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Repository revision

Revision: 10:9e47c4855b18

Repository 'openms_peakpickerwavelet'

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

PeakPickerWavelet tool metadata

Miscellaneous

Name: PeakPickerWavelet

Description: Finds mass spectrometric peaks in profile mass spectra.

Id: PeakPickerWavelet

Guid: toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peakpickerwavelet/PeakPickerWavelet/2.5+galaxy0

Version: 2.5+galaxy0

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/openms_peakpickerwavelet/PeakPickerWavelet/2.6+galaxy0

toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peakpickerwavelet/PeakPickerWavelet/2.5+galaxy0 (this tool)

toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peakpickerwavelet/PeakPickerWavelet/2.3.0

toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peakpickerwavelet/PeakPickerWavelet/2.2.0

toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peakpickerwavelet/PeakPickerWavelet/2.1.0

PeakPickerWavelet

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

Requirements:

name

version

type

openms

2.5

package

openms-thirdparty

2.5

package

blast

2.9.0

package

openjdk

8.0.192

package

ctdopts

1.4

package

Functional tests

name

inputs

outputs

required files

Test-1

in: PeakPickerWavelet_input.mzML
algorithm|signal_to_noise: 3.0
algorithm|centroid_percentage: 0.6
algorithm|peak_width: 0.2
algorithm|estimate_peak_width: False
algorithm|fwhm_lower_bound_factor: 0.5
algorithm|fwhm_upper_bound_factor: 20.0
algorithm|optimization|iterations: 400
algorithm|optimization|penalties|position: 0.0
algorithm|optimization|penalties|left_width: 1.0
algorithm|optimization|penalties|right_width: 1.0
algorithm|optimization|penalties|height: 1.0
algorithm|optimization|2d|tolerance_mz: 2.2
algorithm|optimization|2d|max_peak_distance: 1.2
algorithm|thresholds|peak_bound: 100.0
algorithm|thresholds|peak_bound_ms2_level: 10.0
algorithm|thresholds|correlation: 0.5
algorithm|thresholds|noise_level: 0.1
algorithm|thresholds|search_radius: 3
algorithm|wavelet_transform|spacing: 0.001
algorithm|deconvolution|deconvolution: False
algorithm|deconvolution|asym_threshold: 0.3
algorithm|deconvolution|left_width: 2.0
algorithm|deconvolution|right_width: 2.0
algorithm|deconvolution|scaling: 0.12
algorithm|deconvolution|fitting|fwhm_threshold: 0.7
algorithm|deconvolution|fitting|eps_abs: 9.999999747378752e-06
algorithm|deconvolution|fitting|eps_rel: 9.999999747378752e-06
algorithm|deconvolution|fitting|max_iteration: 10
algorithm|deconvolution|fitting|penalties|position: 0.0
algorithm|deconvolution|fitting|penalties|height: 1.0
algorithm|deconvolution|fitting|penalties|left_width: 0.0
algorithm|deconvolution|fitting|penalties|right_width: 0.0
algorithm|SignalToNoiseEstimationParameter|max_intensity: -1
algorithm|SignalToNoiseEstimationParameter|auto_max_stdev_factor: 3.0
algorithm|SignalToNoiseEstimationParameter|auto_max_percentile: 95
algorithm|SignalToNoiseEstimationParameter|auto_mode: 0
algorithm|SignalToNoiseEstimationParameter|win_len: 200.0
algorithm|SignalToNoiseEstimationParameter|bin_count: 30
algorithm|SignalToNoiseEstimationParameter|stdev_mp: 3.0
algorithm|SignalToNoiseEstimationParameter|min_required_elements: 10
algorithm|SignalToNoiseEstimationParameter|noise_for_empty_window: 1e+20
adv_opts_cond|write_peak_meta_data: True
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ctd_out_FLAG

name: value
name: value

PeakPickerWavelet_input.mzML
value

Test-2

in: PeakPickerWavelet_deconv_input.mzML
algorithm|signal_to_noise: 2.0
algorithm|centroid_percentage: 0.8
algorithm|peak_width: 0.15
algorithm|estimate_peak_width: False
algorithm|fwhm_lower_bound_factor: 1.0
algorithm|fwhm_upper_bound_factor: 20.0
algorithm|optimization|iterations: 400
algorithm|optimization|penalties|position: 0.0
algorithm|optimization|penalties|left_width: 1.0
algorithm|optimization|penalties|right_width: 1.0
algorithm|optimization|penalties|height: 1.0
algorithm|optimization|2d|tolerance_mz: 2.2
algorithm|optimization|2d|max_peak_distance: 1.2
algorithm|thresholds|peak_bound: 200.0
algorithm|thresholds|peak_bound_ms2_level: 50.0
algorithm|thresholds|correlation: 0.5
algorithm|thresholds|noise_level: 0.1
algorithm|thresholds|search_radius: 3
algorithm|wavelet_transform|spacing: 0.001
algorithm|deconvolution|deconvolution: True
algorithm|deconvolution|asym_threshold: 0.3
algorithm|deconvolution|left_width: 2.0
algorithm|deconvolution|right_width: 2.0
algorithm|deconvolution|scaling: 0.1
algorithm|deconvolution|fitting|fwhm_threshold: 0.7
algorithm|deconvolution|fitting|eps_abs: 9.999999747378752e-06
algorithm|deconvolution|fitting|eps_rel: 9.999999747378752e-06
algorithm|deconvolution|fitting|max_iteration: 100
algorithm|deconvolution|fitting|penalties|position: 1.0
algorithm|deconvolution|fitting|penalties|height: 1.0
algorithm|deconvolution|fitting|penalties|left_width: 0.0
algorithm|deconvolution|fitting|penalties|right_width: 0.0
algorithm|SignalToNoiseEstimationParameter|max_intensity: -1
algorithm|SignalToNoiseEstimationParameter|auto_max_stdev_factor: 3.0
algorithm|SignalToNoiseEstimationParameter|auto_max_percentile: 95
algorithm|SignalToNoiseEstimationParameter|auto_mode: 0
algorithm|SignalToNoiseEstimationParameter|win_len: 200.0
algorithm|SignalToNoiseEstimationParameter|bin_count: 30
algorithm|SignalToNoiseEstimationParameter|stdev_mp: 3.0
algorithm|SignalToNoiseEstimationParameter|min_required_elements: 10
algorithm|SignalToNoiseEstimationParameter|noise_for_empty_window: 1e+20
adv_opts_cond|write_peak_meta_data: True
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ctd_out_FLAG

name: value
name: value

PeakPickerWavelet_deconv_input.mzML
value

Test-3

in: PeakPickerWavelet_input.mzML
algorithm|signal_to_noise: 3.0
algorithm|centroid_percentage: 0.6
algorithm|peak_width: 0.2
algorithm|estimate_peak_width: False
algorithm|fwhm_lower_bound_factor: 0.5
algorithm|fwhm_upper_bound_factor: 20.0
algorithm|optimization|iterations: 400
algorithm|optimization|penalties|position: 0.0
algorithm|optimization|penalties|left_width: 1.0
algorithm|optimization|penalties|right_width: 1.0
algorithm|optimization|penalties|height: 1.0
algorithm|optimization|2d|tolerance_mz: 2.2
algorithm|optimization|2d|max_peak_distance: 1.2
algorithm|thresholds|peak_bound: 100.0
algorithm|thresholds|peak_bound_ms2_level: 10.0
algorithm|thresholds|correlation: 0.5
algorithm|thresholds|noise_level: 0.1
algorithm|thresholds|search_radius: 3
algorithm|wavelet_transform|spacing: 0.001
algorithm|deconvolution|deconvolution: False
algorithm|deconvolution|asym_threshold: 0.3
algorithm|deconvolution|left_width: 2.0
algorithm|deconvolution|right_width: 2.0
algorithm|deconvolution|scaling: 0.12
algorithm|deconvolution|fitting|fwhm_threshold: 0.7
algorithm|deconvolution|fitting|eps_abs: 9.999999747378752e-06
algorithm|deconvolution|fitting|eps_rel: 9.999999747378752e-06
algorithm|deconvolution|fitting|max_iteration: 10
algorithm|deconvolution|fitting|penalties|position: 0.0
algorithm|deconvolution|fitting|penalties|height: 1.0
algorithm|deconvolution|fitting|penalties|left_width: 0.0
algorithm|deconvolution|fitting|penalties|right_width: 0.0
algorithm|SignalToNoiseEstimationParameter|max_intensity: -1
algorithm|SignalToNoiseEstimationParameter|auto_max_stdev_factor: 3.0
algorithm|SignalToNoiseEstimationParameter|auto_max_percentile: 95
algorithm|SignalToNoiseEstimationParameter|auto_mode: 0
algorithm|SignalToNoiseEstimationParameter|win_len: 200.0
algorithm|SignalToNoiseEstimationParameter|bin_count: 30
algorithm|SignalToNoiseEstimationParameter|stdev_mp: 3.0
algorithm|SignalToNoiseEstimationParameter|min_required_elements: 10
algorithm|SignalToNoiseEstimationParameter|noise_for_empty_window: 1e+20
adv_opts_cond|write_peak_meta_data: True
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ctd_out_FLAG

name: value
name: value

PeakPickerWavelet_input.mzML
value

Test-4

in: PeakPickerWavelet_input.mzML
algorithm|signal_to_noise: 3.0
algorithm|centroid_percentage: 0.6
algorithm|peak_width: 0.2
algorithm|estimate_peak_width: False
algorithm|fwhm_lower_bound_factor: 0.5
algorithm|fwhm_upper_bound_factor: 20.0
algorithm|optimization|iterations: 400
algorithm|optimization|penalties|position: 0.0
algorithm|optimization|penalties|left_width: 1.0
algorithm|optimization|penalties|right_width: 1.0
algorithm|optimization|penalties|height: 1.0
algorithm|optimization|2d|tolerance_mz: 2.2
algorithm|optimization|2d|max_peak_distance: 1.2
algorithm|thresholds|peak_bound: 100.0
algorithm|thresholds|peak_bound_ms2_level: 10.0
algorithm|thresholds|correlation: 0.5
algorithm|thresholds|noise_level: 0.1
algorithm|thresholds|search_radius: 3
algorithm|wavelet_transform|spacing: 0.001
algorithm|deconvolution|deconvolution: False
algorithm|deconvolution|asym_threshold: 0.3
algorithm|deconvolution|left_width: 2.0
algorithm|deconvolution|right_width: 2.0
algorithm|deconvolution|scaling: 0.12
algorithm|deconvolution|fitting|fwhm_threshold: 0.7
algorithm|deconvolution|fitting|eps_abs: 9.999999747378752e-06
algorithm|deconvolution|fitting|eps_rel: 9.999999747378752e-06
algorithm|deconvolution|fitting|max_iteration: 10
algorithm|deconvolution|fitting|penalties|position: 0.0
algorithm|deconvolution|fitting|penalties|height: 1.0
algorithm|deconvolution|fitting|penalties|left_width: 0.0
algorithm|deconvolution|fitting|penalties|right_width: 0.0
algorithm|SignalToNoiseEstimationParameter|max_intensity: -1
algorithm|SignalToNoiseEstimationParameter|auto_max_stdev_factor: 3.0
algorithm|SignalToNoiseEstimationParameter|auto_max_percentile: 95
algorithm|SignalToNoiseEstimationParameter|auto_mode: 0
algorithm|SignalToNoiseEstimationParameter|win_len: 200.0
algorithm|SignalToNoiseEstimationParameter|bin_count: 30
algorithm|SignalToNoiseEstimationParameter|stdev_mp: 3.0
algorithm|SignalToNoiseEstimationParameter|min_required_elements: 10
algorithm|SignalToNoiseEstimationParameter|noise_for_empty_window: 1e+20
adv_opts_cond|write_peak_meta_data: False
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ctd_out_FLAG

name: value
name: value

PeakPickerWavelet_input.mzML
value