Repository revision
5:528fb09022be

Repository 'cardinal_filtering'
hg clone https://toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering

MSI filtering tool metadata
Miscellaneous
tool for filtering mass spectrometry imaging data
cardinal_filtering
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/1.12.1.3
1.12.1.3
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: ")
True
Version lineage of this tool (guids ordered most recent to oldest)
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 (this tool)
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)
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