Repository revision
7:392b2dfd261d

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

MSI combine tool metadata
Miscellaneous
MSI combine
combine several mass spectrometry imaging datasets into one
cardinal_combine
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/2.4.0.0
2.4.0.0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/2.4.0.1
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/2.4.0.0 (this tool)
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/2.2.6.1
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/2.2.6.0
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/1.12.1.3
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/1.12.1.2
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/1.12.1.1
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/1.12.1.0
cardinal_combine
Requirements (dependencies defined in the <requirements> tag set)
name version type
bioconductor-cardinal 2.4.0 package
r-base 3.6.1 package
r-ggplot2 3.2.1 package
r-maldiquantforeign 0.12 package
r-maldiquant 1.19.3 package
Functional tests
name inputs outputs required files
Test-1 combine_conditional|combine_method: xy_shifts
infiles: ['msidata_1.RData', 'msidata_2.RData', 'msidata_3.RData']
annotation_cond|annotation_files: ['annotations_file1.tabular', 'annotations_file2.tabular', 'annotations_file3.tabular']
combine_conditional|coordinates_file: xy_coordinates.tabular
annotation_cond|tabular_header: True
combine_conditional|column_names: 3
annotation_cond|annotation_tabular: annotation
combine_conditional|column_y: 2
combine_conditional|column_x: 1
processed_true: False
attributes: name
attributes: name
attributes: name
msidata_1.RData
msidata_2.RData
msidata_3.RData
annotations_file1.tabular
annotations_file2.tabular
annotations_file3.tabular
xy_coordinates.tabular
name
Test-2 combine_conditional|combine_method: xy_shifts
infiles: ['123_combined_picked.rdata', '123_combined_picked2.rdata']
combine_conditional|coordinates_file: xy_coordinates2.tabular
combine_conditional|column_names: 3
centroids: True
combine_conditional|column_y: 2
combine_conditional|column_x: 1
processed_true: True
attributes: name
attributes: name
attributes: name
123_combined_picked.rdata
123_combined_picked2.rdata
xy_coordinates2.tabular
name
Test-3 annotation_cond|annotation_tabular: no_annotation
combine_conditional|combine_method: automatic_combine
processed_true: False
infiles: ['msidata_1.RData', 'msidata_2.RData', 'msidata_3.RData']
attributes: name
attributes: name
attributes: name
msidata_1.RData
msidata_2.RData
msidata_3.RData
name
Test-4 combine_conditional|combine_method: automatic_combine
infiles: ['msidata_1.RData', 'msidata_2.RData']
annotation_cond|annotation_files: ['annotations_file1.tabular', 'annotations_file2.tabular']
annotation_cond|tabular_header: True
annotation_cond|annotation_tabular: annotation
processed_true: False
attributes: name
attributes: name
attributes: name
msidata_1.RData
msidata_2.RData
annotations_file1.tabular
annotations_file2.tabular
name
Test-5 combine_conditional|combine_method: automatic_combine
infiles: ['msidata_1.RData', '123_combined.RData']
annotation_cond|annotation_files: ['annotations_file1.tabular', '123_annotation.tabular']
annotation_cond|tabular_header: True
annotation_cond|annotation_tabular: annotation
processed_true: False
attributes: name
attributes: name
attributes: name
msidata_1.RData
123_combined.RData
annotations_file1.tabular
123_annotation.tabular
name
Test-6 annotation_cond|annotation_tabular: no_annotation
combine_conditional|combine_method: automatic_combine
processed_true: False
infiles: ['msidata_2.RData', '123_combined.RData']
attributes: name
attributes: name
attributes: name
msidata_2.RData
123_combined.RData
name