Repository revision
6:d286ff4600dd

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

MALDIquant peak detection tool metadata
Miscellaneous
Peak detection, binning and filtering for mass-spectrometry imaging data
maldi_quant_peak_detection
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection/1.18.0.6
1.18.0.6
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection/1.22.0.0
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection/1.18.0.6 (this tool)
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection/1.18.0.5
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection/1.18.0.4
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection/1.18.0.3
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection/1.18.0.2
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection/1.18.0.1
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection/1.18.0.0
maldi_quant_peak_detection
Requirements (dependencies defined in the <requirements> tag set)
name version type
r-base 3.5.1 package
bioconductor-cardinal 1.12.1 package
r-maldiquantforeign 0.11.5 package
r-maldiquant 1.18 package
r-ggplot2 3.0 package
r-gridextra 2.3 package
Functional tests
name inputs outputs required files
Test-1 methods_0|methods_conditional|use_annotations: True
tabular_annotation|column_y: 2
tabular_annotation|column_x: 1
methods_0|methods_conditional|peak_method: SuperSmoother
tabular_annotation|load_annotation: yes_annotation
tabular_annotation|annotation_file: pixel_annotations.tabular
methods_0|methods_conditional|halfWindowSize: 1
methods_0|methods_conditional|method: Peak_detection
tabular_annotation|column_names: 3
tabular_annotation|tabular_header: True
methods_0|methods_conditional|snr: 5
infile:
attributes: name
attributes: name
attributes: name

pixel_annotations.tabular
name
Test-2 methods_0|methods_conditional|method: monoisotopic_peaks
centroids: True
infile: masspeaks3_forinput.tabular
methods_0|methods_conditional|tolerance: 0.0004
methods_0|methods_conditional|size: 3
attributes: name
attributes: name
attributes: name
attributes: name
masspeaks3_forinput.tabular
name
Test-3 methods_2|methods_conditional|filter_annot_groups: True
tabular_annotation|column_y: 2
tabular_annotation|column_x: 1
tabular_annotation|tabular_header: True
methods_0|methods_conditional|peak_method: MAD
tabular_annotation|load_annotation: yes_annotation
methods_1|methods_conditional|method: Binning
tabular_annotation|annotation_file: pixel_annotations.tabular
methods_0|methods_conditional|halfWindowSize: 1
methods_2|methods_conditional|method: Filtering
methods_2|methods_conditional|minFrequency: 0.5
methods_0|methods_conditional|method: Peak_detection
methods_2|methods_conditional|minNumber: 3
tabular_annotation|column_names: 3
methods_2|methods_conditional|mergeWhitelists: False
methods_0|methods_conditional|snr: 2
infile:
methods_1|methods_conditional|bin_tolerance: 0.01
attributes: name
attributes: name
attributes: name
attributes: name

pixel_annotations.tabular
name
Test-4 methods_0|methods_conditional|halfWindowSize: 20
methods_0|methods_conditional|peak_method: MAD
methods_0|methods_conditional|method: Peak_detection
infile: testfile_squares.rdata
methods_0|methods_conditional|snr: 2
attributes: name
attributes: name
attributes: name
attributes: name
testfile_squares.rdata
name