Revision: 13:b8c79e70516d

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering

Miscellaneous

Name: MSI filtering

Description: tool for filtering mass spectrometry imaging data

Id: cardinal_filtering

Guid: toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/2.6.0.0

Version: 2.6.0.0

Version command string: echo $(R --version | grep version | grep -v GNU)", Cardinal version" $(R --vanilla --slave -e "library(Cardinal); cat(sessionInfo()\$otherPkgs\$Cardinal\$Version)" 2> /dev/null | grep -v -i "WARNING: ")

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/2.10.0.0

toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/2.6.0.0 (this tool)

toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/2.4.0.0

toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/1.12.1.3

toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/1.12.1.2

toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/1.12.1.1

toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/1.12.1.0

cardinal_filtering

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name	version	type
bioconductor-cardinal	2.6.0	package
r-gridextra	2.3	package
r-ggplot2	3.3.2	package

Functional tests

name	inputs	outputs	required files
Test-1	infile: pixels_cond|min_x_range: 1 pixels_cond|max_x_range: 20 pixels_cond|min_y_range: 2 pixels_cond|max_y_range: 2 pixels_cond|pixel_filtering: pixel_range features_cond|min_mz: 350 features_cond|max_mz: 500 features_cond|features_filtering: features_range	name: value name: value	value
Test-2	infile: pixels_cond|annotation_file: inputpixels_2column.tabular pixels_cond|column_x: 1 pixels_cond|column_y: 3 pixels_cond|pixel_filtering: two_columns	name: value name: value	inputpixels_2column.tabular value
Test-3	infile: pixels_cond|min_x_range: 0 pixels_cond|max_x_range: 10 pixels_cond|min_y_range: 2 pixels_cond|max_y_range: 20 pixels_cond|pixel_filtering: pixel_range features_cond|mz_tabular: featuresofinterest5.tabular features_cond|feature_column: 1 features_cond|feature_header: False features_cond|features_filtering: features_list	name: value name: value	featuresofinterest5.tabular value
Test-4	infile:	name: value name: value	value
Test-5	infile: preprocessed.RData	name: value name: value	preprocessed.RData value
Test-6	infile: processed_cond|accuracy: 200 processed_cond|units: ppm processed_cond|processed_file: processed pixels_cond|annotation_file: inputpixels_2column.tabular pixels_cond|column_x: 1 pixels_cond|column_y: 3 pixels_cond|pixel_filtering: two_columns features_cond|mz_tabular: featuresofinterest5.tabular features_cond|feature_column: 1 features_cond|feature_header: False features_cond|removal_plusminus: 100 features_cond|units_removal: ppm features_cond|features_filtering: remove_features	name: value name: value	inputpixels_2column.tabular featuresofinterest5.tabular value