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Revision: 13:9f0e189d093c

Repository 'openms_tofcalibration'

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

TOFCalibration tool metadata

Miscellaneous

Name: TOFCalibration

Description: Applies time of flight calibration.

Id: TOFCalibration

Guid: toolshed.g2.bx.psu.edu/repos/galaxyp/openms_tofcalibration/TOFCalibration/2.8+galaxy0

Version: 2.8+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_tofcalibration/TOFCalibration/3.1+galaxy0

toolshed.g2.bx.psu.edu/repos/galaxyp/openms_tofcalibration/TOFCalibration/2.8+galaxy0 (this tool)

toolshed.g2.bx.psu.edu/repos/galaxyp/openms_tofcalibration/TOFCalibration/2.6+galaxy0

toolshed.g2.bx.psu.edu/repos/galaxyp/openms_tofcalibration/TOFCalibration/2.5+galaxy0

toolshed.g2.bx.psu.edu/repos/galaxyp/openms_tofcalibration/TOFCalibration/2.3.0

toolshed.g2.bx.psu.edu/repos/galaxyp/openms_tofcalibration/TOFCalibration/2.2.0

toolshed.g2.bx.psu.edu/repos/galaxyp/openms_tofcalibration/TOFCalibration/2.1.0

TOFCalibration

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

Requirements:

name

version

type

openms

2.8

package

openms-thirdparty

2.8

package

omssa

2.1.9

package

blast

2.13.0

package

ctdopts

1.4

package

Functional tests

name

inputs

outputs

required files

Test-1

in: TOFCalibration_1_input.mzML
ext_calibrants: TOFCalibration_1_calibrants.mzML
ref_masses: TOFCalibration_ref_masses.tsv
tof_const: TOFCalibration_const.tsv
peak_data: False
algorithm|PeakPicker|signal_to_noise: 3.0
algorithm|PeakPicker|centroid_percentage: 0.6
algorithm|PeakPicker|peak_width: 0.15
algorithm|PeakPicker|estimate_peak_width: False
algorithm|PeakPicker|fwhm_lower_bound_factor: 0.7
algorithm|PeakPicker|fwhm_upper_bound_factor: 20.0
algorithm|PeakPicker|optimization|iterations: 400
algorithm|PeakPicker|optimization|penalties|position: 0.0
algorithm|PeakPicker|optimization|penalties|left_width: 1.0
algorithm|PeakPicker|optimization|penalties|right_width: 1.0
algorithm|PeakPicker|optimization|penalties|height: 1.0
algorithm|PeakPicker|optimization|2d|tolerance_mz: 2.2
algorithm|PeakPicker|optimization|2d|max_peak_distance: 1.2
algorithm|PeakPicker|thresholds|peak_bound: 400.0
algorithm|PeakPicker|thresholds|peak_bound_ms2_level: 10.0
algorithm|PeakPicker|thresholds|correlation: 0.0
algorithm|PeakPicker|thresholds|noise_level: 0.1
algorithm|PeakPicker|thresholds|search_radius: 3
algorithm|PeakPicker|wavelet_transform|spacing: 0.001
algorithm|PeakPicker|deconvolution|deconvolution: False
algorithm|PeakPicker|deconvolution|asym_threshold: 0.3
algorithm|PeakPicker|deconvolution|left_width: 2.0
algorithm|PeakPicker|deconvolution|right_width: 2.0
algorithm|PeakPicker|deconvolution|scaling: 0.12
algorithm|PeakPicker|deconvolution|fitting|fwhm_threshold: 0.7
algorithm|PeakPicker|deconvolution|fitting|eps_abs: 9.999999747378752e-06
algorithm|PeakPicker|deconvolution|fitting|eps_rel: 9.999999747378752e-06
algorithm|PeakPicker|deconvolution|fitting|max_iteration: 10
algorithm|PeakPicker|deconvolution|fitting|penalties|position: 0.0
algorithm|PeakPicker|deconvolution|fitting|penalties|height: 1.0
algorithm|PeakPicker|deconvolution|fitting|penalties|left_width: 0.0
algorithm|PeakPicker|deconvolution|fitting|penalties|right_width: 0.0
algorithm|PeakPicker|SignalToNoiseEstimationParameter|max_intensity: -1
algorithm|PeakPicker|SignalToNoiseEstimationParameter|auto_max_stdev_factor: 3.0
algorithm|PeakPicker|SignalToNoiseEstimationParameter|auto_max_percentile: 95
algorithm|PeakPicker|SignalToNoiseEstimationParameter|auto_mode: 0
algorithm|PeakPicker|SignalToNoiseEstimationParameter|win_len: 200.0
algorithm|PeakPicker|SignalToNoiseEstimationParameter|bin_count: 30
algorithm|PeakPicker|SignalToNoiseEstimationParameter|stdev_mp: 3.0
algorithm|PeakPicker|SignalToNoiseEstimationParameter|min_required_elements: 10
algorithm|PeakPicker|SignalToNoiseEstimationParameter|noise_for_empty_window: 1e+20
adv_opts|force: False
adv_opts|test: true
OPTIONAL_OUTPUTS: ctd_out_FLAG

name: value
name: value

TOFCalibration_1_input.mzML
TOFCalibration_1_calibrants.mzML
TOFCalibration_ref_masses.tsv
TOFCalibration_const.tsv
value

Test-2

in: TOFCalibration_2_input.mzML
ext_calibrants: TOFCalibration_2_calibrants.mzML
ref_masses: TOFCalibration_ref_masses.tsv
tof_const: TOFCalibration_const.tsv
peak_data: True
algorithm|PeakPicker|signal_to_noise: 3.0
algorithm|PeakPicker|centroid_percentage: 0.6
algorithm|PeakPicker|peak_width: 0.15
algorithm|PeakPicker|estimate_peak_width: False
algorithm|PeakPicker|fwhm_lower_bound_factor: 0.7
algorithm|PeakPicker|fwhm_upper_bound_factor: 20.0
algorithm|PeakPicker|optimization|iterations: 400
algorithm|PeakPicker|optimization|penalties|position: 0.0
algorithm|PeakPicker|optimization|penalties|left_width: 1.0
algorithm|PeakPicker|optimization|penalties|right_width: 1.0
algorithm|PeakPicker|optimization|penalties|height: 1.0
algorithm|PeakPicker|optimization|2d|tolerance_mz: 2.2
algorithm|PeakPicker|optimization|2d|max_peak_distance: 1.2
algorithm|PeakPicker|thresholds|peak_bound: 400.0
algorithm|PeakPicker|thresholds|peak_bound_ms2_level: 10.0
algorithm|PeakPicker|thresholds|correlation: 0.0
algorithm|PeakPicker|thresholds|noise_level: 0.1
algorithm|PeakPicker|thresholds|search_radius: 3
algorithm|PeakPicker|wavelet_transform|spacing: 0.001
algorithm|PeakPicker|deconvolution|deconvolution: False
algorithm|PeakPicker|deconvolution|asym_threshold: 0.3
algorithm|PeakPicker|deconvolution|left_width: 2.0
algorithm|PeakPicker|deconvolution|right_width: 2.0
algorithm|PeakPicker|deconvolution|scaling: 0.12
algorithm|PeakPicker|deconvolution|fitting|fwhm_threshold: 0.7
algorithm|PeakPicker|deconvolution|fitting|eps_abs: 9.999999747378752e-06
algorithm|PeakPicker|deconvolution|fitting|eps_rel: 9.999999747378752e-06
algorithm|PeakPicker|deconvolution|fitting|max_iteration: 10
algorithm|PeakPicker|deconvolution|fitting|penalties|position: 0.0
algorithm|PeakPicker|deconvolution|fitting|penalties|height: 1.0
algorithm|PeakPicker|deconvolution|fitting|penalties|left_width: 0.0
algorithm|PeakPicker|deconvolution|fitting|penalties|right_width: 0.0
algorithm|PeakPicker|SignalToNoiseEstimationParameter|max_intensity: -1
algorithm|PeakPicker|SignalToNoiseEstimationParameter|auto_max_stdev_factor: 3.0
algorithm|PeakPicker|SignalToNoiseEstimationParameter|auto_max_percentile: 95
algorithm|PeakPicker|SignalToNoiseEstimationParameter|auto_mode: 0
algorithm|PeakPicker|SignalToNoiseEstimationParameter|win_len: 200.0
algorithm|PeakPicker|SignalToNoiseEstimationParameter|bin_count: 30
algorithm|PeakPicker|SignalToNoiseEstimationParameter|stdev_mp: 3.0
algorithm|PeakPicker|SignalToNoiseEstimationParameter|min_required_elements: 10
algorithm|PeakPicker|SignalToNoiseEstimationParameter|noise_for_empty_window: 1e+20
adv_opts|force: False
adv_opts|test: true
OPTIONAL_OUTPUTS: ctd_out_FLAG

name: value
name: value

TOFCalibration_2_input.mzML
TOFCalibration_2_calibrants.mzML
TOFCalibration_ref_masses.tsv
TOFCalibration_const.tsv
value