# HG changeset patch # User galaxyp # Date 1488391169 18000 # Node ID 7c2b85eb3ccf3f532fe3cb27414f7fad77fe4864 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 diff -r 000000000000 -r 7c2b85eb3ccf MSSimulator.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MSSimulator.xml Wed Mar 01 12:59:29 2017 -0500 @@ -0,0 +1,940 @@ + + + + + A highly configurable simulator for mass spectrometry experiments. + + MSSimulator + macros.xml + + + + + MSSimulator + +-in + #for token in $param_in: + $token + #end for +#if $param_out: + -out $param_out +#end if +#if $param_out_pm: + -out_pm $param_out_pm +#end if +#if $param_out_fm: + -out_fm $param_out_fm +#end if +#if $param_out_cm: + -out_cm $param_out_cm +#end if +#if $param_out_lcm: + -out_lcm $param_out_lcm +#end if +#if $param_out_cntm: + -out_cntm $param_out_cntm +#end if +#if $param_out_id: + -out_id $param_out_id +#end if +#if $param_algorithm_MSSim_Digestion_enzyme: + -algorithm:MSSim:Digestion:enzyme $param_algorithm_MSSim_Digestion_enzyme +#end if +#if $param_algorithm_MSSim_Digestion_model: + -algorithm:MSSim:Digestion:model $param_algorithm_MSSim_Digestion_model +#end if +#if $param_algorithm_MSSim_Digestion_min_peptide_length: + -algorithm:MSSim:Digestion:min_peptide_length $param_algorithm_MSSim_Digestion_min_peptide_length +#end if +#if $param_algorithm_MSSim_Digestion_model_trained_threshold: + -algorithm:MSSim:Digestion:model_trained:threshold $param_algorithm_MSSim_Digestion_model_trained_threshold +#end if +#if $param_algorithm_MSSim_Digestion_model_naive_missed_cleavages: + -algorithm:MSSim:Digestion:model_naive:missed_cleavages $param_algorithm_MSSim_Digestion_model_naive_missed_cleavages +#end if +#if $param_algorithm_MSSim_RT_rt_column: + -algorithm:MSSim:RT:rt_column $param_algorithm_MSSim_RT_rt_column +#end if +#if $param_algorithm_MSSim_RT_auto_scale: + -algorithm:MSSim:RT:auto_scale $param_algorithm_MSSim_RT_auto_scale +#end if +#if $param_algorithm_MSSim_RT_total_gradient_time: + -algorithm:MSSim:RT:total_gradient_time $param_algorithm_MSSim_RT_total_gradient_time +#end if +#if $param_algorithm_MSSim_RT_sampling_rate: + -algorithm:MSSim:RT:sampling_rate $param_algorithm_MSSim_RT_sampling_rate +#end if +#if $param_algorithm_MSSim_RT_scan_window_min: + -algorithm:MSSim:RT:scan_window:min $param_algorithm_MSSim_RT_scan_window_min +#end if +#if $param_algorithm_MSSim_RT_scan_window_max: + -algorithm:MSSim:RT:scan_window:max $param_algorithm_MSSim_RT_scan_window_max +#end if +#if $param_algorithm_MSSim_RT_variation_feature_stddev: + -algorithm:MSSim:RT:variation:feature_stddev $param_algorithm_MSSim_RT_variation_feature_stddev +#end if +#if $param_algorithm_MSSim_RT_variation_affine_offset: + -algorithm:MSSim:RT:variation:affine_offset $param_algorithm_MSSim_RT_variation_affine_offset +#end if +#if $param_algorithm_MSSim_RT_variation_affine_scale: + -algorithm:MSSim:RT:variation:affine_scale $param_algorithm_MSSim_RT_variation_affine_scale +#end if +#if $param_algorithm_MSSim_RT_column_condition_distortion: + -algorithm:MSSim:RT:column_condition:distortion $param_algorithm_MSSim_RT_column_condition_distortion +#end if +#if $param_algorithm_MSSim_RT_profile_shape_width_value: + -algorithm:MSSim:RT:profile_shape:width:value $param_algorithm_MSSim_RT_profile_shape_width_value +#end if +#if $param_algorithm_MSSim_RT_profile_shape_width_variance: + -algorithm:MSSim:RT:profile_shape:width:variance $param_algorithm_MSSim_RT_profile_shape_width_variance +#end if +#if $param_algorithm_MSSim_RT_profile_shape_skewness_value: + -algorithm:MSSim:RT:profile_shape:skewness:value $param_algorithm_MSSim_RT_profile_shape_skewness_value +#end if +#if $param_algorithm_MSSim_RT_profile_shape_skewness_variance: + -algorithm:MSSim:RT:profile_shape:skewness:variance $param_algorithm_MSSim_RT_profile_shape_skewness_variance +#end if +#if $param_algorithm_MSSim_RT_HPLC_model_file: + -algorithm:MSSim:RT:HPLC:model_file "$param_algorithm_MSSim_RT_HPLC_model_file" +#end if +#if $param_algorithm_MSSim_RT_CE_pH: + -algorithm:MSSim:RT:CE:pH $param_algorithm_MSSim_RT_CE_pH +#end if +#if $param_algorithm_MSSim_RT_CE_alpha: + -algorithm:MSSim:RT:CE:alpha $param_algorithm_MSSim_RT_CE_alpha +#end if +#if $param_algorithm_MSSim_RT_CE_mu_eo: + -algorithm:MSSim:RT:CE:mu_eo $param_algorithm_MSSim_RT_CE_mu_eo +#end if +#if $param_algorithm_MSSim_RT_CE_lenght_d: + -algorithm:MSSim:RT:CE:lenght_d $param_algorithm_MSSim_RT_CE_lenght_d +#end if +#if $param_algorithm_MSSim_RT_CE_length_total: + -algorithm:MSSim:RT:CE:length_total $param_algorithm_MSSim_RT_CE_length_total +#end if +#if $param_algorithm_MSSim_RT_CE_voltage: + -algorithm:MSSim:RT:CE:voltage $param_algorithm_MSSim_RT_CE_voltage +#end if +#if $param_algorithm_MSSim_Detectability_dt_simulation_on: + -algorithm:MSSim:Detectability:dt_simulation_on +#end if +#if $param_algorithm_MSSim_Detectability_min_detect: + -algorithm:MSSim:Detectability:min_detect $param_algorithm_MSSim_Detectability_min_detect +#end if +#if $param_algorithm_MSSim_Detectability_dt_model_file: + -algorithm:MSSim:Detectability:dt_model_file "$param_algorithm_MSSim_Detectability_dt_model_file" +#end if + +#if $rep_param_algorithm_MSSim_Ionization_esi_ionized_residues: +-algorithm:MSSim:Ionization:esi:ionized_residues + #for token in $rep_param_algorithm_MSSim_Ionization_esi_ionized_residues: + #if " " in str(token): + "$token.param_algorithm_MSSim_Ionization_esi_ionized_residues" + #else + $token.param_algorithm_MSSim_Ionization_esi_ionized_residues + #end if + #end for +#end if + +#if $rep_param_algorithm_MSSim_Ionization_esi_charge_impurity: +-algorithm:MSSim:Ionization:esi:charge_impurity + #for token in $rep_param_algorithm_MSSim_Ionization_esi_charge_impurity: + #if " " in str(token): + "$token.param_algorithm_MSSim_Ionization_esi_charge_impurity" + #else + $token.param_algorithm_MSSim_Ionization_esi_charge_impurity + #end if + #end for +#end if +#if $param_algorithm_MSSim_Ionization_esi_ionization_probability: + -algorithm:MSSim:Ionization:esi:ionization_probability $param_algorithm_MSSim_Ionization_esi_ionization_probability +#end if + +#if $rep_param_algorithm_MSSim_Ionization_maldi_ionization_probabilities: +-algorithm:MSSim:Ionization:maldi:ionization_probabilities + #for token in $rep_param_algorithm_MSSim_Ionization_maldi_ionization_probabilities: + #if " " in str(token): + "$token.param_algorithm_MSSim_Ionization_maldi_ionization_probabilities" + #else + $token.param_algorithm_MSSim_Ionization_maldi_ionization_probabilities + #end if + #end for +#end if +#if $param_algorithm_MSSim_Ionization_mz_lower_measurement_limit: + -algorithm:MSSim:Ionization:mz:lower_measurement_limit $param_algorithm_MSSim_Ionization_mz_lower_measurement_limit +#end if +#if $param_algorithm_MSSim_Ionization_mz_upper_measurement_limit: + -algorithm:MSSim:Ionization:mz:upper_measurement_limit $param_algorithm_MSSim_Ionization_mz_upper_measurement_limit +#end if +#if $param_algorithm_MSSim_RawSignal_enabled: + -algorithm:MSSim:RawSignal:enabled $param_algorithm_MSSim_RawSignal_enabled +#end if +#if $param_algorithm_MSSim_RawSignal_peak_shape: + -algorithm:MSSim:RawSignal:peak_shape $param_algorithm_MSSim_RawSignal_peak_shape +#end if +#if $param_algorithm_MSSim_RawSignal_resolution_value: + -algorithm:MSSim:RawSignal:resolution:value $param_algorithm_MSSim_RawSignal_resolution_value +#end if +#if $param_algorithm_MSSim_RawSignal_resolution_type: + -algorithm:MSSim:RawSignal:resolution:type $param_algorithm_MSSim_RawSignal_resolution_type +#end if +#if $param_algorithm_MSSim_RawSignal_baseline_scaling: + -algorithm:MSSim:RawSignal:baseline:scaling $param_algorithm_MSSim_RawSignal_baseline_scaling +#end if +#if $param_algorithm_MSSim_RawSignal_baseline_shape: + -algorithm:MSSim:RawSignal:baseline:shape $param_algorithm_MSSim_RawSignal_baseline_shape +#end if +#if $param_algorithm_MSSim_RawSignal_mz_sampling_points: + -algorithm:MSSim:RawSignal:mz:sampling_points $param_algorithm_MSSim_RawSignal_mz_sampling_points +#end if +#if $param_algorithm_MSSim_RawSignal_contaminants_file: + -algorithm:MSSim:RawSignal:contaminants:file "$param_algorithm_MSSim_RawSignal_contaminants_file" +#end if +#if $param_algorithm_MSSim_RawSignal_variation_mz_error_stddev: + -algorithm:MSSim:RawSignal:variation:mz:error_stddev $param_algorithm_MSSim_RawSignal_variation_mz_error_stddev +#end if +#if $param_algorithm_MSSim_RawSignal_variation_mz_error_mean: + -algorithm:MSSim:RawSignal:variation:mz:error_mean $param_algorithm_MSSim_RawSignal_variation_mz_error_mean +#end if +#if $param_algorithm_MSSim_RawSignal_variation_intensity_scale: + -algorithm:MSSim:RawSignal:variation:intensity:scale $param_algorithm_MSSim_RawSignal_variation_intensity_scale +#end if +#if $param_algorithm_MSSim_RawSignal_variation_intensity_scale_stddev: + -algorithm:MSSim:RawSignal:variation:intensity:scale_stddev $param_algorithm_MSSim_RawSignal_variation_intensity_scale_stddev +#end if +#if $param_algorithm_MSSim_RawSignal_noise_shot_rate: + -algorithm:MSSim:RawSignal:noise:shot:rate $param_algorithm_MSSim_RawSignal_noise_shot_rate +#end if +#if $param_algorithm_MSSim_RawSignal_noise_shot_intensity_mean: + -algorithm:MSSim:RawSignal:noise:shot:intensity-mean $param_algorithm_MSSim_RawSignal_noise_shot_intensity_mean +#end if +#if $param_algorithm_MSSim_RawSignal_noise_white_mean: + -algorithm:MSSim:RawSignal:noise:white:mean $param_algorithm_MSSim_RawSignal_noise_white_mean +#end if +#if $param_algorithm_MSSim_RawSignal_noise_white_stddev: + -algorithm:MSSim:RawSignal:noise:white:stddev $param_algorithm_MSSim_RawSignal_noise_white_stddev +#end if +#if $param_algorithm_MSSim_RawSignal_noise_detector_mean: + -algorithm:MSSim:RawSignal:noise:detector:mean $param_algorithm_MSSim_RawSignal_noise_detector_mean +#end if +#if $param_algorithm_MSSim_RawSignal_noise_detector_stddev: + -algorithm:MSSim:RawSignal:noise:detector:stddev $param_algorithm_MSSim_RawSignal_noise_detector_stddev +#end if +#if $param_algorithm_MSSim_RawTandemSignal_status: + -algorithm:MSSim:RawTandemSignal:status $param_algorithm_MSSim_RawTandemSignal_status +#end if +#if $param_algorithm_MSSim_RawTandemSignal_tandem_mode: + -algorithm:MSSim:RawTandemSignal:tandem_mode $param_algorithm_MSSim_RawTandemSignal_tandem_mode +#end if +#if $param_algorithm_MSSim_RawTandemSignal_svm_model_set_file: + -algorithm:MSSim:RawTandemSignal:svm_model_set_file "$param_algorithm_MSSim_RawTandemSignal_svm_model_set_file" +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ms2_spectra_per_rt_bin: + -algorithm:MSSim:RawTandemSignal:Precursor:ms2_spectra_per_rt_bin $param_algorithm_MSSim_RawTandemSignal_Precursor_ms2_spectra_per_rt_bin +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_min_mz_peak_distance: + -algorithm:MSSim:RawTandemSignal:Precursor:min_mz_peak_distance $param_algorithm_MSSim_RawTandemSignal_Precursor_min_mz_peak_distance +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_mz_isolation_window: + -algorithm:MSSim:RawTandemSignal:Precursor:mz_isolation_window $param_algorithm_MSSim_RawTandemSignal_Precursor_mz_isolation_window +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_exclude_overlapping_peaks: + -algorithm:MSSim:RawTandemSignal:Precursor:exclude_overlapping_peaks +#end if + +#if $rep_param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter: +-algorithm:MSSim:RawTandemSignal:Precursor:charge_filter + #for token in $rep_param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter: + #if " " in str(token): + "$token.param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter" + #else + $token.param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter + #end if + #end for +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_use_dynamic_exclusion: + -algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:use_dynamic_exclusion +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_exclusion_time: + -algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:exclusion_time $param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_exclusion_time +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_max_list_size: + -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:max_list_size $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_max_list_size +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_min_rt: + -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:min_rt $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_min_rt +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_max_rt: + -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:max_rt $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_max_rt +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_step_size: + -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_step_size $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_step_size +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_window_size: + -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_window_size $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_window_size +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_protein_id_probability: + -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_protein_id_probability $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_protein_id_probability +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_pt_weight: + -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_pt_weight $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_pt_weight +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_mz: + -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_mz $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_mz +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_max_mz: + -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:max_mz $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_max_mz +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_use_peptide_rule: + -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:use_peptide_rule +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_ids: + -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_ids $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_ids +#end if +#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_probability: + -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_probability $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_probability +#end if +#if $param_algorithm_MSSim_RawTandemSignal_MS_E_add_single_spectra: + -algorithm:MSSim:RawTandemSignal:MS_E:add_single_spectra +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_isotopes: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_isotopes +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_max_isotope: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:max_isotope $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_max_isotope +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_metainfo: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_metainfo +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_losses: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_precursor_peaks: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_abundant_immonium_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_first_prefix_ion: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_y_ions $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_b_ions $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_a_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_a_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_c_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_c_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_x_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_x_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_z_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_z_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_y_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:y_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_y_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_b_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:b_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_b_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_a_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:a_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_a_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_c_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:c_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_c_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_x_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:x_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_x_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_z_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:z_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_z_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_relative_loss_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:relative_loss_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_relative_loss_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_H2O_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_H2O_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_H2O_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_NH3_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_NH3_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_NH3_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_isotopes: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_isotopes +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_max_isotope: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:max_isotope $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_max_isotope +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_metainfo: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_metainfo +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_first_prefix_ion: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_first_prefix_ion +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_y_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_y2_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y2_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_b_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_b2_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b2_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_a_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_a_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_c_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_c_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_x_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_x_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_z_ions: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_z_ions +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_losses: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_losses +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_y_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:y_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_y_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_b_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:b_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_b_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_a_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:a_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_a_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_c_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:c_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_c_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_x_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:x_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_x_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_z_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:z_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_z_intensity +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_relative_loss_intensity: + -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:relative_loss_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_relative_loss_intensity +#end if +#if $param_algorithm_MSSim_Global_ionization_type: + -algorithm:MSSim:Global:ionization_type $param_algorithm_MSSim_Global_ionization_type +#end if +#if $param_algorithm_MSSim_Labeling_type: + -algorithm:MSSim:Labeling:type $param_algorithm_MSSim_Labeling_type +#end if +#if $param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift: + -algorithm:MSSim:Labeling:ICPL:ICPL_fixed_rtshift $param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift +#end if +#if $param_algorithm_MSSim_Labeling_ICPL_label_proteins: + -algorithm:MSSim:Labeling:ICPL:label_proteins $param_algorithm_MSSim_Labeling_ICPL_label_proteins +#end if +#if $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift: + -algorithm:MSSim:Labeling:SILAC:fixed_rtshift $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift +#end if +#if $param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_lysine: + -algorithm:MSSim:Labeling:SILAC:medium_channel:modification_lysine "$param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_lysine" +#end if +#if $param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_arginine: + -algorithm:MSSim:Labeling:SILAC:medium_channel:modification_arginine "$param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_arginine" +#end if +#if $param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_lysine: + -algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_lysine "$param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_lysine" +#end if +#if $param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine: + -algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_arginine "$param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine" +#end if +#if $param_algorithm_MSSim_Labeling_itraq_iTRAQ: + -algorithm:MSSim:Labeling:itraq:iTRAQ $param_algorithm_MSSim_Labeling_itraq_iTRAQ +#end if +#if $param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift: + -algorithm:MSSim:Labeling:itraq:reporter_mass_shift $param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift +#end if + +#if $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_4plex: +-algorithm:MSSim:Labeling:itraq:channel_active_4plex + #for token in $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_4plex: + #if " " in str(token): + "$token.param_algorithm_MSSim_Labeling_itraq_channel_active_4plex" + #else + $token.param_algorithm_MSSim_Labeling_itraq_channel_active_4plex + #end if + #end for +#end if + +#if $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_8plex: +-algorithm:MSSim:Labeling:itraq:channel_active_8plex + #for token in $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_8plex: + #if " " in str(token): + "$token.param_algorithm_MSSim_Labeling_itraq_channel_active_8plex" + #else + $token.param_algorithm_MSSim_Labeling_itraq_channel_active_8plex + #end if + #end for +#end if +#if $param_algorithm_MSSim_Labeling_itraq_Y_contamination: + -algorithm:MSSim:Labeling:itraq:Y_contamination $param_algorithm_MSSim_Labeling_itraq_Y_contamination +#end if +#if $param_algorithm_MSSim_Labeling_o18_labeling_efficiency: + -algorithm:MSSim:Labeling:o18:labeling_efficiency $param_algorithm_MSSim_Labeling_o18_labeling_efficiency +#end if +#if $param_algorithm_RandomNumberGenerators_biological: + -algorithm:RandomNumberGenerators:biological $param_algorithm_RandomNumberGenerators_biological +#end if +#if $param_algorithm_RandomNumberGenerators_technical: + -algorithm:RandomNumberGenerators:technical $param_algorithm_RandomNumberGenerators_technical +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_MSSim_Ionization_esi_max_impurity_set_size: + -algorithm:MSSim:Ionization:esi:max_impurity_set_size $adv_opts.param_algorithm_MSSim_Ionization_esi_max_impurity_set_size +#end if + #if $adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_light_channel_label: + -algorithm:MSSim:Labeling:ICPL:ICPL_light_channel_label "$adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_light_channel_label" +#end if + #if $adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_medium_channel_label: + -algorithm:MSSim:Labeling:ICPL:ICPL_medium_channel_label "$adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_medium_channel_label" +#end if + #if $adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_heavy_channel_label: + -algorithm:MSSim:Labeling:ICPL:ICPL_heavy_channel_label "$adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_heavy_channel_label" +#end if + +#if $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex: +-algorithm:MSSim:Labeling:itraq:isotope_correction_values_4plex + #for token in $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex: + #if " " in str(token): + "$token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex" + #else + $token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex + #end if + #end for +#end if + +#if $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex: +-algorithm:MSSim:Labeling:itraq:isotope_correction_values_8plex + #for token in $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex: + #if " " in str(token): + "$token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex" + #else + $token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex + #end if + #end for +#end if +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A highly configurable simulator for mass spectrometry experiments. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MSSimulator.html + diff -r 000000000000 -r 7c2b85eb3ccf SKIP_TOOLS_FILE.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SKIP_TOOLS_FILE.txt Wed Mar 01 12:59:29 2017 -0500 @@ -0,0 +1,9 @@ +OMSSAAdapter +MyriMatchAdapter +PepNovoAdapter +SeedListGenerator +SpecLibSearcher +MapAlignerIdentification +MapAlignerPoseClustering +MapAlignerSpectrum +MapAlignerRTTransformer diff -r 000000000000 -r 7c2b85eb3ccf datatypes_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes_conf.xml Wed Mar 01 12:59:29 2017 -0500 @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r 7c2b85eb3ccf filetypes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filetypes.txt Wed Mar 01 12:59:29 2017 -0500 @@ -0,0 +1,29 @@ +# CTD type # Galaxy type # Long Galaxy data type # Mimetype +csv tabular galaxy.datatypes.tabular:Tabular +fasta fasta galaxy.datatypes.sequence:Fasta +FASTA fasta galaxy.datatypes.sequence:Fasta +ini txt galaxy.datatypes.data:Text +txt txt galaxy.datatypes.data:Text +options txt galaxy.datatypes.data:Text +grid grid galaxy.datatypes.data:Grid +html html galaxy.datatypes.text:Html text/html +HTML html galaxy.datatypes.text:Html text/html +TraML traml galaxy.datatypes.proteomics:TraML application/xml +traML traml galaxy.datatypes.proteomics:TraML application/xml +XML xml galaxy.datatypes.xml:GenericXml application/xml +consensusXML consensusxml galaxy.datatypes.proteomics:ConsensusXML application/xml +edta tabular galaxy.datatypes.tabular:Tabular +featureXML featurexml galaxy.datatypes.proteomics:FeatureXML application/xml +idXML idxml galaxy.datatypes.proteomics:IdXM application/xml +mzML mzml galaxy.datatypes.proteomics:MzML application/xml +mzXML mzxml galaxy.datatypes.proteomics:MzXML application/xml +pepXML pepxml galaxy.datatypes.proteomics:PepXml application/xml +qcML qcml galaxy.datatypes.xml:GenericXml application/xml +trafoXML trafoxml galaxy.datatypes.xml:GenericXml application/xml +tsv tabular galaxy.datatypes.tabular:Tabular +xsd txt galaxy.datatypes.data:Text +mzq mzq galaxy.datatypes.proteomics:MzQuantML application/xml +msp msp galaxy.datatypes.proteomics:Msp +mzid mzid galaxy.datatypes.proteomics:MzIdentML application/xml +png png galaxy.datatypes.images:Png image/png +mgf mgf galaxy.datatypes.proteomics:Mgf \ No newline at end of file diff -r 000000000000 -r 7c2b85eb3ccf macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Mar 01 12:59:29 2017 -0500 @@ -0,0 +1,35 @@ + + + + + openms + xtandem + fido + msgf_plus + + + + + + + + + + + + doi:10.1186/1471-2105-9-163 + + + + + + + + + + + + + + + diff -r 000000000000 -r 7c2b85eb3ccf readme.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.md Wed Mar 01 12:59:29 2017 -0500 @@ -0,0 +1,165 @@ +Galaxy wrapper for OpenMS +========================= + +OpenMS is an open-source software C++ library for LC/MS data management and analyses. +It offers an infrastructure for the rapid development of mass spectrometry related software. +OpenMS is free software available under the three clause BSD license and runs under Windows, MacOSX and Linux. + +More informations are available at: + + * https://github.com/OpenMS/OpenMS + * http://open-ms.sourceforge.net + + +Generating OpenMS wrappers +========================== + + * install OpenMS (you can do this automatically through the Tool Shed) + * create a folder called CTD + * inside of your new installed openms/bin folder, execute the following command: + + ```bash + for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done; + ``` + + * `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`). + + * clone or install CTDopts + + ```bash + git clone https://github.com/genericworkflownodes/CTDopts + ``` + + * add CTDopts to your `$PYTHONPATH` + + ```bash + export PYTHONPATH=/home/user/CTDopts/ + ``` + + * clone or install CTD2Galaxy + + ```bash + git clone https://github.com/blankclemens/CTD2Galaxy.git + ``` + + * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. + + ```bash + python generator.py \ + -i /PATH/TO/YOUR/CTD/*.ctd \ + -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \ + -d datatypes_conf.xml -g openms \ + -b version log debug test no_progress threads \ + in_type executable myrimatch_executable \ + fido_executable fidocp_executable \ + omssa_executable pepnovo_executable \ + xtandem_executable param_model_directory \ + java_executable java_memory java_permgen \ + -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \ + -s PATH/TO/SKIP_TOOLS_FILES.txt + ``` + + + * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example: + + ``` + sed -i '13 a\-fido_executable fido' wrappers/FidoAdapter.xml + sed -i '13 a\-fidocp_executable fido_choose_parameters' wrappers/FidoAdapter.xml + sed -i '13 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml + sed -i '13 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml + sed -i '13 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml + ``` + + * For some tools, additional work has to be done. In `MSGFPlusAdapter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where): + + ``` + + ``` + * In `PeakPickerHiRes.xml`, the parameter `report_FWHM_unit` has to be put in quotation marks. Look for the following line + + -algorithm:report_FWHM_unit $param_algorithm_report_FWHM_unit + + and change it to + + -algorithm:report_FWHM_unit "$param_algorithm_report_FWHM_unit" + + * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.: + + + + * To add an example test case to `DecoyDatabase.xml` add the following after the output section. If standard settings change you might have to adjust the options and/or the test files. + + ``` + + + + + + + ``` + + + * These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in Galaxy-stable and are therefore in `SKIP_TOOLS_FILES.txt`: + * SeedListGenerator + * SpecLibSearcher + * MapAlignerIdentification + * MapAlignerPoseClustering + * MapAlignerSpectrum + * MapAlignerRTTransformer + + * Additionally cause of lacking dependencies, the following adapters have been removed in `SKIP_TOOLS_FILES.txt` as well: + * OMSSAAdapter + * MyrimatchAdapter + + * Additionally cause of a problematic parameter (-model_directory), the following adapter has been removed: + * PepNovoAdapter + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. + diff -r 000000000000 -r 7c2b85eb3ccf repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Wed Mar 01 12:59:29 2017 -0500 @@ -0,0 +1,4 @@ + + + + diff -r 000000000000 -r 7c2b85eb3ccf test-data/DecoyDatabase_input.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DecoyDatabase_input.fasta Wed Mar 01 12:59:29 2017 -0500 @@ -0,0 +1,146 @@ +>12 +MERMLPLLALGLLAAGFCPAVLCHPNSPLDEENLTQENQDRGTHVDLGLASANVDFAFSLYKQLVLKAPDKNVIFSPLSI +STALAFLSLGAHNTTLTEILKGLKFNLTETSEAEIHQSFQHLLRTLNQSSDELQLSMGNAMFVKEQLSLLDRFTEDAKRL +YGSEAFATDFQDSAAAKKLINDYVKNGTRGKITDLIKDLDSQTMMVLVNYIFFKAKWEMPFDPQDTHQSRFYLSKKKWVM +VPMMSLHHLTIPYFRDEELSCTVVELKYTGNASALFILPDQDKMEEVEAMLLPETLKRWRDSLEFREIGELYLPKFSISR +DYNLNDILLQLGIEEAFTSKADLSGITGARNLAVSQVVHKAVLDVFEEGTEASAATAVKITLLSALVETRTIVRFNRPFL +MIIVPTDTQNIFFMSKVTNPKQA +>18 +MASMLLAQRLACSFQHSYRLLVPGSRHISQAAAKVDVEFDYDGPLMKTEVPGPRSQELMK +QLNIIQNAEAVHFFCNYEESRGNYLVDVDGNRMLDLYSQISSVPIGYSHPALLKLIQQPQ +NASMFVNRPALGILPPENFVEKLRQSLLSVAPKGMSQLITMACGSCSNENALKTIFMWYR +SKERGQRGFSQEELETCMINQAPGCPDYSILSFMGAFHGRTMGCLATTHSKAIHKIDIPS +FDWPIAPFPRLKYPLEEFVKENQQEEARCLEEVEDLIVKYRKKKKTVAGIIVEPIQSEGG +DNHASDDFFRKLRDIARKHGCAFLVDEVQTGGGCTGKFWAHEHWGLDDPADVMTFSKKMM +TGGFFHKEEFRPNAPYRIFNTWLGDPSKNLLLAEVINIIKREDLLNNAAHAGKALLTGLL +DLQARYPQFISRVRGRGTFCSFDTPDDSIRNKLILIARNKGVVLGGCGDKSIRFRPTLVF +RDHHAHLFLNIFSDILADFK +>88 +MNQIEPGVQYNYVYDEDEYMIQEEEWDRDLLLDPAWEKQQRKTFTAWCNSHLRKAGTQIE +NIEEDFRNGLKLMLLLEVISGERLPKPDRGKMRFHKIANVNKALDYIASKGVKLVSIGAE +EIVDGNVKMTLGMIWTIILRFAIQDISVEETSAKEGLLLWCQRKTAPYRNVNIQNFHTSW +KDGLGLCALIHRHRPDLIDYSKLNKDDPIGNINLAMEIAEKHLDIPKMLDAEDIVNTPKP +DERAIMTYVSCFYHAFAGAEQAETAANRICKVLAVNQENERLMEEYERLASELLEWIRRT +IPWLENRTPEKTMQAMQKKLEDFRDYRRKHKPPKVQEKCQLEINFNTLQTKLRISNRPAF +MPSEGKMVSDIAGAWQRLEQAEKGYEEWLLNEIRRLERLEHLAEKFRQKASTHETWAYGK +EQILLQKDYESASLTEVRALLRKHEAFESDLAAHQDRVEQIAAIAQELNELDYHDAVNVN +DRCQKICDQWDRLGTLTQKRREALERMEKLLETIDQLHLEFAKRAAPFNNWMEGAMEDLQ +DMFIVHSIEEIQSLITAHEQFKATLPEADGERQSIMAIQNEVEKVIQSYNIRISSSNPYS +TVTMDELRTKWDKVKQLVPIRDQSLQEELARQHANERLRRQFAAQANAIGPWIQNKMEEI +ARSSIQITGALEDQMNQLKQYEHNIINYKNNIDKLEGDHQLIQEALVFDNKHTNYTMEHI +RVGWELLLTTIARTINEVETQILTRDAKGITQEQMNEFRASFNHFDRRKNGLMDHEDFRA +CLISMGYDLGEAEFARIMTLVDPNGQGTVTFQSFIDFMTRETADTDTAEQVIASFRILAS +DKPYILAEELRRELPPDQAQYCIKRMPAYSGPGSVPGALDYAAFSSALYGESDL +>112 +MSWFSGLLVPKVDERKTAWGERNGQKRSRRRGTRAGGFCTPRYMSCLRDAEPPSPTPAGP +PRCPWQDDAFIRRGGPGKGKELGLRAVALGFEDTEVTTTAGGTAEVAPDAVPRSGRSCWR +RLVQVFQSKQFRSAKLERLYQRYFFQMNQSSLTLLMAVLVLLTAVLLAFHAAPARPQPAY +VALLACAAALFVGLMVVCNRHSFRQDSMWVVSYVVLGILAAVQVGGALAADPRSPSAGLW +CPVFFVYIAYTLLPIRMRAAVLSGLGLSTLHLILAWQLNRGDAFLWKQLGANVLLFLCTN +VIGICTHYPAEVSQRQAFQETRGYIQARLHLQHENRQQERLLLSVLPQHVAMEMKEDINT +KKEDMMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHC +LRIKILGDCYYCVSGLPEARADHAHCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRV +HCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQYLNGDYEVEPGRGGERNA +YLKEQHIETFLILGASQKRKEEKAMLAKLQRTRANSMEGLMPRWVPDRAFSRTKDSKAFR +QMGIDDSSKDNRGTQDALNPEDEVDEFLSRAIDARSIDQLRKDHVRRFLLTFQREDLEKK +YSRKVDPRFGAYVACALLVFCFICFIQLLIFPHSTLMLGIYASIFLLLLITVLICAVYSC +GSLFPKALQRLSRSIVRSRAHSTAVGIFSVLLVFTSAIANMFTCNHTPIRSCAARMLNLT +PADITACHLQQLNYSLGLDAPLCEGTMPTCSFPEYFIGNMLLSLLASSVFLHISSIGKLA +MIFVLGLIYLVLLLLGPPATIFDNYDLLLGVHGLASSNETFDGLDCPAAGRVALKYMTPV +ILLVFALALYLHAQQVESTARLDFLWKLQATGEKEEMEELQAYNRRLLHNILPKDVAAHF +LARERRNDELYYQSCECVAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIIS +EERFRQLEKIKTIGSTYMAASGLNASTYDQVGRSHITALADYAMRLMEQMKHINEHSFNN +FQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDSTGVPDRIQVTTDLYQVLAAKG +YQLECRGVVKVKGKGEMTTYFLNGGPSS +>114 +MELSDVRCLTGSEELYTIHPTPPAGDGRSASRPQRLLWQTAVRHITEQRFIHGHRGGSGS +GSGGSGKASDPAGGGPNHHAPQLSGDSALPLYSLGPGERAHSTCGTKVFPERSGSGSASG +SGGGGDLGFLHLDCAPSNSDFFLNGGYSYRGVIFPTLRNSFKSRDLERLYQRYFLGQRRK +SEVVMNVLDVLTKLTLLVLHLSLASAPMDPLKGILLGFFTGIEVVICALVVVRKDTTSHT +YLQYSGVVTWVAMTTQILAAGLGYGLLGDGIGYVLFTLFATYSMLPLPLTWAILAGLGTS +LLQVILQVVIPRLAVISINQVVAQAVLFMCMNTAGIFISYLSDRAQRQAFLETRRCVEAR +LRLETENQRQERLVLSVLPRFVVLEMINDMTNVEDEHLQHQFHRIYIHRYENVSILFADV +KGFTNLSTTLSAQELVRMLNELFARFDRLAHEHHCLRIKILGDCYYCVSGLPEPRQDHAH +CCVEMGLSMIKTIRYVRSRTKHDVDMRIGIHSGSVLCGVLGLRKWQFDVWSWDVDIANKL +ESGGIPGRIHISKATLDCLNGDYNVEEGHGKERNEFLRKHNIETYLIKQPEDSLLSLPED +IVKESVSSSDRRNSGATFTEGSWSPELPFDNIVGKQNTLAALTRNSINLLPNHLAQALHV +QSGPEEINKRIEHTIDLRSGDKLRREHIKPFSLMFKDSSLEHKYSQMRDEVFKSNLVCAF +IVLLFITAIQSLLPSSRVMPMTIQFSILIMLHSALVLITTAEDYKCLPLILRKTCCWINE +TYLARNVIIFASILINFLGAILNILWCDFDKSIPLKNLTFNSSAVFTDICSYPEYFVFTG +VLAMVTCAVFLRLNSVLKLAVLLIMIAIYALLTETVYAGLFLRYDNLNHSGEDFLGTKEV +SLLLMAMFLLAVFYHGQQLEYTARLDFLWRVQAKEEINEMKELREHNENMLRNILPSHVA +RHFLEKDRDNEELYSQSYDAVGVMFASIPGFADFYSQTEMNNQGVECLRLLNEIIADFDE +LLGEDRFQDIEKIKTIGSTYMAVSGLSPEKQQCEDKWGHLCALADFSLALTESIQEINKH +SFNNFELRIGISHGSVVAGVIGAKKPQYDIWGKTVNLASRMDSTGVSGRIQVPEETYLIL +KDQGFAFDYRGEIYVKGISEQEGKIKTYFLLGRVQPNPFILPPRRLPGQYSLAAVVLGLV +QSLNRQRQKQLLNENNNTGIIKGHYNRRTLLSPSGTEPGAQAEGTDKSDLP +>143 +MVMGIFANCIFCLKVKYLPQQQKKKLQTDIKENGGKFSFSLNPQCTHIILDNADVLSQYQ +LNSIQKNHVHIANPDFIWKSIREKRLLDVKNYDPYKPLDITPPPDQKASSSEVKTEGLCP +DSATEEEDTVELTEFGMQNVEIPHLPQDFEVAKYNTLEKVGMEGGQEAVVVELQCSRDSR +DCPFLISSHFLLDDGMETRRQFAIKKTSEDASEYFENYIEELKKQGFLLREHFTPEATQL +ASEQLQALLLEEVMNSSTLSQEVSDLVEMIWAEALGHLEHMLLKPVNRISLNDVSKAEGI +LLLVKAALKNGETAEQLQKMMTEFYRLIPHKGTMPKEVNLGLLAKKADLCQLIRDMVNVC +ETNLSKPNPPSLAKYRALRCKIEHVEQNTEEFLRVRKEVLQNHHSKSPVDVLQIFRVGRV +NETTEFLSKLGNVRPLLHGSPVQNIVGILCRGLLLPKVVEDRGVQRTDVGNLGSGIYFSD +SLSTSIKYSHPGETDGTRLLLICDVALGKCMDLHEKDFSLTEAPPGYDSVHGVSQTASVT +TDFEDDEFVVYKTNQVKMKYIIKFSMPGDQIKDFHPSDHTELEEYRPEFSNFSKVEDYQL +PDAKTSSSTKAGLQDASGNLVPLEDVHIKGRIIDTVAQVIVFQTYTNKSHVPIEAKYIFP +LDDKAAVCGFEAFINGKHIVGEIKEKEEAQQEYLEAVTQGHGAYLMSQDAPDVFTVSVGN +LPPKAKVLIKITYITELSILGTVGVFFMPATVAPWQQDKALNENLQDTVEKICIKEIGTK +QSFSLTMSIEMPYVIEFIFSDTHELKQKRTDCKAVISTMEGSSLDSSGFSLHIGLSAAYL +PRMWVEKHPEKESEACMLVFQPDLDVDLPDLASESEVIICLDCSSSMEGVTFLQAKQIAL +HALSLVGEKQKVNIIQFGTGYKELFSYPKHITSNTMAAEFIMSATPTMGNTDFWKTLRYL +SLLYPARGSRNILLVSDGHLQDESLTLQLVKRSRPHTRLFACGIGSTANRHVLRILSQCG +AGVFEYFNAKSKHSWRKQIEDQMTRLCSPSCHSVSVKWQQLNPDVPEALQAPAQVPSLFL +NDRLLVYGFIPHCTQATLCALIQEKEFRTMVSTTELQKTTGTMIHKLAARALIRDYEDGI +LHENETSHEMKKQTLKSLIIKLSKENSLITQFTSFVAVEKRDENESPFPDIPKVSELIAK +EDVDFLPYMSWQGEPQEAVRNQSLLASSEWPELRLSKRKHRKIPFSKRKMELSQPEVSED +FEEDGLGVLPAFTSNLERGGVEKLLDLSWTESCKPTATEPLFKKVSPWETSTSSFFPILA +PAVGSYLPPTARAHSPASLSFASYRQVASFGSAAPPRQFDASQFSQGPVPGTCADWIPQS +ASCPTGPPQNPPSSPYCGIVFSGSSLSSAQSAPLQHPGGFTTRPSAGTFPELDSPQLHFS +LPTDPDPIRGFGSYHPSASSPFHFQPSAASLTANLRLPMASALPEALCSQSRTTPVDLCL +LEESVGSLEGSRCPVFAFQSSDTESDELSEVLQDSCFLQIKCDTKDDSILCFLEVKEEDE +IVCIQHWQDAVPWTELLSLQTEDGFWKLTPELGLILNLNTNGLHSFLKQKGIQSLGVKGR +ECLLDLIATMLVLQFIRTRLEKEGIVFKSLMKMDDASISRNIPWAFEAIKQASEWVRRTE +GQYPSICPRLELGNDWDSATKQLLGLQPISTVSPLHRVLHYSQG +>213 +MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF +EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP +ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF +FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV +ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK +ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR +RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE +QLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV +LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL +SEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV +AASQAALGL +>230 +MPHSYPALSAEQKKELSDIALRIVAPGKGILAADESVGSMAKRLSQIGVENTEENRRLYR +QVLFSADDRVKKCIGGVIFFHETLYQKDDNGVPFVRTIQDKGIVVGIKVDKGVVPLAGTD +GETTTQGLDGLSERCAQYKKDGADFAKWRCVLKISERTPSALAILENANVLARYASICQQ +NGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHVYLEGTLLKPNMVTPGHAC +PIKYTPEEIAMATVTALRRTVPPAVPGVTFLSGGQSEEEASFNLNAINRCPLPRPWALTF +SYGRALQASALNAWRGQRDNAGAATEEFIKRAEVNGLAAQGKYEGSGEDGGAAAQSLYIA +NHAY +>231 +MASRLLLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQ +EKLREQVVKREELFIVSKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGK +EFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGISNFNHLQVEMILNKPGLKYKP +AVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAK +HNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCA +LLSCTSHKDYPFHEEF +>242 +MATYKVRVATGTDLLSGTRDSISLTIVGTQGESHKQLLNHFGRDFATGAVGQYTVQCPQD +LGELIIIRLHKERYAFFPKDPWYCNYVQICAPNGRIYHFPAYQWMDGYETLALREATGKT +TADDSLPVLLEHRKEEIRAKQDFYHWRVFLPGLPSYVHIPSYRPPVRRHRNPNRPEWNGY +IPGFPILINFKATKFLNLNLRYSFLKTASFFVRLGPMALAFKVRGLLDCKHSWKRLKDIR +KIFPGKKSVVSEYVAEHWAEDTFFGYQYLNGVNPGLIRRCTRIPDKFPVTDDMVAPFLGE +GTCLQAELEKGNIYLADYRIMEGIPTVELSGRKQHHCAPLCLLHFGPEGKMMPIAIQLSQ +TPGPDCPIFLPSDSEWDWLLAKTWVRYAEFYSHEAIAHLLETHLIAEAFCLALLRNLPMC +HPLYKLLIPHTRYTVQINSIGRAVLLNEGGLSAKGMSLGVEGFAGVMVRALSELTYDSLY +LPNDFVERGVQDLPGYYYRDDSLAVWNALEKYVTEIITYYYPSDAAVEGDPELQSWVQEI +FKECLLGRESSGFPRCLRTVPELIRYVTIVIYTCSAKHAAVNTGQMEFTAWMPNFPASMR +NPPIQTKGLTTLETFMDTLPDVKTTCITLLVLWTLSREPDDRRPLGHFPDIHFVEEAPRR +SIEAFRQRLNQISHDIRQRNKCLPIPYYYLDPVLIENSISI diff -r 000000000000 -r 7c2b85eb3ccf test-data/DecoyDatabase_output.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DecoyDatabase_output.fasta Wed Mar 01 12:59:29 2017 -0500 @@ -0,0 +1,228 @@ +>12 +MERMLPLLALGLLAAGFCPAVLCHPNSPLDEENLTQENQDRGTHVDLGLASANVDFAFSLYKQLVLKAPDKNVIFSPLSI +STALAFLSLGAHNTTLTEILKGLKFNLTETSEAEIHQSFQHLLRTLNQSSDELQLSMGNAMFVKEQLSLLDRFTEDAKRL +YGSEAFATDFQDSAAAKKLINDYVKNGTRGKITDLIKDLDSQTMMVLVNYIFFKAKWEMPFDPQDTHQSRFYLSKKKWVM +VPMMSLHHLTIPYFRDEELSCTVVELKYTGNASALFILPDQDKMEEVEAMLLPETLKRWRDSLEFREIGELYLPKFSISR +DYNLNDILLQLGIEEAFTSKADLSGITGARNLAVSQVVHKAVLDVFEEGTEASAATAVKITLLSALVETRTIVRFNRPFL +MIIVPTDTQNIFFMSKVTNPKQA +>18 +MASMLLAQRLACSFQHSYRLLVPGSRHISQAAAKVDVEFDYDGPLMKTEVPGPRSQELMKQLNIIQNAEAVHFFCNYEES +RGNYLVDVDGNRMLDLYSQISSVPIGYSHPALLKLIQQPQNASMFVNRPALGILPPENFVEKLRQSLLSVAPKGMSQLIT +MACGSCSNENALKTIFMWYRSKERGQRGFSQEELETCMINQAPGCPDYSILSFMGAFHGRTMGCLATTHSKAIHKIDIPS +FDWPIAPFPRLKYPLEEFVKENQQEEARCLEEVEDLIVKYRKKKKTVAGIIVEPIQSEGGDNHASDDFFRKLRDIARKHG +CAFLVDEVQTGGGCTGKFWAHEHWGLDDPADVMTFSKKMMTGGFFHKEEFRPNAPYRIFNTWLGDPSKNLLLAEVINIIK +REDLLNNAAHAGKALLTGLLDLQARYPQFISRVRGRGTFCSFDTPDDSIRNKLILIARNKGVVLGGCGDKSIRFRPTLVF +RDHHAHLFLNIFSDILADFK +>88 +MNQIEPGVQYNYVYDEDEYMIQEEEWDRDLLLDPAWEKQQRKTFTAWCNSHLRKAGTQIENIEEDFRNGLKLMLLLEVIS +GERLPKPDRGKMRFHKIANVNKALDYIASKGVKLVSIGAEEIVDGNVKMTLGMIWTIILRFAIQDISVEETSAKEGLLLW +CQRKTAPYRNVNIQNFHTSWKDGLGLCALIHRHRPDLIDYSKLNKDDPIGNINLAMEIAEKHLDIPKMLDAEDIVNTPKP +DERAIMTYVSCFYHAFAGAEQAETAANRICKVLAVNQENERLMEEYERLASELLEWIRRTIPWLENRTPEKTMQAMQKKL +EDFRDYRRKHKPPKVQEKCQLEINFNTLQTKLRISNRPAFMPSEGKMVSDIAGAWQRLEQAEKGYEEWLLNEIRRLERLE +HLAEKFRQKASTHETWAYGKEQILLQKDYESASLTEVRALLRKHEAFESDLAAHQDRVEQIAAIAQELNELDYHDAVNVN +DRCQKICDQWDRLGTLTQKRREALERMEKLLETIDQLHLEFAKRAAPFNNWMEGAMEDLQDMFIVHSIEEIQSLITAHEQ +FKATLPEADGERQSIMAIQNEVEKVIQSYNIRISSSNPYSTVTMDELRTKWDKVKQLVPIRDQSLQEELARQHANERLRR +QFAAQANAIGPWIQNKMEEIARSSIQITGALEDQMNQLKQYEHNIINYKNNIDKLEGDHQLIQEALVFDNKHTNYTMEHI +RVGWELLLTTIARTINEVETQILTRDAKGITQEQMNEFRASFNHFDRRKNGLMDHEDFRACLISMGYDLGEAEFARIMTL +VDPNGQGTVTFQSFIDFMTRETADTDTAEQVIASFRILASDKPYILAEELRRELPPDQAQYCIKRMPAYSGPGSVPGALD +YAAFSSALYGESDL +>112 +MSWFSGLLVPKVDERKTAWGERNGQKRSRRRGTRAGGFCTPRYMSCLRDAEPPSPTPAGPPRCPWQDDAFIRRGGPGKGK +ELGLRAVALGFEDTEVTTTAGGTAEVAPDAVPRSGRSCWRRLVQVFQSKQFRSAKLERLYQRYFFQMNQSSLTLLMAVLV +LLTAVLLAFHAAPARPQPAYVALLACAAALFVGLMVVCNRHSFRQDSMWVVSYVVLGILAAVQVGGALAADPRSPSAGLW +CPVFFVYIAYTLLPIRMRAAVLSGLGLSTLHLILAWQLNRGDAFLWKQLGANVLLFLCTNVIGICTHYPAEVSQRQAFQE +TRGYIQARLHLQHENRQQERLLLSVLPQHVAMEMKEDINTKKEDMMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQEL +VMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHAHCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRV +HCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQYLNGDYEVEPGRGGERNAYLKEQHIETFLILGASQKRK +EEKAMLAKLQRTRANSMEGLMPRWVPDRAFSRTKDSKAFRQMGIDDSSKDNRGTQDALNPEDEVDEFLSRAIDARSIDQL +RKDHVRRFLLTFQREDLEKKYSRKVDPRFGAYVACALLVFCFICFIQLLIFPHSTLMLGIYASIFLLLLITVLICAVYSC +GSLFPKALQRLSRSIVRSRAHSTAVGIFSVLLVFTSAIANMFTCNHTPIRSCAARMLNLTPADITACHLQQLNYSLGLDA +PLCEGTMPTCSFPEYFIGNMLLSLLASSVFLHISSIGKLAMIFVLGLIYLVLLLLGPPATIFDNYDLLLGVHGLASSNET +FDGLDCPAAGRVALKYMTPVILLVFALALYLHAQQVESTARLDFLWKLQATGEKEEMEELQAYNRRLLHNILPKDVAAHF +LARERRNDELYYQSCECVAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEERFRQLEKIKTIGSTYMAA +SGLNASTYDQVGRSHITALADYAMRLMEQMKHINEHSFNNFQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDST +GVPDRIQVTTDLYQVLAAKGYQLECRGVVKVKGKGEMTTYFLNGGPSS +>114 +MELSDVRCLTGSEELYTIHPTPPAGDGRSASRPQRLLWQTAVRHITEQRFIHGHRGGSGSGSGGSGKASDPAGGGPNHHA +PQLSGDSALPLYSLGPGERAHSTCGTKVFPERSGSGSASGSGGGGDLGFLHLDCAPSNSDFFLNGGYSYRGVIFPTLRNS +FKSRDLERLYQRYFLGQRRKSEVVMNVLDVLTKLTLLVLHLSLASAPMDPLKGILLGFFTGIEVVICALVVVRKDTTSHT +YLQYSGVVTWVAMTTQILAAGLGYGLLGDGIGYVLFTLFATYSMLPLPLTWAILAGLGTSLLQVILQVVIPRLAVISINQ +VVAQAVLFMCMNTAGIFISYLSDRAQRQAFLETRRCVEARLRLETENQRQERLVLSVLPRFVVLEMINDMTNVEDEHLQH +QFHRIYIHRYENVSILFADVKGFTNLSTTLSAQELVRMLNELFARFDRLAHEHHCLRIKILGDCYYCVSGLPEPRQDHAH +CCVEMGLSMIKTIRYVRSRTKHDVDMRIGIHSGSVLCGVLGLRKWQFDVWSWDVDIANKLESGGIPGRIHISKATLDCLN +GDYNVEEGHGKERNEFLRKHNIETYLIKQPEDSLLSLPEDIVKESVSSSDRRNSGATFTEGSWSPELPFDNIVGKQNTLA +ALTRNSINLLPNHLAQALHVQSGPEEINKRIEHTIDLRSGDKLRREHIKPFSLMFKDSSLEHKYSQMRDEVFKSNLVCAF +IVLLFITAIQSLLPSSRVMPMTIQFSILIMLHSALVLITTAEDYKCLPLILRKTCCWINETYLARNVIIFASILINFLGA +ILNILWCDFDKSIPLKNLTFNSSAVFTDICSYPEYFVFTGVLAMVTCAVFLRLNSVLKLAVLLIMIAIYALLTETVYAGL +FLRYDNLNHSGEDFLGTKEVSLLLMAMFLLAVFYHGQQLEYTARLDFLWRVQAKEEINEMKELREHNENMLRNILPSHVA +RHFLEKDRDNEELYSQSYDAVGVMFASIPGFADFYSQTEMNNQGVECLRLLNEIIADFDELLGEDRFQDIEKIKTIGSTY +MAVSGLSPEKQQCEDKWGHLCALADFSLALTESIQEINKHSFNNFELRIGISHGSVVAGVIGAKKPQYDIWGKTVNLASR +MDSTGVSGRIQVPEETYLILKDQGFAFDYRGEIYVKGISEQEGKIKTYFLLGRVQPNPFILPPRRLPGQYSLAAVVLGLV +QSLNRQRQKQLLNENNNTGIIKGHYNRRTLLSPSGTEPGAQAEGTDKSDLP +>143 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