |
name: value |
common.cppipe value |
| Test-2 |
input_pipeline: common.cppipe con_advanced|input_from_nat: DNA con_advanced|name_to_be_identified: Nuclei con_advanced|min_diameter: 15 con_advanced|max_diameter: 200 con_advanced|discard_outside_border: Yes con_advanced|discard_touching_border: Yes con_advanced|con_threshold_strategy|con_threshold_method|con_threshold_class|assign_pixel: Foreground con_advanced|con_threshold_strategy|con_threshold_method|con_threshold_class|threshold_class: Three classes con_advanced|con_threshold_strategy|con_threshold_method|threshold_method: Otsu con_advanced|con_threshold_strategy|adaptive_window: 50 con_advanced|con_threshold_strategy|threshold_smoothing_scale: 1.5 con_advanced|con_threshold_strategy|threshold_correction_factor: 1 con_advanced|con_threshold_strategy|threshold_lower: 0.0 con_advanced|con_threshold_strategy|threshold_upper: 1.0 con_advanced|con_threshold_strategy|threshold_strategy: Adaptive con_advanced|con_distinguish_clumped_objects|con_dividing_lines|con_smoothing_filter|size_smoothing_filter: 1 con_advanced|con_distinguish_clumped_objects|con_dividing_lines|con_smoothing_filter|smoothing_filter: No con_advanced|con_distinguish_clumped_objects|con_dividing_lines|con_min_distance|min_allowed_distance: 1 con_advanced|con_distinguish_clumped_objects|con_dividing_lines|con_min_distance|min_distance: No con_advanced|con_distinguish_clumped_objects|con_dividing_lines|speed_up: Yes con_advanced|con_distinguish_clumped_objects|con_dividing_lines|dividing_lines: Shape con_advanced|con_distinguish_clumped_objects|distinguish_clumped_objects: Shape con_advanced|fill_hole: After both thresholding and declumping con_advanced|con_handling_excessive|excessive_handling: Continue con_advanced|advanced: Yes |
name: value |
common.cppipe value |
| Test-3 |
input_pipeline: common.cppipe con_advanced|input_from_nat: DNA con_advanced|name_to_be_identified: Nuclei con_advanced|min_diameter: 5 con_advanced|max_diameter: 20 con_advanced|discard_outside_border: No con_advanced|discard_touching_border: Yes con_advanced|con_threshold_strategy|con_threshold_method|manual_threshold: 1 con_advanced|con_threshold_strategy|con_threshold_method|threshold_method: Manual con_advanced|con_threshold_strategy|threshold_strategy: Global con_advanced|con_distinguish_clumped_objects|con_dividing_lines|con_smoothing_filter|size_smoothing_filter: 1 con_advanced|con_distinguish_clumped_objects|con_dividing_lines|con_smoothing_filter|smoothing_filter: No con_advanced|con_distinguish_clumped_objects|con_dividing_lines|con_min_distance|min_allowed_distance: 1 con_advanced|con_distinguish_clumped_objects|con_dividing_lines|con_min_distance|min_distance: No con_advanced|con_distinguish_clumped_objects|con_dividing_lines|speed_up: Yes con_advanced|con_distinguish_clumped_objects|con_dividing_lines|dividing_lines: Shape con_advanced|con_distinguish_clumped_objects|distinguish_clumped_objects: Shape con_advanced|fill_hole: After both thresholding and declumping con_advanced|con_handling_excessive|max_obj: 499 con_advanced|con_handling_excessive|excessive_handling: Erase con_advanced|advanced: Yes |
name: value |
common.cppipe value |
| Test-4 |
input_pipeline: common.cppipe con_advanced|input_from_nat: DNA con_advanced|name_to_be_identified: Nuclei con_advanced|min_diameter: 5 con_advanced|max_diameter: 20 con_advanced|discard_outside_border: Yes con_advanced|discard_touching_border: No con_advanced|con_threshold_strategy|con_threshold_method|global_measurement_threshold_cat: FileName con_advanced|con_threshold_strategy|con_threshold_method|global_measurement_threshold_measurement: DNA con_advanced|con_threshold_strategy|con_threshold_method|threshold_correction_factor: 1 con_advanced|con_threshold_strategy|con_threshold_method|threshold_lower: 0.1 con_advanced|con_threshold_strategy|con_threshold_method|threshold_upper: 0.4 con_advanced|con_threshold_strategy|con_threshold_method|threshold_method: Measurement con_advanced|con_threshold_strategy|threshold_strategy: Global con_advanced|con_distinguish_clumped_objects|con_dividing_lines|con_smoothing_filter|smoothing_filter: Yes con_advanced|con_distinguish_clumped_objects|con_dividing_lines|con_min_distance|min_allowed_distance: 6 con_advanced|con_distinguish_clumped_objects|con_dividing_lines|con_min_distance|min_distance: No con_advanced|con_distinguish_clumped_objects|con_dividing_lines|speed_up: Yes con_advanced|con_distinguish_clumped_objects|con_dividing_lines|dividing_lines: Shape con_advanced|con_distinguish_clumped_objects|distinguish_clumped_objects: Intensity con_advanced|fill_hole: After both thresholding and declumping con_advanced|con_handling_excessive|excessive_handling: Continue con_advanced|advanced: Yes |
name: value |
common.cppipe value |
| Test-5 |
input_pipeline: common.cppipe con_advanced|input_from_nat: DNA con_advanced|name_to_be_identified: Nuclei con_advanced|min_diameter: 15 con_advanced|max_diameter: 40 con_advanced|discard_outside_border: Yes con_advanced|discard_touching_border: Yes con_advanced|con_threshold_strategy|con_threshold_method|threshold_smoothing_scale: 1.5 con_advanced|con_threshold_strategy|con_threshold_method|threshold_correction_factor: 1 con_advanced|con_threshold_strategy|con_threshold_method|threshold_lower: 0.0 con_advanced|con_threshold_strategy|con_threshold_method|threshold_upper: 1.0 con_advanced|con_threshold_strategy|con_threshold_method|threshold_method: Minimum cross entropy con_advanced|con_threshold_strategy|threshold_strategy: Global con_advanced|con_distinguish_clumped_objects|con_dividing_lines|con_smoothing_filter|size_smoothing_filter: 1 con_advanced|con_distinguish_clumped_objects|con_dividing_lines|con_smoothing_filter|smoothing_filter: No con_advanced|con_distinguish_clumped_objects|con_dividing_lines|con_min_distance|min_allowed_distance: 7 con_advanced|con_distinguish_clumped_objects|con_dividing_lines|con_min_distance|min_distance: No con_advanced|con_distinguish_clumped_objects|con_dividing_lines|speed_up: Yes con_advanced|con_distinguish_clumped_objects|con_dividing_lines|dividing_lines: Shape con_advanced|con_distinguish_clumped_objects|distinguish_clumped_objects: Shape con_advanced|fill_hole: After both thresholding and declumping con_advanced|con_handling_excessive|excessive_handling: Continue con_advanced|advanced: Yes |
name: value |
common.cppipe value |
| Test-6 |
input_pipeline: common.cppipe con_advanced|input_from_nat: DNA con_advanced|name_to_be_identified: Nuclei con_advanced|min_diameter: 10 con_advanced|max_diameter: 40 con_advanced|discard_outside_border: Yes con_advanced|discard_touching_border: Yes con_advanced|con_threshold_strategy|con_threshold_method|lower_outlier_fraction: 0.06 con_advanced|con_threshold_strategy|con_threshold_method|upper_outlier_fraction: 0.07 con_advanced|con_threshold_strategy|con_threshold_method|avg_method: Median con_advanced|con_threshold_strategy|con_threshold_method|variance_method: Median absolute deviation con_advanced|con_threshold_strategy|con_threshold_method|no_of_deviations: 3.0 con_advanced|con_threshold_strategy|con_threshold_method|threshold_smoothing_scale: 1.4 con_advanced|con_threshold_strategy|con_threshold_method|threshold_correction_factor: 1 con_advanced|con_threshold_strategy|con_threshold_method|threshold_lower: 0.0 con_advanced|con_threshold_strategy|con_threshold_method|threshold_upper: 1.0 con_advanced|con_threshold_strategy|con_threshold_method|threshold_method: RobustBackground con_advanced|con_threshold_strategy|threshold_strategy: Global con_advanced|con_distinguish_clumped_objects|con_dividing_lines|con_smoothing_filter|size_smoothing_filter: 1 con_advanced|con_distinguish_clumped_objects|con_dividing_lines|con_smoothing_filter|smoothing_filter: No con_advanced|con_distinguish_clumped_objects|con_dividing_lines|con_min_distance|min_allowed_distance: 7 con_advanced|con_distinguish_clumped_objects|con_dividing_lines|con_min_distance|min_distance: No con_advanced|con_distinguish_clumped_objects|con_dividing_lines|speed_up: Yes con_advanced|con_distinguish_clumped_objects|con_dividing_lines|dividing_lines: Shape con_advanced|con_distinguish_clumped_objects|distinguish_clumped_objects: Shape con_advanced|fill_hole: After both thresholding and declumping con_advanced|con_handling_excessive|excessive_handling: Continue con_advanced|advanced: Yes |
name: value |
common.cppipe value |