Detects two-dimensional features in LC-MS data.
FeatureFinderCentroided
macros.xml
FeatureFinderCentroided
#if $param_in:
-in $param_in
#end if
#if $param_out:
-out $param_out
#end if
#if $param_seeds:
-seeds $param_seeds
#end if
#if $param_out_mzq:
-out_mzq $param_out_mzq
#end if
#if $param_algorithm_intensity_bins:
-algorithm:intensity:bins $param_algorithm_intensity_bins
#end if
#if $param_algorithm_mass_trace_mz_tolerance:
-algorithm:mass_trace:mz_tolerance $param_algorithm_mass_trace_mz_tolerance
#end if
#if $param_algorithm_mass_trace_min_spectra:
-algorithm:mass_trace:min_spectra $param_algorithm_mass_trace_min_spectra
#end if
#if $param_algorithm_mass_trace_max_missing:
-algorithm:mass_trace:max_missing $param_algorithm_mass_trace_max_missing
#end if
#if $param_algorithm_mass_trace_slope_bound:
-algorithm:mass_trace:slope_bound $param_algorithm_mass_trace_slope_bound
#end if
#if $param_algorithm_isotopic_pattern_charge_low:
-algorithm:isotopic_pattern:charge_low $param_algorithm_isotopic_pattern_charge_low
#end if
#if $param_algorithm_isotopic_pattern_charge_high:
-algorithm:isotopic_pattern:charge_high $param_algorithm_isotopic_pattern_charge_high
#end if
#if $param_algorithm_isotopic_pattern_mz_tolerance:
-algorithm:isotopic_pattern:mz_tolerance $param_algorithm_isotopic_pattern_mz_tolerance
#end if
#if $param_algorithm_seed_min_score:
-algorithm:seed:min_score $param_algorithm_seed_min_score
#end if
#if $param_algorithm_feature_min_score:
-algorithm:feature:min_score $param_algorithm_feature_min_score
#end if
#if $param_algorithm_feature_reported_mz:
-algorithm:feature:reported_mz
#if " " in str($param_algorithm_feature_reported_mz):
"$param_algorithm_feature_reported_mz"
#else
$param_algorithm_feature_reported_mz
#end if
#end if
#if $param_algorithm_user_seed_rt_tolerance:
-algorithm:user-seed:rt_tolerance $param_algorithm_user_seed_rt_tolerance
#end if
#if $param_algorithm_user_seed_mz_tolerance:
-algorithm:user-seed:mz_tolerance $param_algorithm_user_seed_mz_tolerance
#end if
#if $param_algorithm_user_seed_min_score:
-algorithm:user-seed:min_score $param_algorithm_user_seed_min_score
#end if
#if $adv_opts.adv_opts_selector=='advanced':
#if $adv_opts.param_force:
-force
#end if
#if $adv_opts.param_algorithm_debug_pseudo_rt_shift:
-algorithm:debug:pseudo_rt_shift $adv_opts.param_algorithm_debug_pseudo_rt_shift
#end if
#if $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage:
-algorithm:isotopic_pattern:intensity_percentage $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage
#end if
#if $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage_optional:
-algorithm:isotopic_pattern:intensity_percentage_optional $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage_optional
#end if
#if $adv_opts.param_algorithm_isotopic_pattern_optional_fit_improvement:
-algorithm:isotopic_pattern:optional_fit_improvement $adv_opts.param_algorithm_isotopic_pattern_optional_fit_improvement
#end if
#if $adv_opts.param_algorithm_isotopic_pattern_mass_window_width:
-algorithm:isotopic_pattern:mass_window_width $adv_opts.param_algorithm_isotopic_pattern_mass_window_width
#end if
#if $adv_opts.param_algorithm_isotopic_pattern_abundance_12C:
-algorithm:isotopic_pattern:abundance_12C $adv_opts.param_algorithm_isotopic_pattern_abundance_12C
#end if
#if $adv_opts.param_algorithm_isotopic_pattern_abundance_14N:
-algorithm:isotopic_pattern:abundance_14N $adv_opts.param_algorithm_isotopic_pattern_abundance_14N
#end if
#if $adv_opts.param_algorithm_fit_max_iterations:
-algorithm:fit:max_iterations $adv_opts.param_algorithm_fit_max_iterations
#end if
#if $adv_opts.param_algorithm_feature_min_isotope_fit:
-algorithm:feature:min_isotope_fit $adv_opts.param_algorithm_feature_min_isotope_fit
#end if
#if $adv_opts.param_algorithm_feature_min_trace_score:
-algorithm:feature:min_trace_score $adv_opts.param_algorithm_feature_min_trace_score
#end if
#if $adv_opts.param_algorithm_feature_min_rt_span:
-algorithm:feature:min_rt_span $adv_opts.param_algorithm_feature_min_rt_span
#end if
#if $adv_opts.param_algorithm_feature_max_rt_span:
-algorithm:feature:max_rt_span $adv_opts.param_algorithm_feature_max_rt_span
#end if
#if $adv_opts.param_algorithm_feature_rt_shape:
-algorithm:feature:rt_shape
#if " " in str($adv_opts.param_algorithm_feature_rt_shape):
"$adv_opts.param_algorithm_feature_rt_shape"
#else
$adv_opts.param_algorithm_feature_rt_shape
#end if
#end if
#if $adv_opts.param_algorithm_feature_max_intersection:
-algorithm:feature:max_intersection $adv_opts.param_algorithm_feature_max_intersection
#end if
#end if
Detects two-dimensional features in LC-MS data.
For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderCentroided.html