Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_tofcalibration/TOFCalibration/2.8+galaxy0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_tofcalibration/TOFCalibration/2.6+galaxy0 (this tool) |
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) |
name | version | type |
openms | 2.6 | package |
openms-thirdparty | 2.6 | package |
blast | 2.9.0 | 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_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced 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_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced 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 |