Revision: 3:4b5513e25902

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/1.12.1.2

Version: 1.12.1.2

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/1.12.1.3

toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/1.12.1.2 (this tool)

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	1.12.1	package
r-base	3.5.1	package
r-gridextra	2.3	package
r-ggplot2	3.0	package

Functional tests

name	inputs	outputs	required files
Test-1	pixels_cond|max_x_range: 20 pixels_cond|max_y_range: 2 features_cond|max_mz: 500 pixels_cond|min_x_range: 1 infile: pixels_cond|min_y_range: 2 features_cond|min_mz: 350 features_cond|features_filtering: features_range imzml_output: imzml_format pixels_cond|pixel_filtering: pixel_range	attributes: name attributes: name	name
Test-2	pixels_cond|column_y: 3 pixels_cond|column_x: 1 infile: pixels_cond|pixel_filtering: two_columns pixels_cond|annotation_file: inputpixels_2column.tabular imzml_output: imzml_format	attributes: name attributes: name	inputpixels_2column.tabular name
Test-3	pixels_cond|max_x_range: 10 infile: pixels_cond|max_y_range: 20 pixels_cond|min_x_range: 0 features_cond|feature_column: 1 features_cond|mz_tabular: featuresofinterest5.tabular features_cond|feature_header: False features_cond|features_filtering: features_list pixels_cond|min_y_range: 2 imzml_output: imzml_format pixels_cond|pixel_filtering: pixel_range	attributes: name attributes: name	featuresofinterest5.tabular name
Test-4	infile: imzml_output: imzml_format	attributes: name attributes: name	name
Test-5	infile: preprocessed.RData imzml_output: imzml_format	attributes: name attributes: name	preprocessed.RData name