Mercurial > repos > bgruening > openms
diff MSSimulator.xml @ 4:6ead64a594bd draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
| author | bgruening |
|---|---|
| date | Wed, 27 Jan 2016 10:06:49 -0500 |
| parents | 3d84209d3178 |
| children |
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--- a/MSSimulator.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/MSSimulator.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,392 +1,981 @@ -<?xml version='1.0' encoding='UTF-8'?> -<tool id="MSSimulator" name="MSSimulator" version="1.12.0"> - <description>A highly configurable simulator for mass spectrometry experiments.</description> - <macros> - <token name="@EXECUTABLE@">MSSimulator</token> - <import>macros.xml</import> - </macros> - <expand macro="stdio"/> - <expand macro="requirements"/> - <command>MSSimulator +<?xml version="1.0" encoding="UTF-8"?> + <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> + <!--Proposed Tool Section: [Utilities]--> + <tool id="MSSimulator" name="MSSimulator" version="2.0.0"> + <description>A highly configurable simulator for mass spectrometry experiments.</description> + <macros> + <token name="@EXECUTABLE@">MSSimulator</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>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 +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_MSSim_Digestion_enzyme: + -algorithm:MSSim:Digestion:enzyme + #if " " in str($param_algorithm_MSSim_Digestion_enzyme): + "$param_algorithm_MSSim_Digestion_enzyme" + #else + $param_algorithm_MSSim_Digestion_enzyme + #end if +#end if +#if $param_algorithm_MSSim_Digestion_model: + -algorithm:MSSim:Digestion:model + #if " " in str($param_algorithm_MSSim_Digestion_model): + "$param_algorithm_MSSim_Digestion_model" + #else + $param_algorithm_MSSim_Digestion_model + #end if +#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 $param_algorithm_MSSim_RT_rt_column: + -algorithm:MSSim:RT:rt_column + #if " " in str($param_algorithm_MSSim_RT_rt_column): + "$param_algorithm_MSSim_RT_rt_column" + #else + $param_algorithm_MSSim_RT_rt_column + #end if +#end if +#if $param_algorithm_MSSim_RT_auto_scale: + -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 +#end if +#if $param_algorithm_MSSim_RawSignal_peak_shape: + -algorithm:MSSim:RawSignal:peak_shape + #if " " in str($param_algorithm_MSSim_RawSignal_peak_shape): + "$param_algorithm_MSSim_RawSignal_peak_shape" + #else + $param_algorithm_MSSim_RawSignal_peak_shape + #end if +#end if +#if $param_algorithm_MSSim_RawSignal_resolution_value: + -algorithm:MSSim:RawSignal:resolution:value $param_algorithm_MSSim_RawSignal_resolution_value +#end if +#if $param_algorithm_MSSim_RawSignal_resolution_type: + -algorithm:MSSim:RawSignal:resolution:type + #if " " in str($param_algorithm_MSSim_RawSignal_resolution_type): + "$param_algorithm_MSSim_RawSignal_resolution_type" + #else + $param_algorithm_MSSim_RawSignal_resolution_type + #end if +#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 $param_algorithm_MSSim_RawTandemSignal_status: + -algorithm:MSSim:RawTandemSignal:status + #if " " in str($param_algorithm_MSSim_RawTandemSignal_status): + "$param_algorithm_MSSim_RawTandemSignal_status" + #else + $param_algorithm_MSSim_RawTandemSignal_status + #end if +#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 --in ${param_in} --out ${param_out} --out_pm ${param_out_pm} --out_fm ${param_out_fm} --out_cm ${param_out_cm} --out_lcm ${param_out_lcm} --out_cntm ${param_out_cntm} --out_id ${param_out_id} --threads \${GALAXY_SLOTS:-24} --algorithm:MSSim:Digestion:enzyme ${param_enzyme} --algorithm:MSSim:Digestion:model ${param_model} --algorithm:MSSim:Digestion:min_peptide_length ${param_min_peptide_length} --algorithm:MSSim:Digestion:model_trained:threshold ${param_threshold} --algorithm:MSSim:Digestion:model_naive:missed_cleavages ${param_missed_cleavages} --algorithm:MSSim:RT:rt_column ${param_rt_column} -${param_auto_scale} --algorithm:MSSim:RT:total_gradient_time ${param_total_gradient_time} --algorithm:MSSim:RT:sampling_rate ${param_sampling_rate} --algorithm:MSSim:RT:scan_window:min ${param_min} --algorithm:MSSim:RT:scan_window:max ${param_max} --algorithm:MSSim:RT:variation:feature_stddev ${param_feature_stddev} --algorithm:MSSim:RT:variation:affine_offset ${param_affine_offset} --algorithm:MSSim:RT:variation:affine_scale ${param_affine_scale} --algorithm:MSSim:RT:column_condition:distortion ${param_distortion} --algorithm:MSSim:RT:profile_shape:width:value ${param_value} --algorithm:MSSim:RT:profile_shape:width:variance ${param_variance} --algorithm:MSSim:RT:profile_shape:skewness:value ${param_value} --algorithm:MSSim:RT:profile_shape:skewness:variance ${param_variance} --algorithm:MSSim:RT:HPLC:model_file ${param_model_file} --algorithm:MSSim:RT:CE:pH ${param_pH} --algorithm:MSSim:RT:CE:alpha ${param_alpha} --algorithm:MSSim:RT:CE:mu_eo ${param_mu_eo} --algorithm:MSSim:RT:CE:lenght_d ${param_lenght_d} --algorithm:MSSim:RT:CE:length_total ${param_length_total} --algorithm:MSSim:RT:CE:voltage ${param_voltage} -${param_dt_simulation_on} --algorithm:MSSim:Detectability:min_detect ${param_min_detect} --algorithm:MSSim:Detectability:dt_model_file ${param_dt_model_file} --algorithm:MSSim:Ionization:esi:ionized_residues ${param_ionized_residues} --algorithm:MSSim:Ionization:esi:charge_impurity ${param_charge_impurity} --algorithm:MSSim:Ionization:esi:ionization_probability ${param_ionization_probability} --algorithm:MSSim:Ionization:maldi:ionization_probabilities ${param_ionization_probabilities} --algorithm:MSSim:Ionization:mz:lower_measurement_limit ${param_lower_measurement_limit} --algorithm:MSSim:Ionization:mz:upper_measurement_limit ${param_upper_measurement_limit} -${param_enabled} --algorithm:MSSim:RawSignal:peak_shape ${param_peak_shape} --algorithm:MSSim:RawSignal:resolution:value ${param_value} --algorithm:MSSim:RawSignal:resolution:type ${param_type} --algorithm:MSSim:RawSignal:baseline:scaling ${param_scaling} --algorithm:MSSim:RawSignal:baseline:shape ${param_shape} --algorithm:MSSim:RawSignal:mz:sampling_points ${param_sampling_points} --algorithm:MSSim:RawSignal:contaminants:file ${param_file} --algorithm:MSSim:RawSignal:variation:mz:error_stddev ${param_error_stddev} --algorithm:MSSim:RawSignal:variation:mz:error_mean ${param_error_mean} --algorithm:MSSim:RawSignal:variation:intensity:scale ${param_scale} --algorithm:MSSim:RawSignal:variation:intensity:scale_stddev ${param_scale_stddev} --algorithm:MSSim:RawSignal:noise:shot:rate ${param_rate} --algorithm:MSSim:RawSignal:noise:shot:intensity-mean ${param_intensity-mean} --algorithm:MSSim:RawSignal:noise:white:mean ${param_mean} --algorithm:MSSim:RawSignal:noise:white:stddev ${param_stddev} --algorithm:MSSim:RawSignal:noise:detector:mean ${param_mean} --algorithm:MSSim:RawSignal:noise:detector:stddev ${param_stddev} --algorithm:MSSim:RawTandemSignal:status ${param_status} --algorithm:MSSim:RawTandemSignal:tandem_mode ${param_tandem_mode} --algorithm:MSSim:RawTandemSignal:svm_model_set_file ${param_svm_model_set_file} --algorithm:MSSim:RawTandemSignal:Precursor:ms2_spectra_per_rt_bin ${param_ms2_spectra_per_rt_bin} --algorithm:MSSim:RawTandemSignal:Precursor:min_peak_distance ${param_min_peak_distance} --algorithm:MSSim:RawTandemSignal:Precursor:selection_window ${param_selection_window} -${param_exclude_overlapping_peaks} --algorithm:MSSim:RawTandemSignal:Precursor:charge_filter ${param_charge_filter} -${param_use_dynamic_exclusion} --algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:exclusion_time ${param_exclusion_time} --algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:max_list_size ${param_max_list_size} --algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:min_rt ${param_min_rt} --algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:max_rt ${param_max_rt} --algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_step_size ${param_rt_step_size} --algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_window_size ${param_rt_window_size} --algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_protein_id_probability ${param_min_protein_id_probability} --algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_pt_weight ${param_min_pt_weight} --algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_mz ${param_min_mz} --algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:max_mz ${param_max_mz} -${param_use_peptide_rule} --algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_ids ${param_min_peptide_ids} --algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_probability ${param_min_peptide_probability} -${param_add_single_spectra} -${param_add_isotopes} --algorithm:MSSim:RawTandemSignal:TandemSim:Simple:max_isotope ${param_max_isotope} -${param_add_metainfo} -${param_add_losses} -${param_add_precursor_peaks} -${param_add_abundant_immonium_ions} -${param_add_first_prefix_ion} -${param_add_y_ions} -${param_add_b_ions} -${param_add_a_ions} -${param_add_c_ions} -${param_add_x_ions} -${param_add_z_ions} --algorithm:MSSim:RawTandemSignal:TandemSim:Simple:y_intensity ${param_y_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:Simple:b_intensity ${param_b_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:Simple:a_intensity ${param_a_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:Simple:c_intensity ${param_c_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:Simple:x_intensity ${param_x_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:Simple:z_intensity ${param_z_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:Simple:relative_loss_intensity ${param_relative_loss_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_intensity ${param_precursor_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_H2O_intensity ${param_precursor_H2O_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_NH3_intensity ${param_precursor_NH3_intensity} -${param_add_isotopes} --algorithm:MSSim:RawTandemSignal:TandemSim:SVM:max_isotope ${param_max_isotope} -${param_add_metainfo} -${param_add_first_prefix_ion} -${param_hide_y_ions} -${param_hide_y2_ions} -${param_hide_b_ions} -${param_hide_b2_ions} -${param_hide_a_ions} -${param_hide_c_ions} -${param_hide_x_ions} -${param_hide_z_ions} -${param_hide_losses} --algorithm:MSSim:RawTandemSignal:TandemSim:SVM:y_intensity ${param_y_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:SVM:b_intensity ${param_b_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:SVM:a_intensity ${param_a_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:SVM:c_intensity ${param_c_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:SVM:x_intensity ${param_x_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:SVM:z_intensity ${param_z_intensity} --algorithm:MSSim:RawTandemSignal:TandemSim:SVM:relative_loss_intensity ${param_relative_loss_intensity} --algorithm:MSSim:Global:ionization_type ${param_ionization_type} --algorithm:MSSim:Labeling:type ${param_type} --algorithm:MSSim:Labeling:ICPL:ICPL_fixed_rtshift ${param_ICPL_fixed_rtshift} -${param_label_proteins} --algorithm:MSSim:Labeling:SILAC:fixed_rtshift ${param_fixed_rtshift} --algorithm:MSSim:Labeling:SILAC:medium_channel:modification_lysine ${param_modification_lysine} --algorithm:MSSim:Labeling:SILAC:medium_channel:modification_arginine ${param_modification_arginine} --algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_lysine ${param_modification_lysine} --algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_arginine ${param_modification_arginine} --algorithm:MSSim:Labeling:itraq:iTRAQ ${param_iTRAQ} --algorithm:MSSim:Labeling:itraq:reporter_mass_shift ${param_reporter_mass_shift} --algorithm:MSSim:Labeling:itraq:channel_active_4plex ${param_channel_active_4plex} --algorithm:MSSim:Labeling:itraq:channel_active_8plex ${param_channel_active_8plex} --algorithm:MSSim:Labeling:itraq:Y_contamination ${param_Y_contamination} --algorithm:MSSim:Labeling:o18:labeling_efficiency ${param_labeling_efficiency} --algorithm:RandomNumberGenerators:biological ${param_biological} --algorithm:RandomNumberGenerators:technical ${param_technical} +#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 +#end if +#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions: + -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 $param_algorithm_MSSim_Global_ionization_type: + -algorithm:MSSim:Global:ionization_type + #if " " in str($param_algorithm_MSSim_Global_ionization_type): + "$param_algorithm_MSSim_Global_ionization_type" + #else + $param_algorithm_MSSim_Global_ionization_type + #end if +#end if +#if $param_algorithm_MSSim_Labeling_type: + -algorithm:MSSim:Labeling:type + #if " " in str($param_algorithm_MSSim_Labeling_type): + "$param_algorithm_MSSim_Labeling_type" + #else + $param_algorithm_MSSim_Labeling_type + #end if +#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 +#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 $param_algorithm_MSSim_Labeling_itraq_iTRAQ: + -algorithm:MSSim:Labeling:itraq:iTRAQ + #if " " in str($param_algorithm_MSSim_Labeling_itraq_iTRAQ): + "$param_algorithm_MSSim_Labeling_itraq_iTRAQ" + #else + $param_algorithm_MSSim_Labeling_itraq_iTRAQ + #end if +#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 $param_algorithm_RandomNumberGenerators_biological: + -algorithm:RandomNumberGenerators:biological + #if " " in str($param_algorithm_RandomNumberGenerators_biological): + "$param_algorithm_RandomNumberGenerators_biological" + #else + $param_algorithm_RandomNumberGenerators_biological + #end if +#end if +#if $param_algorithm_RandomNumberGenerators_technical: + -algorithm:RandomNumberGenerators:technical + #if " " in str($param_algorithm_RandomNumberGenerators_technical): + "$param_algorithm_RandomNumberGenerators_technical" + #else + $param_algorithm_RandomNumberGenerators_technical + #end if +#end if #if $adv_opts.adv_opts_selector=='advanced': - -algorithm:MSSim:Ionization:esi:max_impurity_set_size ${adv_opts.param_max_impurity_set_size} - -algorithm:MSSim:Labeling:ICPL:ICPL_light_channel_label ${adv_opts.param_ICPL_light_channel_label} - -algorithm:MSSim:Labeling:ICPL:ICPL_medium_channel_label ${adv_opts.param_ICPL_medium_channel_label} - -algorithm:MSSim:Labeling:ICPL:ICPL_heavy_channel_label ${adv_opts.param_ICPL_heavy_channel_label} - -algorithm:MSSim:Labeling:itraq:isotope_correction_values_4plex ${adv_opts.param_isotope_correction_values_4plex} - -algorithm:MSSim:Labeling:itraq:isotope_correction_values_8plex ${adv_opts.param_isotope_correction_values_8plex} + #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 </command> - <inputs> - <param name="param_in" type="data" format="" optional="False" size="20" label="Input protein sequences" help="(-in)"/> - <param name="param_enzyme" type="select" optional="True" value="Trypsin" label="Enzyme to use for digestion (select 'none' to skip digestion)" help="(-enzyme)"> - <option value="Trypsin">Trypsin</option> - <option value="none">none</option> - </param> - <param name="param_model" type="select" optional="True" value="naive" label="The cleavage model to use for digestion. 'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u)." help="(-model)"> - <option value="trained">trained</option> - <option value="naive">naive</option> - </param> - <param name="param_min_peptide_length" type="integer" min="1" optional="True" value="3" label="Minimum peptide length after digestion (shorter ones will be discarded)" help="(-min_peptide_length)"/> - <param name="param_threshold" type="float" min="-2.0" max="4.0" optional="True" value="0.5" label="Model threshold for calling a cleavage. Higher values increase the number of cleavages. -2 will give no cleavages, +4 almost full cleavage." help="(-threshold)"/> - <param name="param_missed_cleavages" type="integer" min="0" optional="True" value="1" label="Maximum number of missed cleavages considered. All possible resulting peptides will be created." help="(-missed_cleavages)"/> - <param name="param_rt_column" type="select" optional="True" value="HPLC" label="Modelling of an RT or CE column" help="(-rt_column)"> - <option value="none">none</option> - <option value="HPLC">HPLC</option> - <option value="CE">CE</option> - </param> - <param name="param_auto_scale" type="boolean" truevalue="-algorithm:MSSim:RT:auto_scale true" falsevalue="-algorithm:MSSim:RT:auto_scale false" checked="true" optional="True" label="Scale predicted RT's/MT's to given 'total_gradient_time'? If 'true', for CE this means that 'CE:lenght_d', 'CE:length_total', 'CE:voltage' have no influence." help="(-auto_scale)"/> - <param name="param_total_gradient_time" type="float" min="1e-05" optional="True" value="2500.0" label="The duration [s] of the gradient." help="(-total_gradient_time)"/> - <param name="param_sampling_rate" type="float" min="0.01" max="60.0" optional="True" value="2.0" label="Time interval [s] between consecutive scans" help="(-sampling_rate)"/> - <param name="param_min" type="float" min="0.0" optional="True" value="500.0" label="Start of RT Scan Window [s]" help="(-min)"/> - <param name="param_max" type="float" min="1.0" optional="True" value="1500.0" label="End of RT Scan Window [s]" help="(-max)"/> - <param name="param_feature_stddev" type="integer" value="3" label="Standard deviation of shift in retention time [s] from predicted model (applied to every single feature independently)" help="(-feature_stddev)"/> - <param name="param_affine_offset" type="integer" value="0" label="Global offset in retention time [s] from predicted model" help="(-affine_offset)"/> - <param name="param_affine_scale" type="integer" value="1" label="Global scaling in retention time from predicted model" help="(-affine_scale)"/> - <param name="param_distortion" type="integer" min="0" max="10" optional="True" value="0" label="Distortion of the elution profiles. Good presets are 0 for a perfect elution profile, 1 for a slightly distorted elution profile etc... For trapping instruments (e.g. Orbitrap) distortion should be >4." help="(-distortion)"/> - <param name="param_value" type="float" min="0.0" optional="True" value="9.0" label="Width of the Exponential Gaussian Hybrid distribution shape of the elution profile. This does not correspond directly to the width in [s]." help="(-value)"/> - <param name="param_variance" type="float" min="0.0" optional="True" value="1.6" label="Random component of the width (set to 0 to disable randomness), i.e. scale parameter for the lorentzian variation of the variance (Note: The scale parameter has to be >= 0)." help="(-variance)"/> - <param name="param_value" type="float" value="0.1" label="Asymmetric component of the EGH. Higher absolute(!) values lead to more skewness (negative values cause fronting, positive values cause tailing). Tau parameter of the EGH, i.e. time constant of the exponential decay of the Exponential Gaussian Hybrid distribution shape of the elution profile." help="(-value)"/> - <param name="param_variance" type="float" min="0.0" optional="True" value="0.3" label="Random component of skewness (set to 0 to disable randomness), i.e. scale parameter for the lorentzian variation of the time constant (Note: The scale parameter has to be > 0)." help="(-variance)"/> - <param name="param_model_file" type="text" size="20" value="examples/simulation/RTPredict.model" label="SVM model for retention time prediction" help="(-model_file)"/> - <param name="param_pH" type="float" min="0.0" max="14.0" optional="True" value="3.0" label="pH of buffer" help="(-pH)"/> - <param name="param_alpha" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Exponent Alpha used to calculate mobility" help="(-alpha)"/> - <param name="param_mu_eo" type="float" min="0.0" max="5.0" optional="True" value="0.0" label="Electroosmotic flow" help="(-mu_eo)"/> - <param name="param_lenght_d" type="float" min="0.0" max="1000.0" optional="True" value="70.0" label="Length of capillary [cm] from injection site to MS" help="(-lenght_d)"/> - <param name="param_length_total" type="float" min="0.0" max="1000.0" optional="True" value="75.0" label="Total length of capillary [cm]" help="(-length_total)"/> - <param name="param_voltage" type="float" min="0.0" optional="True" value="1000.0" label="Voltage applied to capillary" help="(-voltage)"/> - <param name="param_dt_simulation_on" type="boolean" truevalue="-algorithm:MSSim:Detectability:dt_simulation_on true" falsevalue="-algorithm:MSSim:Detectability:dt_simulation_on false" checked="false" optional="True" label="Modelling detectibility enabled? This can serve as a filter to remove peptides which ionize badly, thus reducing peptide count" help="(-dt_simulation_on)"/> - <param name="param_min_detect" type="float" value="0.5" label="Minimum peptide detectability accepted. Peptides with a lower score will be removed" help="(-min_detect)"/> - <param name="param_dt_model_file" type="text" size="20" value="examples/simulation/DTPredict.model" label="SVM model for peptide detectability prediction" help="(-dt_model_file)"/> - <param name="param_ionized_residues" type="select" optional="True" value="Arg Lys His" label="List of residues (as three letter code) that will be considered during ES ionization. The N-term is always assumed to carry a charge. This parameter will be ignored during MALDI ionization." help="(-ionized_residues)"> - <option value="Ala">Ala</option> - <option value="Cys">Cys</option> - <option value="Asp">Asp</option> - <option value="Glu">Glu</option> - <option value="Phe">Phe</option> - <option value="Gly">Gly</option> - <option value="His">His</option> - <option value="Ile">Ile</option> - <option value="Lys">Lys</option> - <option value="Leu">Leu</option> - <option value="Met">Met</option> - <option value="Asn">Asn</option> - <option value="Pro">Pro</option> - <option value="Gln">Gln</option> - <option value="Arg">Arg</option> - <option value="Sec">Sec</option> - <option value="Ser">Ser</option> - <option value="Thr">Thr</option> - <option value="Val">Val</option> - <option value="Trp">Trp</option> - <option value="Tyr">Tyr</option> - </param> - <param name="param_charge_impurity" type="text" size="20" value="H+:1" label="List of charged ions that contribute to charge with weight of occurrence (their sum is scaled to 1 internally), e.g. ['H:1'] or ['H:0.7' 'Na:0.3'], ['H:4' 'Na:1'] (which internally translates to ['H:0.8' 'Na:0.2'])" help="(-charge_impurity)"/> - <param name="param_ionization_probability" type="float" value="0.8" label="Probability for the binomial distribution of the ESI charge states" help="(-ionization_probability)"/> - <param name="param_ionization_probabilities" type="text" size="20" value="0.9 0.1" label="List of probabilities for the different charge states during MALDI ionization (the list must sum up to 1.0)" help="(-ionization_probabilities)"/> - <param name="param_lower_measurement_limit" type="float" min="0.0" optional="True" value="200.0" label="Lower m/z detector limit." help="(-lower_measurement_limit)"/> - <param name="param_upper_measurement_limit" type="float" min="0.0" optional="True" value="2500.0" label="Upper m/z detector limit." help="(-upper_measurement_limit)"/> - <param name="param_enabled" type="boolean" truevalue="-algorithm:MSSim:RawSignal:enabled true" falsevalue="-algorithm:MSSim:RawSignal:enabled false" checked="true" optional="True" label="Enable RAW signal simulation? (select 'false' if you only need feature-maps)" help="(-enabled)"/> - <param name="param_peak_shape" type="select" optional="True" value="Gaussian" label="Peak Shape used around each isotope peak (be aware that the area under the curve is constant for both types, but the maximal height will differ (~ 2:3 = Lorentz:Gaussian) due to the wider base of the Lorentzian." help="(-peak_shape)"> - <option value="Gaussian">Gaussian</option> - <option value="Lorentzian">Lorentzian</option> - </param> - <param name="param_value" type="integer" value="50000" label="Instrument resolution at 400 Th." help="(-value)"/> - <param name="param_type" type="select" optional="True" value="linear" label="How does resolution change with increasing m/z?! QTOFs usually show 'constant' behavior, FTs have linear degradation, and on Orbitraps the resolution decreases with square root of mass." help="(-type)"> - <option value="constant">constant</option> - <option value="linear">linear</option> - <option value="sqrt">sqrt</option> - </param> - <param name="param_scaling" type="float" min="0.0" optional="True" value="0.0" label="Scale of baseline. Set to 0 to disable simulation of baseline." help="(-scaling)"/> - <param name="param_shape" type="float" min="0.0" optional="True" value="0.5" label="The baseline is modeled by an exponential probability density function (pdf) with f(x) = shape*e^(- shape*x)" help="(-shape)"/> - <param name="param_sampling_points" type="integer" min="2" optional="True" value="3" label="Number of raw data points per FWHM of the peak." help="(-sampling_points)"/> - <param name="param_file" type="text" size="20" value="examples/simulation/contaminants.csv" label="Contaminants file with sum formula and absolute RT interval. See 'OpenMS/examples/simulation/contaminants.txt' for details." help="(-file)"/> - <param name="param_error_stddev" type="float" value="0.0" label="Standard deviation for m/z errors. Set to 0 to disable simulation of m/z errors." help="(-error_stddev)"/> - <param name="param_error_mean" type="float" value="0.0" label="Average systematic m/z error (Da)" help="(-error_mean)"/> - <param name="param_scale" type="float" min="0.0" optional="True" value="100.0" label="Constant scale factor of the feature intensity. Set to 1.0 to get the real intensity values provided in the FASTA file." help="(-scale)"/> - <param name="param_scale_stddev" type="float" min="0.0" optional="True" value="0.0" label="Standard deviation of peak intensity (relative to the scaled peak height). Set to 0 to get simple rescaled intensities." help="(-scale_stddev)"/> - <param name="param_rate" type="float" min="0.0" optional="True" value="0.0" label="Poisson rate of shot noise per unit m/z. Set this to 0 to disable simulation of shot noise." help="(-rate)"/> - <param name="param_intensity-mean" type="float" value="1.0" label="Shot noise intensity mean (exponentially distributed with given mean)." help="(-intensity-mean)"/> - <param name="param_mean" type="float" value="0.0" label="Mean value of white noise being added to each measured signal." help="(-mean)"/> - <param name="param_stddev" type="float" value="0.0" label="Standard deviation of white noise being added to each measured signal." help="(-stddev)"/> - <param name="param_mean" type="float" value="0.0" label="Mean value of the detector noise being added to the complete measurement." help="(-mean)"/> - <param name="param_stddev" type="float" value="0.0" label="Standard deviation of the detector noise being added to the complete measurement." help="(-stddev)"/> - <param name="param_status" type="select" optional="True" value="disabled" label="Create Tandem-MS scans?" help="(-status)"> - <option value="disabled">disabled</option> - <option value="precursor">precursor</option> - <option value="MS^E">MS^E</option> - </param> - <param name="param_tandem_mode" type="integer" min="0" max="2" optional="True" value="0" label="Algorithm to generate the tandem-MS spectra. 0 - fixed intensities, 1 - SVC prediction (abundant/missing), 2 - SVR prediction of peak intensity #br#" help="(-tandem_mode)"/> - <param name="param_svm_model_set_file" type="text" size="20" value="examples/simulation/SvmModelSet.model" label="File containing the filenames of SVM Models for different charge variants" help="(-svm_model_set_file)"/> - <param name="param_ms2_spectra_per_rt_bin" type="integer" min="1" optional="True" value="5" label="Number of allowed MS/MS spectra in a retention time bin." help="(-ms2_spectra_per_rt_bin)"/> - <param name="param_min_peak_distance" type="float" min="0.0" optional="True" value="3.0" label="The minimal distance (in Da) of two peaks in one spectrum so that they can be selected." help="(-min_peak_distance)"/> - <param name="param_selection_window" type="float" min="0.0" optional="True" value="2.0" label="All peaks within a mass window (in Da) of a selected peak are also selected for fragmentation." help="(-selection_window)"/> - <param name="param_exclude_overlapping_peaks" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:Precursor:exclude_overlapping_peaks true" falsevalue="-algorithm:MSSim:RawTandemSignal:Precursor:exclude_overlapping_peaks false" checked="false" optional="True" label="If true overlapping or nearby peaks (within min_peak_distance) are excluded for selection." help="(-exclude_overlapping_peaks)"/> - <param name="param_charge_filter" type="text" min="1" max="5" optional="True" size="20" value="2 3" label="Charges considered for MS2 fragmentation." help="(-charge_filter)"/> - <param name="param_use_dynamic_exclusion" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:use_dynamic_exclusion true" falsevalue="-algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:use_dynamic_exclusion false" checked="false" optional="True" label="If true dynamic exclusion is applied." help="(-use_dynamic_exclusion)"/> - <param name="param_exclusion_time" type="float" min="0.0" optional="True" value="100.0" label="The time (in seconds) a feature is excluded." help="(-exclusion_time)"/> - <param name="param_max_list_size" type="integer" min="1" optional="True" value="1000" label="The maximal number of precursors in the inclusion list." help="(-max_list_size)"/> - <param name="param_min_rt" type="float" min="0.0" optional="True" value="960.0" label="Minimal rt in seconds." help="(-min_rt)"/> - <param name="param_max_rt" type="float" min="0.0" optional="True" value="3840.0" label="Maximal rt in seconds." help="(-max_rt)"/> - <param name="param_rt_step_size" type="float" min="1.0" optional="True" value="30.0" label="rt step size in seconds." help="(-rt_step_size)"/> - <param name="param_rt_window_size" type="integer" min="1" optional="True" value="100" label="rt window size in seconds." help="(-rt_window_size)"/> - <param name="param_min_protein_id_probability" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="Minimal protein probability for a protein to be considered identified." help="(-min_protein_id_probability)"/> - <param name="param_min_pt_weight" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal pt weight of a precursor" help="(-min_pt_weight)"/> - <param name="param_min_mz" type="float" min="0.0" optional="True" value="500.0" label="Minimal mz to be considered in protein based LP formulation." help="(-min_mz)"/> - <param name="param_max_mz" type="float" min="0.0" optional="True" value="5000.0" label="Minimal mz to be considered in protein based LP formulation." help="(-max_mz)"/> - <param name="param_use_peptide_rule" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:use_peptide_rule true" falsevalue="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:use_peptide_rule false" checked="false" optional="True" label="Use peptide rule instead of minimal protein id probability" help="(-use_peptide_rule)"/> - <param name="param_min_peptide_ids" type="integer" min="1" optional="True" value="2" label="If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id" help="(-min_peptide_ids)"/> - <param name="param_min_peptide_probability" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified" help="(-min_peptide_probability)"/> - <param name="param_add_single_spectra" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:MS_E:add_single_spectra true" falsevalue="-algorithm:MSSim:RawTandemSignal:MS_E:add_single_spectra false" checked="false" optional="True" label="If true, the MS2 spectra for each peptide signal are included in the output (might be a lot). They will have a meta value 'MSE_DebugSpectrum' attached, so they can be filtered out. Native MS_E spectra will have 'MSE_Spectrum' instead." help="(-add_single_spectra)"/> - <param name="param_add_isotopes" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_isotopes true" falsevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_isotopes false" checked="false" optional="True" label="If set to 1 isotope peaks of the product ion peaks are added" help="(-add_isotopes)"/> - <param name="param_max_isotope" type="integer" value="2" label="Defines the maximal isotopic peak which is added, add_isotopes must be set to 1" help="(-max_isotope)"/> - <param name="param_add_metainfo" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_metainfo true" falsevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_metainfo false" checked="false" optional="True" label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" help="(-add_metainfo)"/> - <param name="param_add_losses" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses true" falsevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses false" checked="false" optional="True" label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" help="(-add_losses)"/> - <param name="param_add_precursor_peaks" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks true" falsevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks false" checked="false" optional="True" label="Adds peaks of the precursor to the spectrum, which happen to occur sometimes" help="(-add_precursor_peaks)"/> - <param name="param_add_abundant_immonium_ions" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions true" falsevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions false" checked="false" optional="True" label="Add most abundant immonium ions" help="(-add_abundant_immonium_ions)"/> - <param name="param_add_first_prefix_ion" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion true" falsevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion false" checked="false" optional="True" label="If set to true e.g. b1 ions are added" help="(-add_first_prefix_ion)"/> - <param name="param_add_y_ions" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_y_ions true" falsevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_y_ions false" checked="true" optional="True" label="Add peaks of y-ions to the spectrum" help="(-add_y_ions)"/> - <param name="param_add_b_ions" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_b_ions true" falsevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_b_ions false" checked="true" optional="True" label="Add peaks of b-ions to the spectrum" help="(-add_b_ions)"/> - <param name="param_add_a_ions" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_a_ions true" falsevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_a_ions false" checked="false" optional="True" label="Add peaks of a-ions to the spectrum" help="(-add_a_ions)"/> - <param name="param_add_c_ions" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_c_ions true" falsevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_c_ions false" checked="false" optional="True" label="Add peaks of c-ions to the spectrum" help="(-add_c_ions)"/> - <param name="param_add_x_ions" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_x_ions true" falsevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_x_ions false" checked="false" optional="True" label="Add peaks of x-ions to the spectrum" help="(-add_x_ions)"/> - <param name="param_add_z_ions" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_z_ions true" falsevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_z_ions false" checked="false" optional="True" label="Add peaks of z-ions to the spectrum" help="(-add_z_ions)"/> - <param name="param_y_intensity" type="float" value="1.0" label="Intensity of the y-ions" help="(-y_intensity)"/> - <param name="param_b_intensity" type="float" value="1.0" label="Intensity of the b-ions" help="(-b_intensity)"/> - <param name="param_a_intensity" type="float" value="1.0" label="Intensity of the a-ions" help="(-a_intensity)"/> - <param name="param_c_intensity" type="float" value="1.0" label="Intensity of the c-ions" help="(-c_intensity)"/> - <param name="param_x_intensity" type="float" value="1.0" label="Intensity of the x-ions" help="(-x_intensity)"/> - <param name="param_z_intensity" type="float" value="1.0" label="Intensity of the z-ions" help="(-z_intensity)"/> - <param name="param_relative_loss_intensity" type="float" value="0.1" label="Intensity of loss ions, in relation to the intact ion intensity" help="(-relative_loss_intensity)"/> - <param name="param_precursor_intensity" type="float" value="1.0" label="Intensity of the precursor peak" help="(-precursor_intensity)"/> - <param name="param_precursor_H2O_intensity" type="float" value="1.0" label="Intensity of the H2O loss peak of the precursor" help="(-precursor_H2O_intensity)"/> - <param name="param_precursor_NH3_intensity" type="float" value="1.0" label="Intensity of the NH3 loss peak of the precursor" help="(-precursor_NH3_intensity)"/> - <param name="param_add_isotopes" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_isotopes true" falsevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_isotopes false" checked="false" optional="True" label="If set to 1 isotope peaks of the product ion peaks are added" help="(-add_isotopes)"/> - <param name="param_max_isotope" type="integer" value="2" label="Defines the maximal isotopic peak which is added, add_isotopes must be set to 1" help="(-max_isotope)"/> - <param name="param_add_metainfo" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_metainfo true" falsevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_metainfo false" checked="false" optional="True" label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" help="(-add_metainfo)"/> - <param name="param_add_first_prefix_ion" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_first_prefix_ion true" falsevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_first_prefix_ion false" checked="false" optional="True" label="If set to true e.g. b1 ions are added" help="(-add_first_prefix_ion)"/> - <param name="param_hide_y_ions" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y_ions true" falsevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y_ions false" checked="false" optional="True" label="Add peaks of y-ions to the spectrum" help="(-hide_y_ions)"/> - <param name="param_hide_y2_ions" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y2_ions true" falsevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y2_ions false" checked="false" optional="True" label="Add peaks of y-ions to the spectrum" help="(-hide_y2_ions)"/> - <param name="param_hide_b_ions" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b_ions true" falsevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b_ions false" checked="false" optional="True" label="Add peaks of b-ions to the spectrum" help="(-hide_b_ions)"/> - <param name="param_hide_b2_ions" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b2_ions true" falsevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b2_ions false" checked="false" optional="True" label="Add peaks of b-ions to the spectrum" help="(-hide_b2_ions)"/> - <param name="param_hide_a_ions" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_a_ions true" falsevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_a_ions false" checked="false" optional="True" label="Add peaks of a-ions to the spectrum" help="(-hide_a_ions)"/> - <param name="param_hide_c_ions" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_c_ions true" falsevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_c_ions false" checked="false" optional="True" label="Add peaks of c-ions to the spectrum" help="(-hide_c_ions)"/> - <param name="param_hide_x_ions" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_x_ions true" falsevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_x_ions false" checked="false" optional="True" label="Add peaks of x-ions to the spectrum" help="(-hide_x_ions)"/> - <param name="param_hide_z_ions" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_z_ions true" falsevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_z_ions false" checked="false" optional="True" label="Add peaks of z-ions to the spectrum" help="(-hide_z_ions)"/> - <param name="param_hide_losses" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_losses true" falsevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_losses false" checked="false" optional="True" label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" help="(-hide_losses)"/> - <param name="param_y_intensity" type="float" value="1.0" label="Intensity of the y-ions" help="(-y_intensity)"/> - <param name="param_b_intensity" type="float" value="1.0" label="Intensity of the b-ions" help="(-b_intensity)"/> - <param name="param_a_intensity" type="float" value="1.0" label="Intensity of the a-ions" help="(-a_intensity)"/> - <param name="param_c_intensity" type="float" value="1.0" label="Intensity of the c-ions" help="(-c_intensity)"/> - <param name="param_x_intensity" type="float" value="1.0" label="Intensity of the x-ions" help="(-x_intensity)"/> - <param name="param_z_intensity" type="float" value="1.0" label="Intensity of the z-ions" help="(-z_intensity)"/> - <param name="param_relative_loss_intensity" type="float" value="0.1" label="Intensity of loss ions, in relation to the intact ion intensity" help="(-relative_loss_intensity)"/> - <param name="param_ionization_type" type="select" optional="True" value="ESI" label="Type of Ionization (MALDI or ESI)" help="(-ionization_type)"> - <option value="MALDI">MALDI</option> - <option value="ESI">ESI</option> - </param> - <param name="param_type" type="select" optional="True" value="labelfree" label="Select the labeling type you want for your experiment" help="(-type)"> - <option value="ICPL">ICPL</option> - <option value="SILAC">SILAC</option> - <option value="itraq">itraq</option> - <option value="labelfree">labelfree</option> - <option value="o18">o18</option> - </param> - <param name="param_ICPL_fixed_rtshift" type="float" value="0.0" label="Fixed retention time shift between labeled pairs. If set to 0.0 only the retention times, computed by the RT model step are used." help="(-ICPL_fixed_rtshift)"/> - <param name="param_label_proteins" type="boolean" truevalue="-algorithm:MSSim:Labeling:ICPL:label_proteins true" falsevalue="-algorithm:MSSim:Labeling:ICPL:label_proteins false" checked="true" optional="True" label="Enables protein-labeling. (select 'false' if you only need peptide-labeling)" help="(-label_proteins)"/> - <param name="param_fixed_rtshift" type="float" min="0.0" optional="True" value="0.0001" label="Fixed retention time shift between labeled peptides. If set to 0.0 only the retention times computed by the RT model step are used." help="(-fixed_rtshift)"/> - <param name="param_modification_lysine" type="text" size="20" value="UniMod:481" label="Modification of Lysine in the medium SILAC channel" help="(-modification_lysine)"/> - <param name="param_modification_arginine" type="text" size="20" value="UniMod:188" label="Modification of Arginine in the medium SILAC channel" help="(-modification_arginine)"/> - <param name="param_modification_lysine" type="text" size="20" value="UniMod:259" label="Modification of Lysine in the heavy SILAC channel. If left empty, two channelSILAC is assumed." help="(-modification_lysine)"/> - <param name="param_modification_arginine" type="text" size="20" value="UniMod:267" label="Modification of Arginine in the heavy SILAC channel. If left empty, two-channel SILAC is assumed." help="(-modification_arginine)"/> - <param name="param_iTRAQ" type="select" optional="True" value="4plex" label="4plex or 8plex iTRAQ?" help="(-iTRAQ)"> - <option value="4plex">4plex</option> - <option value="8plex">8plex</option> - </param> - <param name="param_reporter_mass_shift" type="float" min="0.0" max="0.5" optional="True" value="0.1" label="Allowed shift (uniformly distributed - left to right) in Da from the expected position (of e.g. 114.1, 115.1)" help="(-reporter_mass_shift)"/> - <param name="param_channel_active_4plex" type="text" size="20" value="114:myReference" label="Four-plex only: Each channel that was used in the experiment and its description (114-117) in format <channel>:<name>, e.g. "114:myref","115:liver"." help="(-channel_active_4plex)"/> - <param name="param_channel_active_8plex" type="text" size="20" value="113:myReference" label="Eight-plex only: Each channel that was used in the experiment and its description (113-121) in format <channel>:<name>, e.g. "113:myref","115:liver","118:lung"." help="(-channel_active_8plex)"/> - <param name="param_Y_contamination" type="float" min="0.0" max="1.0" optional="True" value="0.3" label="Efficiency of labeling tyrosine ('Y') residues. 0=off, 1=full labeling" help="(-Y_contamination)"/> - <param name="param_labeling_efficiency" type="float" min="0.0" max="1.0" optional="True" value="1.0" label="Describes the distribution of the labeled peptide over the different states (unlabeled, mono- and di-labeled)" help="(-labeling_efficiency)"/> - <param name="param_biological" type="select" optional="True" value="random" label="Controls the 'biological' randomness of the generated data (e.g. systematic effects like deviations in RT). If set to 'random' each experiment will look different. If set to 'reproducible' each experiment will have the same outcome (given that the input data is the same)." help="(-biological)"> - <option value="reproducible">reproducible</option> - <option value="random">random</option> - </param> - <param name="param_technical" type="select" optional="True" value="random" label="Controls the 'technical' randomness of the generated data (e.g. noise in the raw signal). If set to 'random' each experiment will look different. If set to 'reproducible' each experiment will have the same outcome (given that the input data is the same)." help="(-technical)"> - <option value="reproducible">reproducible</option> - <option value="random">random</option> - </param> - <expand macro="advanced_options"> - <param name="param_max_impurity_set_size" type="integer" value="3" label="Maximal #combinations of charge impurities allowed (each generating one feature) per charge state. E.g. assuming charge=3 and this parameter is 2, then we could choose to allow '3H+, 2H+Na+' features (given a certain 'charge_impurity' constraints), but no '3H+, 2H+Na+, 3Na+'" help="(-max_impurity_set_size)"/> - <param name="param_ICPL_light_channel_label" type="text" size="20" value="UniMod:365" label="UniMod Id of the light channel ICPL label." help="(-ICPL_light_channel_label)"/> - <param name="param_ICPL_medium_channel_label" type="text" size="20" value="UniMod:687" label="UniMod Id of the medium channel ICPL label." help="(-ICPL_medium_channel_label)"/> - <param name="param_ICPL_heavy_channel_label" type="text" size="20" value="UniMod:364" label="UniMod Id of the heavy channel ICPL label." help="(-ICPL_heavy_channel_label)"/> - <param name="param_isotope_correction_values_4plex" type="text" size="20" value="114:0/1/5.9/0.2 115:0/2/5.6/0.1 116:0/3/4.5/0.1 117:0.1/4/3.5/0.1" label="override default values (see Documentation); use the following format: <channel>:<-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2' " help="(-isotope_correction_values_4plex)"/> - <param name="param_isotope_correction_values_8plex" type="text" size="20" value="113:0/0/6.89/0.22 114:0/0.94/5.9/0.16 115:0/1.88/4.9/0.1 116:0/2.82/3.9/0.07 117:0.06/3.77/2.99/0 118:0.09/4.71/1.88/0 119:0.14/5.66/0.87/0 121:0.27/7.44/0.18/0" label="override default values (see Documentation); use the following format: <channel>:<-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '113:0/0.3/4/0' , '116:0.1/0.3/3/0.2' " help="(-isotope_correction_values_8plex)"/> - </expand> - </inputs> - <outputs> - <data name="param_out" label="output: simulated MS raw (profile) data" format="mzML"/> - <data name="param_out_pm" label="output: ground-truth picked (centroided) MS data" format="mzML"/> - <data name="param_out_fm" label="output: ground-truth features" format="featureXML"/> - <data name="param_out_cm" label="output: ground-truth features, grouping ESI charge variants of each parent peptide" format="consensusXML"/> - <data name="param_out_lcm" label="output: ground-truth features, grouping labeled variants" format="consensusXML"/> - <data name="param_out_cntm" label="output: ground-truth features caused by contaminants" format="featureXML"/> - <data name="param_out_id" label="output: ground-truth MS2 peptide identifications" format="idXML"/> - </outputs> - <help>**What it does** - -A highly configurable simulator for mass spectrometry experiments. + <inputs> + <param format="fasta" help="(-in) " label="Input protein sequences" multiple="true" name="param_in" optional="False" size="30" type="data"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param help="(-enzyme) " label="Enzyme to use for digestion (select 'no cleavage' to skip digestion)" name="param_algorithm_MSSim_Digestion_enzyme" optional="True" type="select" value="Trypsin"> + <option value="no cleavage">no cleavage</option> + <option value="V8-E">V8-E</option> + <option value="Trypsin/P">Trypsin/P</option> + <option value="Lys-C/P">Lys-C/P</option> + <option value="unspecific cleavage">unspecific cleavage</option> + <option value="leukocyte elastase">leukocyte elastase</option> + <option value="proline endopeptidase">proline endopeptidase</option> + <option value="V8-DE">V8-DE</option> + <option value="Chymotrypsin">Chymotrypsin</option> + <option value="Asp-N">Asp-N</option> + <option value="2-iodobenzoate">2-iodobenzoate</option> + <option value="Arg-C">Arg-C</option> + <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> + <option value="TrypChymo">TrypChymo</option> + <option value="Trypsin">Trypsin</option> + <option value="Formic_acid">Formic_acid</option> + <option value="CNBr">CNBr</option> + <option value="Asp-N_ambic">Asp-N_ambic</option> + <option value="PepsinA">PepsinA</option> + <option value="Lys-C">Lys-C</option> + </param> + <param help="(-model) 'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u)" label="The cleavage model to use for digestion" name="param_algorithm_MSSim_Digestion_model" optional="True" type="select" value="naive"> + <option value="trained">trained</option> + <option value="naive">naive</option> + </param> + <param help="(-min_peptide_length) " label="Minimum peptide length after digestion (shorter ones will be discarded)" min="1" name="param_algorithm_MSSim_Digestion_min_peptide_length" optional="True" type="integer" value="3"/> + <param help="(-threshold) Higher values increase the number of cleavages. -2 will give no cleavages, +4 almost full cleavage" label="Model threshold for calling a cleavage" max="4.0" min="-2.0" name="param_algorithm_MSSim_Digestion_model_trained_threshold" optional="True" type="float" value="0.5"/> + <param help="(-missed_cleavages) All possible resulting peptides will be created" label="Maximum number of missed cleavages considered" min="0" name="param_algorithm_MSSim_Digestion_model_naive_missed_cleavages" optional="True" type="integer" value="1"/> + <param help="(-rt_column) " label="Modelling of an RT or CE column" name="param_algorithm_MSSim_RT_rt_column" optional="True" type="select" value="HPLC"> + <option value="none">none</option> + <option value="HPLC">HPLC</option> + <option value="CE">CE</option> + </param> + <param checked="true" falsevalue="" help="(-auto_scale) If 'true', for CE this means that 'CE:lenght_d', 'CE:length_total', 'CE:voltage' have no influence" label="Scale predicted RT's/MT's to given 'total_gradient_time'?" name="param_algorithm_MSSim_RT_auto_scale" optional="True" truevalue="-algorithm:MSSim:RT:auto_scale" type="boolean"/> + <param help="(-total_gradient_time) " label="The duration [s] of the gradient" min="1e-05" name="param_algorithm_MSSim_RT_total_gradient_time" optional="True" type="float" value="2500.0"/> + <param help="(-sampling_rate) " label="Time interval [s] between consecutive scans" max="60.0" min="0.01" name="param_algorithm_MSSim_RT_sampling_rate" optional="True" type="float" value="2.0"/> + <param help="(-min) " label="Start of RT Scan Window [s]" min="0.0" name="param_algorithm_MSSim_RT_scan_window_min" optional="True" type="float" value="500.0"/> + <param help="(-max) " label="End of RT Scan Window [s]" min="1.0" name="param_algorithm_MSSim_RT_scan_window_max" optional="True" type="float" value="1500.0"/> + <param help="(-feature_stddev) " label="Standard deviation of shift in retention time [s] from predicted model (applied to every single feature independently)" name="param_algorithm_MSSim_RT_variation_feature_stddev" type="integer" value="3"/> + <param help="(-affine_offset) " label="Global offset in retention time [s] from predicted model" name="param_algorithm_MSSim_RT_variation_affine_offset" type="integer" value="0"/> + <param help="(-affine_scale) " label="Global scaling in retention time from predicted model" name="param_algorithm_MSSim_RT_variation_affine_scale" type="integer" value="1"/> + <param help="(-distortion) e.g. Orbitrap) distortion should be >4" label="Distortion of the elution profiles. Good presets are 0 for a perfect elution profile, 1 for a slightly distorted elution profile etc... For trapping instruments (" max="10" min="0" name="param_algorithm_MSSim_RT_column_condition_distortion" optional="True" type="integer" value="0"/> + <param help="(-value) This does not correspond directly to the width in [s]" label="Width of the Exponential Gaussian Hybrid distribution shape of the elution profile" min="0.0" name="param_algorithm_MSSim_RT_profile_shape_width_value" optional="True" type="float" value="9.0"/> + <param help="(-variance) scale parameter for the lorentzian variation of the variance (Note: The scale parameter has to be >= 0)" label="Random component of the width (set to 0 to disable randomness), i.e" min="0.0" name="param_algorithm_MSSim_RT_profile_shape_width_variance" optional="True" type="float" value="1.6"/> + <param help="(-value) Higher absolute(!) values lead to more skewness (negative values cause fronting, positive values cause tailing). Tau parameter of the EGH, i.e. time constant of the exponential decay of the Exponential Gaussian Hybrid distribution shape of the elution profile" label="Asymmetric component of the EGH" name="param_algorithm_MSSim_RT_profile_shape_skewness_value" type="float" value="0.1"/> + <param help="(-variance) scale parameter for the lorentzian variation of the time constant (Note: The scale parameter has to be > 0)" label="Random component of skewness (set to 0 to disable randomness), i.e" min="0.0" name="param_algorithm_MSSim_RT_profile_shape_skewness_variance" optional="True" type="float" value="0.3"/> + <param help="(-model_file) " label="SVM model for retention time prediction" name="param_algorithm_MSSim_RT_HPLC_model_file" size="30" type="text" value="examples/simulation/RTPredict.model"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param help="(-pH) " label="pH of buffe" max="14.0" min="0.0" name="param_algorithm_MSSim_RT_CE_pH" optional="True" type="float" value="3.0"/> + <param help="(-alpha) " label="Exponent Alpha used to calculate mobility" max="1.0" min="0.0" name="param_algorithm_MSSim_RT_CE_alpha" optional="True" type="float" value="0.5"/> + <param help="(-mu_eo) " label="Electroosmotic flow" max="5.0" min="0.0" name="param_algorithm_MSSim_RT_CE_mu_eo" optional="True" type="float" value="0.0"/> + <param help="(-lenght_d) " label="Length of capillary [cm] from injection site to MS" max="1000.0" min="0.0" name="param_algorithm_MSSim_RT_CE_lenght_d" optional="True" type="float" value="70.0"/> + <param help="(-length_total) " label="Total length of capillary [cm]" max="1000.0" min="0.0" name="param_algorithm_MSSim_RT_CE_length_total" optional="True" type="float" value="75.0"/> + <param help="(-voltage) " label="Voltage applied to capillary" min="0.0" name="param_algorithm_MSSim_RT_CE_voltage" optional="True" type="float" value="1000.0"/> + <param checked="false" falsevalue="" help="(-dt_simulation_on) This can serve as a filter to remove peptides which ionize badly, thus reducing peptide count" label="Modelling detectibility enabled?" name="param_algorithm_MSSim_Detectability_dt_simulation_on" optional="True" truevalue="-algorithm:MSSim:Detectability:dt_simulation_on" type="boolean"/> + <param help="(-min_detect) Peptides with a lower score will be removed" label="Minimum peptide detectability accepted" name="param_algorithm_MSSim_Detectability_min_detect" type="float" value="0.5"/> + <param help="(-dt_model_file) " label="SVM model for peptide detectability prediction" name="param_algorithm_MSSim_Detectability_dt_model_file" size="30" type="text" value="examples/simulation/DTPredict.model"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <repeat max="1" min="0" name="rep_param_algorithm_MSSim_Ionization_esi_ionized_residues" title="param_algorithm_MSSim_Ionization_esi_ionized_residues"> + <param help="(-ionized_residues) The N-term is always assumed to carry a charge. This parameter will be ignored during MALDI ionization" label="List of residues (as three letter code) that will be considered during ES ionization" name="param_algorithm_MSSim_Ionization_esi_ionized_residues" optional="True" type="select" value="Arg Lys His"> + <option value="Ala">Ala</option> + <option value="Cys">Cys</option> + <option value="Asp">Asp</option> + <option value="Glu">Glu</option> + <option value="Phe">Phe</option> + <option value="Gly">Gly</option> + <option value="His">His</option> + <option value="Ile">Ile</option> + <option value="Lys">Lys</option> + <option value="Leu">Leu</option> + <option value="Met">Met</option> + <option value="Asn">Asn</option> + <option value="Pro">Pro</option> + <option value="Gln">Gln</option> + <option value="Arg">Arg</option> + <option value="Sec">Sec</option> + <option value="Ser">Ser</option> + <option value="Thr">Thr</option> + <option value="Val">Val</option> + <option value="Trp">Trp</option> + <option value="Tyr">Tyr</option> + </param> + </repeat> + <repeat max="1" min="0" name="rep_param_algorithm_MSSim_Ionization_esi_charge_impurity" title="param_algorithm_MSSim_Ionization_esi_charge_impurity"> + <param help="(-charge_impurity) e.g. ['H:1'] or ['H:0.7' 'Na:0.3'], ['H:4' 'Na:1'] (which internally translates to ['H:0.8' 'Na:0.2'])" label="List of charged ions that contribute to charge with weight of occurrence (their sum is scaled to 1 internally)," name="param_algorithm_MSSim_Ionization_esi_charge_impurity" size="30" type="text" value="H+:1"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <param help="(-ionization_probability) " label="Probability for the binomial distribution of the ESI charge states" name="param_algorithm_MSSim_Ionization_esi_ionization_probability" type="float" value="0.8"/> + <repeat max="1" min="0" name="rep_param_algorithm_MSSim_Ionization_maldi_ionization_probabilities" title="param_algorithm_MSSim_Ionization_maldi_ionization_probabilities"> + <param help="(-ionization_probabilities) " label="List of probabilities for the different charge states during MALDI ionization (the list must sum up to 1.0)" name="param_algorithm_MSSim_Ionization_maldi_ionization_probabilities" size="30" type="text" value="0.9 0.1"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <param help="(-lower_measurement_limit) " label="Lower m/z detector limit" min="0.0" name="param_algorithm_MSSim_Ionization_mz_lower_measurement_limit" optional="True" type="float" value="200.0"/> + <param help="(-upper_measurement_limit) " label="Upper m/z detector limit" min="0.0" name="param_algorithm_MSSim_Ionization_mz_upper_measurement_limit" optional="True" type="float" value="2500.0"/> + <param checked="true" falsevalue="" help="(-enabled) (select 'false' if you only need feature-maps)" label="Enable RAW signal simulation?" name="param_algorithm_MSSim_RawSignal_enabled" optional="True" truevalue="-algorithm:MSSim:RawSignal:enabled" type="boolean"/> + <param help="(-peak_shape) " label="Peak Shape used around each isotope peak (be aware that the area under the curve is constant for both types, but the maximal height will differ (~ 2:3 = Lorentz:Gaussian) due to the wider base of the Lorentzian" name="param_algorithm_MSSim_RawSignal_peak_shape" optional="True" type="select" value="Gaussian"> + <option value="Gaussian">Gaussian</option> + <option value="Lorentzian">Lorentzian</option> + </param> + <param help="(-value) " label="Instrument resolution at 400 Th" name="param_algorithm_MSSim_RawSignal_resolution_value" type="integer" value="50000"/> + <param help="(-type) " label="How does resolution change with increasing m/z?! QTOFs usually show 'constant' behavior, FTs have linear degradation, and on Orbitraps the resolution decreases with square root of mass" name="param_algorithm_MSSim_RawSignal_resolution_type" optional="True" type="select" value="linear"> + <option value="constant">constant</option> + <option value="linear">linear</option> + <option value="sqrt">sqrt</option> + </param> + <param help="(-scaling) Set to 0 to disable simulation of baseline" label="Scale of baseline" min="0.0" name="param_algorithm_MSSim_RawSignal_baseline_scaling" optional="True" type="float" value="0.0"/> + <param help="(-shape) " label="The baseline is modeled by an exponential probability density function (pdf) with f(x) = shape*e^(- shape*x)" min="0.0" name="param_algorithm_MSSim_RawSignal_baseline_shape" optional="True" type="float" value="0.5"/> + <param help="(-sampling_points) " label="Number of raw data points per FWHM of the peak" min="2" name="param_algorithm_MSSim_RawSignal_mz_sampling_points" optional="True" type="integer" value="3"/> + <param help="(-file) See 'OpenMS/examples/simulation/contaminants.txt' for details" label="Contaminants file with sum formula and absolute RT interval" name="param_algorithm_MSSim_RawSignal_contaminants_file" size="30" type="text" value="examples/simulation/contaminants.csv"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param help="(-error_stddev) Set to 0 to disable simulation of m/z errors" label="Standard deviation for m/z errors" name="param_algorithm_MSSim_RawSignal_variation_mz_error_stddev" type="float" value="0.0"/> + <param help="(-error_mean) " label="Average systematic m/z error (Da)" name="param_algorithm_MSSim_RawSignal_variation_mz_error_mean" type="float" value="0.0"/> + <param help="(-scale) Set to 1.0 to get the real intensity values provided in the FASTA file" label="Constant scale factor of the feature intensity" min="0.0" name="param_algorithm_MSSim_RawSignal_variation_intensity_scale" optional="True" type="float" value="100.0"/> + <param help="(-scale_stddev) Set to 0 to get simple rescaled intensities" label="Standard deviation of peak intensity (relative to the scaled peak height)" min="0.0" name="param_algorithm_MSSim_RawSignal_variation_intensity_scale_stddev" optional="True" type="float" value="0.0"/> + <param help="(-rate) Set this to 0 to disable simulation of shot noise" label="Poisson rate of shot noise per unit m/z" min="0.0" name="param_algorithm_MSSim_RawSignal_noise_shot_rate" optional="True" type="float" value="0.0"/> + <param help="(-intensity-mean) " label="Shot noise intensity mean (exponentially distributed with given mean)" name="param_algorithm_MSSim_RawSignal_noise_shot_intensity_mean" type="float" value="1.0"/> + <param help="(-mean) " label="Mean value of white noise being added to each measured signal" name="param_algorithm_MSSim_RawSignal_noise_white_mean" type="float" value="0.0"/> + <param help="(-stddev) " label="Standard deviation of white noise being added to each measured signal" name="param_algorithm_MSSim_RawSignal_noise_white_stddev" type="float" value="0.0"/> + <param help="(-mean) " label="Mean value of the detector noise being added to the complete measurement" name="param_algorithm_MSSim_RawSignal_noise_detector_mean" type="float" value="0.0"/> + <param help="(-stddev) " label="Standard deviation of the detector noise being added to the complete measurement" name="param_algorithm_MSSim_RawSignal_noise_detector_stddev" type="float" value="0.0"/> + <param help="(-status) " label="Create Tandem-MS scans?" name="param_algorithm_MSSim_RawTandemSignal_status" optional="True" type="select" value="disabled"> + <option value="disabled">disabled</option> + <option value="precursor">precursor</option> + <option value="MS^E">MS^E</option> + </param> + <param help="(-tandem_mode) 0 - fixed intensities, 1 - SVC prediction (abundant/missing), 2 - SVR prediction of peak intensity <br>" label="Algorithm to generate the tandem-MS spectra" max="2" min="0" name="param_algorithm_MSSim_RawTandemSignal_tandem_mode" optional="True" type="integer" value="0"/> + <param help="(-svm_model_set_file) " label="File containing the filenames of SVM Models for different charge variants" name="param_algorithm_MSSim_RawTandemSignal_svm_model_set_file" size="30" type="text" value="examples/simulation/SvmModelSet.model"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param help="(-ms2_spectra_per_rt_bin) " label="Number of allowed MS/MS spectra in a retention time bin" min="1" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ms2_spectra_per_rt_bin" optional="True" type="integer" value="5"/> + <param help="(-min_mz_peak_distance) Also used to define the m/z width of an exclusion window (distance +/- from m/z of precursor). If you set this lower than the isotopic envelope of a peptide, you might get multiple fragment spectra pointing to the same precursor" label="The minimal distance (in Th) between two peaks for concurrent selection for fragmentation" min="0.0001" name="param_algorithm_MSSim_RawTandemSignal_Precursor_min_mz_peak_distance" optional="True" type="float" value="2.0"/> + <param help="(-mz_isolation_window) " label="All peaks within a mass window (in Th) of a selected peak are also selected for fragmentation" min="0.0" name="param_algorithm_MSSim_RawTandemSignal_Precursor_mz_isolation_window" optional="True" type="float" value="2.0"/> + <param checked="false" falsevalue="" help="(-exclude_overlapping_peaks) " label="If true, overlapping or nearby peaks (within 'min_mz_peak_distance') are excluded for selection" name="param_algorithm_MSSim_RawTandemSignal_Precursor_exclude_overlapping_peaks" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:Precursor:exclude_overlapping_peaks" type="boolean"/> + <repeat max="1" min="0" name="rep_param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter" title="param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter"> + <param help="(-charge_filter) " label="Charges considered for MS2 fragmentation" max="5" min="1" name="param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter" optional="True" size="30" type="text" value="2 3"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <param checked="false" falsevalue="" help="(-use_dynamic_exclusion) " label="If true dynamic exclusion is applied" name="param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_use_dynamic_exclusion" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:use_dynamic_exclusion" type="boolean"/> + <param help="(-exclusion_time) " label="The time (in seconds) a feature is excluded" min="0.0" name="param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_exclusion_time" optional="True" type="float" value="100.0"/> + <param help="(-max_list_size) " label="The maximal number of precursors in the inclusion list" min="1" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_max_list_size" optional="True" type="integer" value="1000"/> + <param help="(-min_rt) " label="Minimal rt in seconds" min="0.0" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_min_rt" optional="True" type="float" value="960.0"/> + <param help="(-max_rt) " label="Maximal rt in seconds" min="0.0" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_max_rt" optional="True" type="float" value="3840.0"/> + <param help="(-rt_step_size) " label="rt step size in seconds" min="1.0" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_step_size" optional="True" type="float" value="30.0"/> + <param help="(-rt_window_size) " label="rt window size in seconds" min="1" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_window_size" optional="True" type="integer" value="100"/> + <param help="(-min_protein_id_probability) " label="Minimal protein probability for a protein to be considered identified" max="1.0" min="0.0" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_protein_id_probability" optional="True" type="float" value="0.95"/> + <param help="(-min_pt_weight) " label="Minimal pt weight of a precurso" max="1.0" min="0.0" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_pt_weight" optional="True" type="float" value="0.5"/> + <param help="(-min_mz) " label="Minimal mz to be considered in protein based LP formulation" min="0.0" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_mz" optional="True" type="float" value="500.0"/> + <param help="(-max_mz) " label="Minimal mz to be considered in protein based LP formulation" min="0.0" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_max_mz" optional="True" type="float" value="5000.0"/> + <param checked="false" falsevalue="" help="(-use_peptide_rule) " label="Use peptide rule instead of minimal protein id probability" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_use_peptide_rule" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:use_peptide_rule" type="boolean"/> + <param help="(-min_peptide_ids) " label="If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id" min="1" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_ids" optional="True" type="integer" value="2"/> + <param help="(-min_peptide_probability) " label="If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified" max="1.0" min="0.0" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_probability" optional="True" type="float" value="0.95"/> + <param checked="false" falsevalue="" help="(-add_single_spectra) They will have a meta value 'MSE_DebugSpectrum' attached, so they can be filtered out. Native MS_E spectra will have 'MSE_Spectrum' instead" label="If true, the MS2 spectra for each peptide signal are included in the output (might be a lot)" name="param_algorithm_MSSim_RawTandemSignal_MS_E_add_single_spectra" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:MS_E:add_single_spectra" type="boolean"/> + <param checked="false" falsevalue="" help="(-add_isotopes) " label="If set to 1 isotope peaks of the product ion peaks are added" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_isotopes" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_isotopes" type="boolean"/> + <param help="(-max_isotope) " label="Defines the maximal isotopic peak which is added, add_isotopes must be set to 1" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_max_isotope" type="integer" value="2"/> + <param checked="false" falsevalue="" help="(-add_metainfo) " label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_metainfo" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_metainfo" type="boolean"/> + <param checked="false" falsevalue="" help="(-add_losses) " label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_losses" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses" type="boolean"/> + <param checked="false" falsevalue="" help="(-add_precursor_peaks) " label="Adds peaks of the precursor to the spectrum, which happen to occur sometimes" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_precursor_peaks" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks" type="boolean"/> + <param checked="false" falsevalue="" help="(-add_abundant_immonium_ions) " label="Add most abundant immonium ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_abundant_immonium_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions" type="boolean"/> + <param checked="false" falsevalue="" help="(-add_first_prefix_ion) " label="If set to true e.g. b1 ions are added" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_first_prefix_ion" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion" type="boolean"/> + <param checked="true" falsevalue="" help="(-add_y_ions) " label="Add peaks of y-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_y_ions" type="boolean"/> + <param checked="true" falsevalue="" help="(-add_b_ions) " label="Add peaks of b-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_b_ions" type="boolean"/> + <param checked="false" falsevalue="" help="(-add_a_ions) " label="Add peaks of a-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_a_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_a_ions" type="boolean"/> + <param checked="false" falsevalue="" help="(-add_c_ions) " label="Add peaks of c-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_c_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_c_ions" type="boolean"/> + <param checked="false" falsevalue="" help="(-add_x_ions) " label="Add peaks of x-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_x_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_x_ions" type="boolean"/> + <param checked="false" falsevalue="" help="(-add_z_ions) " label="Add peaks of z-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_z_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_z_ions" type="boolean"/> + <param help="(-y_intensity) " label="Intensity of the y-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_y_intensity" type="float" value="1.0"/> + <param help="(-b_intensity) " label="Intensity of the b-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_b_intensity" type="float" value="1.0"/> + <param help="(-a_intensity) " label="Intensity of the a-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_a_intensity" type="float" value="1.0"/> + <param help="(-c_intensity) " label="Intensity of the c-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_c_intensity" type="float" value="1.0"/> + <param help="(-x_intensity) " label="Intensity of the x-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_x_intensity" type="float" value="1.0"/> + <param help="(-z_intensity) " label="Intensity of the z-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_z_intensity" type="float" value="1.0"/> + <param help="(-relative_loss_intensity) " label="Intensity of loss ions, in relation to the intact ion intensity" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_relative_loss_intensity" type="float" value="0.1"/> + <param help="(-precursor_intensity) " label="Intensity of the precursor peak" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_intensity" type="float" value="1.0"/> + <param help="(-precursor_H2O_intensity) " label="Intensity of the H2O loss peak of the precurso" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_H2O_intensity" type="float" value="1.0"/> + <param help="(-precursor_NH3_intensity) " label="Intensity of the NH3 loss peak of the precurso" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_NH3_intensity" type="float" value="1.0"/> + <param checked="false" falsevalue="" help="(-add_isotopes) " label="If set to 1 isotope peaks of the product ion peaks are added" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_isotopes" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_isotopes" type="boolean"/> + <param help="(-max_isotope) " label="Defines the maximal isotopic peak which is added, add_isotopes must be set to 1" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_max_isotope" type="integer" value="2"/> + <param checked="false" falsevalue="" help="(-add_metainfo) " label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_metainfo" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_metainfo" type="boolean"/> + <param checked="false" falsevalue="" help="(-add_first_prefix_ion) " label="If set to true e.g. b1 ions are added" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_first_prefix_ion" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_first_prefix_ion" type="boolean"/> + <param checked="false" falsevalue="" help="(-hide_y_ions) " label="Add peaks of y-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_y_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y_ions" type="boolean"/> + <param checked="false" falsevalue="" help="(-hide_y2_ions) " label="Add peaks of y-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_y2_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y2_ions" type="boolean"/> + <param checked="false" falsevalue="" help="(-hide_b_ions) " label="Add peaks of b-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_b_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b_ions" type="boolean"/> + <param checked="false" falsevalue="" help="(-hide_b2_ions) " label="Add peaks of b-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_b2_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b2_ions" type="boolean"/> + <param checked="false" falsevalue="" help="(-hide_a_ions) " label="Add peaks of a-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_a_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_a_ions" type="boolean"/> + <param checked="false" falsevalue="" help="(-hide_c_ions) " label="Add peaks of c-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_c_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_c_ions" type="boolean"/> + <param checked="false" falsevalue="" help="(-hide_x_ions) " label="Add peaks of x-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_x_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_x_ions" type="boolean"/> + <param checked="false" falsevalue="" help="(-hide_z_ions) " label="Add peaks of z-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_z_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_z_ions" type="boolean"/> + <param checked="false" falsevalue="" help="(-hide_losses) " label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_losses" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_losses" type="boolean"/> + <param help="(-y_intensity) " label="Intensity of the y-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_y_intensity" type="float" value="1.0"/> + <param help="(-b_intensity) " label="Intensity of the b-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_b_intensity" type="float" value="1.0"/> + <param help="(-a_intensity) " label="Intensity of the a-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_a_intensity" type="float" value="1.0"/> + <param help="(-c_intensity) " label="Intensity of the c-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_c_intensity" type="float" value="1.0"/> + <param help="(-x_intensity) " label="Intensity of the x-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_x_intensity" type="float" value="1.0"/> + <param help="(-z_intensity) " label="Intensity of the z-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_z_intensity" type="float" value="1.0"/> + <param help="(-relative_loss_intensity) " label="Intensity of loss ions, in relation to the intact ion intensity" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_relative_loss_intensity" type="float" value="0.1"/> + <param help="(-ionization_type) " label="Type of Ionization (MALDI or ESI)" name="param_algorithm_MSSim_Global_ionization_type" optional="True" type="select" value="ESI"> + <option value="MALDI">MALDI</option> + <option value="ESI">ESI</option> + </param> + <param help="(-type) " label="Select the labeling type you want for your experiment" name="param_algorithm_MSSim_Labeling_type" optional="True" type="select" value="labelfree"> + <option value="ICPL">ICPL</option> + <option value="SILAC">SILAC</option> + <option value="itraq">itraq</option> + <option value="labelfree">labelfree</option> + <option value="o18">o18</option> + </param> + <param help="(-ICPL_fixed_rtshift) If set to 0.0 only the retention times, computed by the RT model step are used" label="Fixed retention time shift between labeled pairs" name="param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift" type="float" value="0.0"/> + <param checked="true" falsevalue="" help="(-label_proteins) (select 'false' if you only need peptide-labeling)" label="Enables protein-labeling" name="param_algorithm_MSSim_Labeling_ICPL_label_proteins" optional="True" truevalue="-algorithm:MSSim:Labeling:ICPL:label_proteins" type="boolean"/> + <param help="(-fixed_rtshift) If set to 0.0 only the retention times computed by the RT model step are used" label="Fixed retention time shift between labeled peptides" min="0.0" name="param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift" optional="True" type="float" value="0.0001"/> + <param help="(-modification_lysine) " label="Modification of Lysine in the medium SILAC channel" name="param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_lysine" size="30" type="text" value="UniMod:481"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param help="(-modification_arginine) " label="Modification of Arginine in the medium SILAC channel" name="param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_arginine" size="30" type="text" value="UniMod:188"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param help="(-modification_lysine) If left empty, two channelSILAC is assumed" label="Modification of Lysine in the heavy SILAC channel" name="param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_lysine" size="30" type="text" value="UniMod:259"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param help="(-modification_arginine) If left empty, two-channel SILAC is assumed" label="Modification of Arginine in the heavy SILAC channel" name="param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine" size="30" type="text" value="UniMod:267"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param help="(-iTRAQ) " label="4plex or 8plex iTRAQ?" name="param_algorithm_MSSim_Labeling_itraq_iTRAQ" optional="True" type="select" value="4plex"> + <option value="4plex">4plex</option> + <option value="8plex">8plex</option> + </param> + <param help="(-reporter_mass_shift) e.g. 114.1, 115.1)" label="Allowed shift (uniformly distributed - left to right) in Da from the expected position (of" max="0.5" min="0.0" name="param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift" optional="True" type="float" value="0.1"/> + <repeat max="1" min="0" name="rep_param_algorithm_MSSim_Labeling_itraq_channel_active_4plex" title="param_algorithm_MSSim_Labeling_itraq_channel_active_4plex"> + <param help="(-channel_active_4plex) e.g. "114:myref","115:liver"" label="Four-plex only: Each channel that was used in the experiment and its description (114-117) in format <channel>:<name>," name="param_algorithm_MSSim_Labeling_itraq_channel_active_4plex" size="30" type="text" value="114:myReference"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <repeat max="1" min="0" name="rep_param_algorithm_MSSim_Labeling_itraq_channel_active_8plex" title="param_algorithm_MSSim_Labeling_itraq_channel_active_8plex"> + <param help="(-channel_active_8plex) e.g. "113:myref","115:liver","118:lung"" label="Eight-plex only: Each channel that was used in the experiment and its description (113-121) in format <channel>:<name>," name="param_algorithm_MSSim_Labeling_itraq_channel_active_8plex" size="30" type="text" value="113:myReference"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <param help="(-Y_contamination) 0=off, 1=full labeling" label="Efficiency of labeling tyrosine ('Y') residues" max="1.0" min="0.0" name="param_algorithm_MSSim_Labeling_itraq_Y_contamination" optional="True" type="float" value="0.3"/> + <param help="(-labeling_efficiency) " label="Describes the distribution of the labeled peptide over the different states (unlabeled, mono- and di-labeled)" max="1.0" min="0.0" name="param_algorithm_MSSim_Labeling_o18_labeling_efficiency" optional="True" type="float" value="1.0"/> + <param help="(-biological) e.g. systematic effects like deviations in RT). If set to 'random' each experiment will look different. If set to 'reproducible' each experiment will have the same outcome (given that the input data is the same)" label="Controls the 'biological' randomness of the generated data (" name="param_algorithm_RandomNumberGenerators_biological" optional="True" type="select" value="random"> + <option value="reproducible">reproducible</option> + <option value="random">random</option> + </param> + <param help="(-technical) e.g. noise in the raw signal). If set to 'random' each experiment will look different. If set to 'reproducible' each experiment will have the same outcome (given that the input data is the same)" label="Controls the 'technical' randomness of the generated data (" name="param_algorithm_RandomNumberGenerators_technical" optional="True" type="select" value="random"> + <option value="reproducible">reproducible</option> + <option value="random">random</option> + </param> + <expand macro="advanced_options"> + <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/> + <param help="(-max_impurity_set_size) E.g. assuming charge=3 and this parameter is 2, then we could choose to allow '3H+, 2H+Na+' features (given a certain 'charge_impurity' constraints), but no '3H+, 2H+Na+, 3Na+'" label="Maximal #combinations of charge impurities allowed (each generating one feature) per charge state" name="param_algorithm_MSSim_Ionization_esi_max_impurity_set_size" type="integer" value="3"/> + <param help="(-ICPL_light_channel_label) " label="UniMod Id of the light channel ICPL label" name="param_algorithm_MSSim_Labeling_ICPL_ICPL_light_channel_label" size="30" type="text" value="UniMod:365"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param help="(-ICPL_medium_channel_label) " label="UniMod Id of the medium channel ICPL label" name="param_algorithm_MSSim_Labeling_ICPL_ICPL_medium_channel_label" size="30" type="text" value="UniMod:687"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param help="(-ICPL_heavy_channel_label) " label="UniMod Id of the heavy channel ICPL label" name="param_algorithm_MSSim_Labeling_ICPL_ICPL_heavy_channel_label" size="30" type="text" value="UniMod:364"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <repeat max="1" min="0" name="rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex" title="param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex"> + <param help="(-isotope_correction_values_4plex) e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2' " label="override default values (see Documentation); use the following format: <channel>:<-2Da>/<-1Da>/<+1Da>/<+2Da> ;" name="param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex" size="30" type="text" value="114:0/1/5.9/0.2 115:0/2/5.6/0.1 116:0/3/4.5/0.1 117:0.1/4/3.5/0.1"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <repeat max="1" min="0" name="rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex" title="param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex"> + <param help="(-isotope_correction_values_8plex) e.g. '113:0/0.3/4/0' , '116:0.1/0.3/3/0.2' " label="override default values (see Documentation); use the following format: <channel>:<-2Da>/<-1Da>/<+1Da>/<+2Da> ;" name="param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex" size="30" type="text" value="113:0/0/6.89/0.22 114:0/0.94/5.9/0.16 115:0/1.88/4.9/0.1 116:0/2.82/3.9/0.07 117:0.06/3.77/2.99/0 118:0.09/4.71/1.88/0 119:0.14/5.66/0.87/0 121:0.27/7.44/0.18/0"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + </expand> + </inputs> + <outputs> + <data format="mzml" name="param_out"/> + <data format="mzml" name="param_out_pm"/> + <data format="xml" name="param_out_fm"/> + <data format="consensusxml" name="param_out_cm"/> + <data format="consensusxml" name="param_out_lcm"/> + <data format="xml" name="param_out_cntm"/> + <data format="xml" name="param_out_id"/> + </outputs> + <help>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 - -@REFERENCES@ -</help> -</tool> +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MSSimulator.html</help> + </tool>