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Revision: 7:44a4b31fcbf3

Repository 'cardinal_preprocessing'

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

MSI preprocessing tool metadata

Miscellaneous

Name: MSI preprocessing

Description: mass spectrometry imaging preprocessing

Id: cardinal_preprocessing

Guid: toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_preprocessing/cardinal_preprocessing/2.4.0.1

Version: 2.4.0.1

Version command string: None

Display in tool panel: True

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

toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_preprocessing/cardinal_preprocessing/2.4.0.2

toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_preprocessing/cardinal_preprocessing/2.4.0.1 (this tool)

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

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

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

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

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

cardinal_preprocessing

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

Requirements:

name

version

type

bioconductor-cardinal

2.4.0

package

r-base

3.6.1

package

r-gridextra

2.3

package

r-ggplot2

3.2.1

package

Functional tests

name

inputs

outputs

required files

Test-1

methods_2|methods_conditional|imzml_output: False
methods_1|methods_conditional|methods_for_smoothing|sd_gaussian: 4
methods_1|methods_conditional|preprocessing_method: Smoothing
methods_2|methods_conditional|blocks_picking: 3
methods_5|methods_conditional|transf_conditional|trans_type: sqrt
methods_3|methods_conditional|preprocessing_method: Peak_alignment
methods_2|methods_conditional|methods_for_picking|picking_method: adaptive
methods_4|methods_conditional|frequ_filtering: 0.3
infile:
methods_1|methods_conditional|methods_for_smoothing|smoothing_method: gaussian
methods_2|methods_conditional|preprocessing_method: Peak_picking
methods_2|methods_conditional|window_picking: 3
methods_2|methods_conditional|SNR_picking_method: 3
methods_3|methods_conditional|imzml_output: False
methods_4|methods_conditional|preprocessing_method: Peak_filtering
methods_0|methods_conditional|preprocessing_method: Normalization
methods_0|methods_conditional|methods_for_normalization|normalization_method: tic
methods_1|methods_conditional|window_smoothing: 9
methods_5|methods_conditional|preprocessing_method: Transformation

attributes: name
attributes: name

name

Test-2

methods_1|methods_conditional|preprocessing_method: Peak_alignment
methods_0|methods_conditional|window_picking: 5
methods_0|methods_conditional|SNR_picking_method: 2
methods_1|methods_conditional|imzml_output: False
methods_0|methods_conditional|blocks_picking: 3
methods_0|methods_conditional|methods_for_picking|picking_method: adaptive
methods_0|methods_conditional|imzml_output: False
methods_0|methods_conditional|preprocessing_method: Peak_picking
infile: 3_files_combined.RData

attributes: name
attributes: name

3_files_combined.RData
name

Test-3

methods_2|methods_conditional|imzml_output: True
methods_1|methods_conditional|preprocessing_method: Peak_picking
infile:
methods_1|methods_conditional|imzml_output: True
methods_1|methods_conditional|window_picking: 5
methods_2|methods_conditional|preprocessing_method: Peak_alignment
methods_1|methods_conditional|blocks_picking: 20
methods_1|methods_conditional|SNR_picking_method: 2
methods_1|methods_conditional|methods_for_picking|picking_method: mad
methods_0|methods_conditional|preprocessing_method: Normalization
methods_0|methods_conditional|methods_for_normalization|normalization_method: rms

attributes: name
attributes: name

name

Test-4

methods_1|methods_conditional|methods_for_reduction|reduction_method: bin
methods_1|methods_conditional|preprocessing_method: Data_reduction
methods_0|methods_conditional|preprocessing_method: Normalization
infile:
methods_1|methods_conditional|methods_for_reduction|bin_width: 0.1

attributes: name
attributes: name

name

Test-5

processed_cond|units: ppm
methods_1|methods_conditional|preprocessing_method: Baseline_reduction
processed_cond|processed_file: processed
processed_cond|accuracy: 100
methods_0|methods_conditional|transf_conditional|trans_type: log2
methods_0|methods_conditional|preprocessing_method: Transformation
infile:

attributes: name
attributes: name

name