| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermetabo/FeatureFinderMetabo/2.6+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermetabo/FeatureFinderMetabo/2.5+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermetabo/FeatureFinderMetabo/2.3.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermetabo/FeatureFinderMetabo/2.2.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermetabo/FeatureFinderMetabo/2.1.0 |
| FeatureFinderMetabo |
| Requirements (dependencies defined in the <requirements> tag set) |
| 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: FeatureFinderMetabo_1_input.mzML algorithm|common|noise_threshold_int: 10.0 algorithm|common|chrom_peak_snr: 3.0 algorithm|common|chrom_fwhm: 5.0 algorithm|mtd|mass_error_ppm: 20.0 algorithm|mtd|reestimate_mt_sd: True algorithm|mtd|quant_method: area algorithm|mtd|trace_termination_criterion: outlier algorithm|mtd|trace_termination_outliers: 5 algorithm|mtd|min_sample_rate: 0.5 algorithm|mtd|min_trace_length: 5.0 algorithm|mtd|max_trace_length: 300.0 algorithm|epd|enabled: True algorithm|epd|width_filtering: off algorithm|epd|min_fwhm: 3.0 algorithm|epd|max_fwhm: 60.0 algorithm|epd|masstrace_snr_filtering: False algorithm|ffm|local_rt_range: 10.0 algorithm|ffm|local_mz_range: 6.5 algorithm|ffm|charge_lower_bound: 1 algorithm|ffm|charge_upper_bound: 3 algorithm|ffm|report_summed_ints: False algorithm|ffm|enable_RT_filtering: True algorithm|ffm|isotope_filtering_model: metabolites (5% RMS) algorithm|ffm|mz_scoring_13C: True algorithm|ffm|use_smoothed_intensities: True algorithm|ffm|report_convex_hulls: False algorithm|ffm|remove_single_traces: False algorithm|ffm|mz_scoring_by_elements: False algorithm|ffm|elements: CHNOPS 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 |
FeatureFinderMetabo_1_input.mzML value |
| Test-2 |
in: FeatureFinderMetabo_2_input.mzML algorithm|common|noise_threshold_int: 100.0 algorithm|common|chrom_peak_snr: 0.0 algorithm|common|chrom_fwhm: 100.0 algorithm|mtd|mass_error_ppm: 5.0 algorithm|mtd|reestimate_mt_sd: True algorithm|mtd|quant_method: median algorithm|mtd|trace_termination_criterion: sample_rate algorithm|mtd|trace_termination_outliers: 2 algorithm|mtd|min_sample_rate: 0.01 algorithm|mtd|min_trace_length: 30.0 algorithm|mtd|max_trace_length: 3000.0 algorithm|epd|enabled: False algorithm|epd|width_filtering: off algorithm|epd|min_fwhm: 10.0 algorithm|epd|max_fwhm: 80.0 algorithm|epd|masstrace_snr_filtering: False algorithm|ffm|local_rt_range: 10.0 algorithm|ffm|local_mz_range: 4.5 algorithm|ffm|charge_lower_bound: 1 algorithm|ffm|charge_upper_bound: 3 algorithm|ffm|report_summed_ints: False algorithm|ffm|enable_RT_filtering: False algorithm|ffm|isotope_filtering_model: none algorithm|ffm|mz_scoring_13C: False algorithm|ffm|use_smoothed_intensities: False algorithm|ffm|report_convex_hulls: True algorithm|ffm|remove_single_traces: False algorithm|ffm|mz_scoring_by_elements: False algorithm|ffm|elements: CHNOPS 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 |
FeatureFinderMetabo_2_input.mzML value |
| Test-3 |
in: FeatureFinderMetabo_3_input.mzML algorithm|common|noise_threshold_int: 10.0 algorithm|common|chrom_peak_snr: 3.0 algorithm|common|chrom_fwhm: 5.0 algorithm|mtd|mass_error_ppm: 5.0 algorithm|mtd|reestimate_mt_sd: True algorithm|mtd|quant_method: area algorithm|mtd|trace_termination_criterion: outlier algorithm|mtd|trace_termination_outliers: 5 algorithm|mtd|min_sample_rate: 0.5 algorithm|mtd|min_trace_length: 5.0 algorithm|mtd|max_trace_length: -1.0 algorithm|epd|enabled: True algorithm|epd|width_filtering: fixed algorithm|epd|min_fwhm: 3.0 algorithm|epd|max_fwhm: 60.0 algorithm|epd|masstrace_snr_filtering: False algorithm|ffm|local_rt_range: 10.0 algorithm|ffm|local_mz_range: 6.5 algorithm|ffm|charge_lower_bound: 1 algorithm|ffm|charge_upper_bound: 3 algorithm|ffm|report_summed_ints: False algorithm|ffm|enable_RT_filtering: True algorithm|ffm|isotope_filtering_model: none algorithm|ffm|mz_scoring_13C: True algorithm|ffm|use_smoothed_intensities: True algorithm|ffm|report_convex_hulls: True algorithm|ffm|remove_single_traces: False algorithm|ffm|mz_scoring_by_elements: False algorithm|ffm|elements: CHNOPS adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_chrom_FLAG'] |
name: value name: value name: value |
FeatureFinderMetabo_3_input.mzML value |
| Test-4 |
in: FeatureFinderMetabo_3_input.mzML algorithm|common|noise_threshold_int: 10.0 algorithm|common|chrom_peak_snr: 3.0 algorithm|common|chrom_fwhm: 5.0 algorithm|mtd|mass_error_ppm: 5.0 algorithm|mtd|reestimate_mt_sd: True algorithm|mtd|quant_method: area algorithm|mtd|trace_termination_criterion: outlier algorithm|mtd|trace_termination_outliers: 5 algorithm|mtd|min_sample_rate: 0.5 algorithm|mtd|min_trace_length: 5.0 algorithm|mtd|max_trace_length: -1.0 algorithm|epd|enabled: True algorithm|epd|width_filtering: fixed algorithm|epd|min_fwhm: 3.0 algorithm|epd|max_fwhm: 60.0 algorithm|epd|masstrace_snr_filtering: False algorithm|ffm|local_rt_range: 10.0 algorithm|ffm|local_mz_range: 6.5 algorithm|ffm|charge_lower_bound: 1 algorithm|ffm|charge_upper_bound: 3 algorithm|ffm|report_summed_ints: False algorithm|ffm|enable_RT_filtering: True algorithm|ffm|isotope_filtering_model: none algorithm|ffm|mz_scoring_13C: True algorithm|ffm|use_smoothed_intensities: True algorithm|ffm|report_convex_hulls: True algorithm|ffm|remove_single_traces: True algorithm|ffm|mz_scoring_by_elements: False algorithm|ffm|elements: CHNOPS adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_chrom_FLAG'] |
name: value name: value name: value |
FeatureFinderMetabo_3_input.mzML value |
| Test-5 |
in: FeatureFinderMetabo_1_input.mzML algorithm|common|noise_threshold_int: 10.0 algorithm|common|chrom_peak_snr: 3.0 algorithm|common|chrom_fwhm: 5.0 algorithm|mtd|mass_error_ppm: 20.0 algorithm|mtd|reestimate_mt_sd: True algorithm|mtd|quant_method: max_height algorithm|mtd|trace_termination_criterion: outlier algorithm|mtd|trace_termination_outliers: 5 algorithm|mtd|min_sample_rate: 0.5 algorithm|mtd|min_trace_length: 5.0 algorithm|mtd|max_trace_length: 300.0 algorithm|epd|enabled: True algorithm|epd|width_filtering: off algorithm|epd|min_fwhm: 3.0 algorithm|epd|max_fwhm: 60.0 algorithm|epd|masstrace_snr_filtering: False algorithm|ffm|local_rt_range: 10.0 algorithm|ffm|local_mz_range: 6.5 algorithm|ffm|charge_lower_bound: 1 algorithm|ffm|charge_upper_bound: 3 algorithm|ffm|report_summed_ints: False algorithm|ffm|enable_RT_filtering: True algorithm|ffm|isotope_filtering_model: metabolites (5% RMS) algorithm|ffm|mz_scoring_13C: True algorithm|ffm|use_smoothed_intensities: True algorithm|ffm|report_convex_hulls: False algorithm|ffm|remove_single_traces: False algorithm|ffm|mz_scoring_by_elements: False algorithm|ffm|elements: CHNOPS 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 |
FeatureFinderMetabo_1_input.mzML value |