openms: MSSimulator.xml comparison

comparison 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

comparison

equal deleted inserted replaced

-:ec62782f6c68
+:6ead64a594bd
-<?xml version='1.0' encoding='UTF-8'?>
+<?xml version="1.0" encoding="UTF-8"?>
-<tool id="MSSimulator" name="MSSimulator" version="1.12.0">
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
-<description>A highly configurable simulator for mass spectrometry experiments.</description>
+<!--Proposed Tool Section: [Utilities]-->
-<macros>
+<tool id="MSSimulator" name="MSSimulator" version="2.0.0">
-<token name="@EXECUTABLE@">MSSimulator</token>
+<description>A highly configurable simulator for mass spectrometry experiments.</description>
-<import>macros.xml</import>
+<macros>
-</macros>
+<token name="@EXECUTABLE@">MSSimulator</token>
-<expand macro="stdio"/>
+<import>macros.xml</import>
-<expand macro="requirements"/>
+</macros>
-<command>MSSimulator
+<expand macro="references"/>
+<expand macro="stdio"/>
+<expand macro="requirements"/>
+<command>MSSimulator
--in ${param_in}
+-in
--out ${param_out}
+#for token in $param_in:
--out_pm ${param_out_pm}
+$token
--out_fm ${param_out_fm}
+#end for
--out_cm ${param_out_cm}
+#if $param_out:
--out_lcm ${param_out_lcm}
+-out $param_out
--out_cntm ${param_out_cntm}
+#end if
--out_id ${param_out_id}
+#if $param_out_pm:
--threads \${GALAXY_SLOTS:-24}
+-out_pm $param_out_pm
--algorithm:MSSim:Digestion:enzyme ${param_enzyme}
+#end if
--algorithm:MSSim:Digestion:model ${param_model}
+#if $param_out_fm:
--algorithm:MSSim:Digestion:min_peptide_length ${param_min_peptide_length}
+-out_fm $param_out_fm
--algorithm:MSSim:Digestion:model_trained:threshold ${param_threshold}
+#end if
--algorithm:MSSim:Digestion:model_naive:missed_cleavages ${param_missed_cleavages}
+#if $param_out_cm:
--algorithm:MSSim:RT:rt_column ${param_rt_column}
+-out_cm $param_out_cm
-${param_auto_scale}
+#end if
--algorithm:MSSim:RT:total_gradient_time ${param_total_gradient_time}
+#if $param_out_lcm:
--algorithm:MSSim:RT:sampling_rate ${param_sampling_rate}
+-out_lcm $param_out_lcm
--algorithm:MSSim:RT:scan_window:min ${param_min}
+#end if
--algorithm:MSSim:RT:scan_window:max ${param_max}
+#if $param_out_cntm:
--algorithm:MSSim:RT:variation:feature_stddev ${param_feature_stddev}
+-out_cntm $param_out_cntm
--algorithm:MSSim:RT:variation:affine_offset ${param_affine_offset}
+#end if
--algorithm:MSSim:RT:variation:affine_scale ${param_affine_scale}
+#if $param_out_id:
--algorithm:MSSim:RT:column_condition:distortion ${param_distortion}
+-out_id $param_out_id
--algorithm:MSSim:RT:profile_shape:width:value ${param_value}
+#end if
--algorithm:MSSim:RT:profile_shape:width:variance ${param_variance}
+-threads \${GALAXY_SLOTS:-24}
--algorithm:MSSim:RT:profile_shape:skewness:value ${param_value}
+#if $param_algorithm_MSSim_Digestion_enzyme:
--algorithm:MSSim:RT:profile_shape:skewness:variance ${param_variance}
+-algorithm:MSSim:Digestion:enzyme
--algorithm:MSSim:RT:HPLC:model_file ${param_model_file}
+#if &quot; &quot; in str($param_algorithm_MSSim_Digestion_enzyme):
--algorithm:MSSim:RT:CE:pH ${param_pH}
+&quot;$param_algorithm_MSSim_Digestion_enzyme&quot;
--algorithm:MSSim:RT:CE:alpha ${param_alpha}
+#else
--algorithm:MSSim:RT:CE:mu_eo ${param_mu_eo}
+$param_algorithm_MSSim_Digestion_enzyme
--algorithm:MSSim:RT:CE:lenght_d ${param_lenght_d}
+#end if
--algorithm:MSSim:RT:CE:length_total ${param_length_total}
+#end if
--algorithm:MSSim:RT:CE:voltage ${param_voltage}
+#if $param_algorithm_MSSim_Digestion_model:
-${param_dt_simulation_on}
+-algorithm:MSSim:Digestion:model
--algorithm:MSSim:Detectability:min_detect ${param_min_detect}
+#if &quot; &quot; in str($param_algorithm_MSSim_Digestion_model):
--algorithm:MSSim:Detectability:dt_model_file ${param_dt_model_file}
+&quot;$param_algorithm_MSSim_Digestion_model&quot;
--algorithm:MSSim:Ionization:esi:ionized_residues ${param_ionized_residues}
+#else
--algorithm:MSSim:Ionization:esi:charge_impurity ${param_charge_impurity}
+$param_algorithm_MSSim_Digestion_model
--algorithm:MSSim:Ionization:esi:ionization_probability ${param_ionization_probability}
+#end if
--algorithm:MSSim:Ionization:maldi:ionization_probabilities ${param_ionization_probabilities}
+#end if
--algorithm:MSSim:Ionization:mz:lower_measurement_limit ${param_lower_measurement_limit}
+#if $param_algorithm_MSSim_Digestion_min_peptide_length:
--algorithm:MSSim:Ionization:mz:upper_measurement_limit ${param_upper_measurement_limit}
+-algorithm:MSSim:Digestion:min_peptide_length $param_algorithm_MSSim_Digestion_min_peptide_length
-${param_enabled}
+#end if
--algorithm:MSSim:RawSignal:peak_shape ${param_peak_shape}
+#if $param_algorithm_MSSim_Digestion_model_trained_threshold:
--algorithm:MSSim:RawSignal:resolution:value ${param_value}
+-algorithm:MSSim:Digestion:model_trained:threshold $param_algorithm_MSSim_Digestion_model_trained_threshold
--algorithm:MSSim:RawSignal:resolution:type ${param_type}
+#end if
--algorithm:MSSim:RawSignal:baseline:scaling ${param_scaling}
+#if $param_algorithm_MSSim_Digestion_model_naive_missed_cleavages:
--algorithm:MSSim:RawSignal:baseline:shape ${param_shape}
+-algorithm:MSSim:Digestion:model_naive:missed_cleavages $param_algorithm_MSSim_Digestion_model_naive_missed_cleavages
--algorithm:MSSim:RawSignal:mz:sampling_points ${param_sampling_points}
+#end if
--algorithm:MSSim:RawSignal:contaminants:file ${param_file}
+#if $param_algorithm_MSSim_RT_rt_column:
--algorithm:MSSim:RawSignal:variation:mz:error_stddev ${param_error_stddev}
+-algorithm:MSSim:RT:rt_column
--algorithm:MSSim:RawSignal:variation:mz:error_mean ${param_error_mean}
+#if &quot; &quot; in str($param_algorithm_MSSim_RT_rt_column):
--algorithm:MSSim:RawSignal:variation:intensity:scale ${param_scale}
+&quot;$param_algorithm_MSSim_RT_rt_column&quot;
--algorithm:MSSim:RawSignal:variation:intensity:scale_stddev ${param_scale_stddev}
+#else
--algorithm:MSSim:RawSignal:noise:shot:rate ${param_rate}
+$param_algorithm_MSSim_RT_rt_column
--algorithm:MSSim:RawSignal:noise:shot:intensity-mean ${param_intensity-mean}
+#end if
--algorithm:MSSim:RawSignal:noise:white:mean ${param_mean}
+#end if
--algorithm:MSSim:RawSignal:noise:white:stddev ${param_stddev}
+#if $param_algorithm_MSSim_RT_auto_scale:
--algorithm:MSSim:RawSignal:noise:detector:mean ${param_mean}
+-algorithm:MSSim:RT:auto_scale
--algorithm:MSSim:RawSignal:noise:detector:stddev ${param_stddev}
+#end if
--algorithm:MSSim:RawTandemSignal:status ${param_status}
+#if $param_algorithm_MSSim_RT_total_gradient_time:
--algorithm:MSSim:RawTandemSignal:tandem_mode ${param_tandem_mode}
+-algorithm:MSSim:RT:total_gradient_time $param_algorithm_MSSim_RT_total_gradient_time
--algorithm:MSSim:RawTandemSignal:svm_model_set_file ${param_svm_model_set_file}
+#end if
--algorithm:MSSim:RawTandemSignal:Precursor:ms2_spectra_per_rt_bin ${param_ms2_spectra_per_rt_bin}
+#if $param_algorithm_MSSim_RT_sampling_rate:
--algorithm:MSSim:RawTandemSignal:Precursor:min_peak_distance ${param_min_peak_distance}
+-algorithm:MSSim:RT:sampling_rate $param_algorithm_MSSim_RT_sampling_rate
--algorithm:MSSim:RawTandemSignal:Precursor:selection_window ${param_selection_window}
+#end if
-${param_exclude_overlapping_peaks}
+#if $param_algorithm_MSSim_RT_scan_window_min:
--algorithm:MSSim:RawTandemSignal:Precursor:charge_filter ${param_charge_filter}
+-algorithm:MSSim:RT:scan_window:min $param_algorithm_MSSim_RT_scan_window_min
-${param_use_dynamic_exclusion}
+#end if
--algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:exclusion_time ${param_exclusion_time}
+#if $param_algorithm_MSSim_RT_scan_window_max:
--algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:max_list_size ${param_max_list_size}
+-algorithm:MSSim:RT:scan_window:max $param_algorithm_MSSim_RT_scan_window_max
--algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:min_rt ${param_min_rt}
+#end if
--algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:max_rt ${param_max_rt}
+#if $param_algorithm_MSSim_RT_variation_feature_stddev:
--algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_step_size ${param_rt_step_size}
+-algorithm:MSSim:RT:variation:feature_stddev $param_algorithm_MSSim_RT_variation_feature_stddev
--algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_window_size ${param_rt_window_size}
+#end if
--algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_protein_id_probability ${param_min_protein_id_probability}
+#if $param_algorithm_MSSim_RT_variation_affine_offset:
--algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_pt_weight ${param_min_pt_weight}
+-algorithm:MSSim:RT:variation:affine_offset $param_algorithm_MSSim_RT_variation_affine_offset
--algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_mz ${param_min_mz}
+#end if
--algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:max_mz ${param_max_mz}
+#if $param_algorithm_MSSim_RT_variation_affine_scale:
-${param_use_peptide_rule}
+-algorithm:MSSim:RT:variation:affine_scale $param_algorithm_MSSim_RT_variation_affine_scale
--algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_ids ${param_min_peptide_ids}
+#end if
--algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_probability ${param_min_peptide_probability}
+#if $param_algorithm_MSSim_RT_column_condition_distortion:
-${param_add_single_spectra}
+-algorithm:MSSim:RT:column_condition:distortion $param_algorithm_MSSim_RT_column_condition_distortion
-${param_add_isotopes}
+#end if
--algorithm:MSSim:RawTandemSignal:TandemSim:Simple:max_isotope ${param_max_isotope}
+#if $param_algorithm_MSSim_RT_profile_shape_width_value:
-${param_add_metainfo}
+-algorithm:MSSim:RT:profile_shape:width:value $param_algorithm_MSSim_RT_profile_shape_width_value
-${param_add_losses}
+#end if
-${param_add_precursor_peaks}
+#if $param_algorithm_MSSim_RT_profile_shape_width_variance:
-${param_add_abundant_immonium_ions}
+-algorithm:MSSim:RT:profile_shape:width:variance $param_algorithm_MSSim_RT_profile_shape_width_variance
-${param_add_first_prefix_ion}
+#end if
-${param_add_y_ions}
+#if $param_algorithm_MSSim_RT_profile_shape_skewness_value:
-${param_add_b_ions}
+-algorithm:MSSim:RT:profile_shape:skewness:value $param_algorithm_MSSim_RT_profile_shape_skewness_value
-${param_add_a_ions}
+#end if
-${param_add_c_ions}
+#if $param_algorithm_MSSim_RT_profile_shape_skewness_variance:
-${param_add_x_ions}
+-algorithm:MSSim:RT:profile_shape:skewness:variance $param_algorithm_MSSim_RT_profile_shape_skewness_variance
-${param_add_z_ions}
+#end if
--algorithm:MSSim:RawTandemSignal:TandemSim:Simple:y_intensity ${param_y_intensity}
+#if $param_algorithm_MSSim_RT_HPLC_model_file:
--algorithm:MSSim:RawTandemSignal:TandemSim:Simple:b_intensity ${param_b_intensity}
+-algorithm:MSSim:RT:HPLC:model_file     &quot;$param_algorithm_MSSim_RT_HPLC_model_file&quot;
--algorithm:MSSim:RawTandemSignal:TandemSim:Simple:a_intensity ${param_a_intensity}
+#end if
--algorithm:MSSim:RawTandemSignal:TandemSim:Simple:c_intensity ${param_c_intensity}
+#if $param_algorithm_MSSim_RT_CE_pH:
--algorithm:MSSim:RawTandemSignal:TandemSim:Simple:x_intensity ${param_x_intensity}
+-algorithm:MSSim:RT:CE:pH $param_algorithm_MSSim_RT_CE_pH
--algorithm:MSSim:RawTandemSignal:TandemSim:Simple:z_intensity ${param_z_intensity}
+#end if
--algorithm:MSSim:RawTandemSignal:TandemSim:Simple:relative_loss_intensity ${param_relative_loss_intensity}
+#if $param_algorithm_MSSim_RT_CE_alpha:
--algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_intensity ${param_precursor_intensity}
+-algorithm:MSSim:RT:CE:alpha $param_algorithm_MSSim_RT_CE_alpha
--algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_H2O_intensity ${param_precursor_H2O_intensity}
+#end if
--algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_NH3_intensity ${param_precursor_NH3_intensity}
+#if $param_algorithm_MSSim_RT_CE_mu_eo:
-${param_add_isotopes}
+-algorithm:MSSim:RT:CE:mu_eo $param_algorithm_MSSim_RT_CE_mu_eo
--algorithm:MSSim:RawTandemSignal:TandemSim:SVM:max_isotope ${param_max_isotope}
+#end if
-${param_add_metainfo}
+#if $param_algorithm_MSSim_RT_CE_lenght_d:
-${param_add_first_prefix_ion}
+-algorithm:MSSim:RT:CE:lenght_d $param_algorithm_MSSim_RT_CE_lenght_d
-${param_hide_y_ions}
+#end if
-${param_hide_y2_ions}
+#if $param_algorithm_MSSim_RT_CE_length_total:
-${param_hide_b_ions}
+-algorithm:MSSim:RT:CE:length_total $param_algorithm_MSSim_RT_CE_length_total
-${param_hide_b2_ions}
+#end if
-${param_hide_a_ions}
+#if $param_algorithm_MSSim_RT_CE_voltage:
-${param_hide_c_ions}
+-algorithm:MSSim:RT:CE:voltage $param_algorithm_MSSim_RT_CE_voltage
-${param_hide_x_ions}
+#end if
-${param_hide_z_ions}
+#if $param_algorithm_MSSim_Detectability_dt_simulation_on:
-${param_hide_losses}
+-algorithm:MSSim:Detectability:dt_simulation_on
--algorithm:MSSim:RawTandemSignal:TandemSim:SVM:y_intensity ${param_y_intensity}
+#end if
--algorithm:MSSim:RawTandemSignal:TandemSim:SVM:b_intensity ${param_b_intensity}
+#if $param_algorithm_MSSim_Detectability_min_detect:
--algorithm:MSSim:RawTandemSignal:TandemSim:SVM:a_intensity ${param_a_intensity}
+-algorithm:MSSim:Detectability:min_detect $param_algorithm_MSSim_Detectability_min_detect
--algorithm:MSSim:RawTandemSignal:TandemSim:SVM:c_intensity ${param_c_intensity}
+#end if
--algorithm:MSSim:RawTandemSignal:TandemSim:SVM:x_intensity ${param_x_intensity}
+#if $param_algorithm_MSSim_Detectability_dt_model_file:
--algorithm:MSSim:RawTandemSignal:TandemSim:SVM:z_intensity ${param_z_intensity}
+-algorithm:MSSim:Detectability:dt_model_file     &quot;$param_algorithm_MSSim_Detectability_dt_model_file&quot;
--algorithm:MSSim:RawTandemSignal:TandemSim:SVM:relative_loss_intensity ${param_relative_loss_intensity}
+#end if
--algorithm:MSSim:Global:ionization_type ${param_ionization_type}
--algorithm:MSSim:Labeling:type ${param_type}
+#if $rep_param_algorithm_MSSim_Ionization_esi_ionized_residues:
--algorithm:MSSim:Labeling:ICPL:ICPL_fixed_rtshift ${param_ICPL_fixed_rtshift}
+-algorithm:MSSim:Ionization:esi:ionized_residues
-${param_label_proteins}
+#for token in $rep_param_algorithm_MSSim_Ionization_esi_ionized_residues:
--algorithm:MSSim:Labeling:SILAC:fixed_rtshift ${param_fixed_rtshift}
+#if &quot; &quot; in str(token):
--algorithm:MSSim:Labeling:SILAC:medium_channel:modification_lysine ${param_modification_lysine}
+&quot;$token.param_algorithm_MSSim_Ionization_esi_ionized_residues&quot;
--algorithm:MSSim:Labeling:SILAC:medium_channel:modification_arginine ${param_modification_arginine}
+#else
--algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_lysine ${param_modification_lysine}
+$token.param_algorithm_MSSim_Ionization_esi_ionized_residues
--algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_arginine ${param_modification_arginine}
+#end if
--algorithm:MSSim:Labeling:itraq:iTRAQ ${param_iTRAQ}
+#end for
--algorithm:MSSim:Labeling:itraq:reporter_mass_shift ${param_reporter_mass_shift}
+#end if
--algorithm:MSSim:Labeling:itraq:channel_active_4plex ${param_channel_active_4plex}
--algorithm:MSSim:Labeling:itraq:channel_active_8plex ${param_channel_active_8plex}
+#if $rep_param_algorithm_MSSim_Ionization_esi_charge_impurity:
--algorithm:MSSim:Labeling:itraq:Y_contamination ${param_Y_contamination}
+-algorithm:MSSim:Ionization:esi:charge_impurity
--algorithm:MSSim:Labeling:o18:labeling_efficiency ${param_labeling_efficiency}
+#for token in $rep_param_algorithm_MSSim_Ionization_esi_charge_impurity:
--algorithm:RandomNumberGenerators:biological ${param_biological}
+#if &quot; &quot; in str(token):
--algorithm:RandomNumberGenerators:technical ${param_technical}
+&quot;$token.param_algorithm_MSSim_Ionization_esi_charge_impurity&quot;
+#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 $rep_param_algorithm_MSSim_Ionization_maldi_ionization_probabilities:
+#if &quot; &quot; in str(token):
+&quot;$token.param_algorithm_MSSim_Ionization_maldi_ionization_probabilities&quot;
+#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 $param_algorithm_MSSim_RawSignal_peak_shape:
+-algorithm:MSSim:RawSignal:peak_shape
+#if &quot; &quot; in str($param_algorithm_MSSim_RawSignal_peak_shape):
+&quot;$param_algorithm_MSSim_RawSignal_peak_shape&quot;
+#else
+$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 $param_algorithm_MSSim_RawSignal_resolution_type:
+-algorithm:MSSim:RawSignal:resolution:type
+#if &quot; &quot; in str($param_algorithm_MSSim_RawSignal_resolution_type):
+&quot;$param_algorithm_MSSim_RawSignal_resolution_type&quot;
+#else
+$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 $param_algorithm_MSSim_RawSignal_contaminants_file:
+-algorithm:MSSim:RawSignal:contaminants:file     &quot;$param_algorithm_MSSim_RawSignal_contaminants_file&quot;
+#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 $param_algorithm_MSSim_RawTandemSignal_status:
+-algorithm:MSSim:RawTandemSignal:status
+#if &quot; &quot; in str($param_algorithm_MSSim_RawTandemSignal_status):
+&quot;$param_algorithm_MSSim_RawTandemSignal_status&quot;
+#else
+$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 $param_algorithm_MSSim_RawTandemSignal_svm_model_set_file:
+-algorithm:MSSim:RawTandemSignal:svm_model_set_file     &quot;$param_algorithm_MSSim_RawTandemSignal_svm_model_set_file&quot;
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_Precursor_ms2_spectra_per_rt_bin:
+-algorithm:MSSim:RawTandemSignal:Precursor:ms2_spectra_per_rt_bin $param_algorithm_MSSim_RawTandemSignal_Precursor_ms2_spectra_per_rt_bin
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_Precursor_min_mz_peak_distance:
+-algorithm:MSSim:RawTandemSignal:Precursor:min_mz_peak_distance $param_algorithm_MSSim_RawTandemSignal_Precursor_min_mz_peak_distance
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_Precursor_mz_isolation_window:
+-algorithm:MSSim:RawTandemSignal:Precursor:mz_isolation_window $param_algorithm_MSSim_RawTandemSignal_Precursor_mz_isolation_window
+#end if
+#if $param_algorithm_MSSim_RawTandemSignal_Precursor_exclude_overlapping_peaks:
+-algorithm:MSSim:RawTandemSignal:Precursor:exclude_overlapping_peaks
+#end if
+#if $rep_param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter:
+-algorithm:MSSim:RawTandemSignal:Precursor:charge_filter
+#for token in $rep_param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter:
+#if &quot; &quot; in str(token):
+&quot;$token.param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter&quot;
+#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 $param_algorithm_MSSim_Global_ionization_type:
+-algorithm:MSSim:Global:ionization_type
+#if &quot; &quot; in str($param_algorithm_MSSim_Global_ionization_type):
+&quot;$param_algorithm_MSSim_Global_ionization_type&quot;
+#else
+$param_algorithm_MSSim_Global_ionization_type
+#end if
+#end if
+#if $param_algorithm_MSSim_Labeling_type:
+-algorithm:MSSim:Labeling:type
+#if &quot; &quot; in str($param_algorithm_MSSim_Labeling_type):
+&quot;$param_algorithm_MSSim_Labeling_type&quot;
+#else
+$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 $param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_lysine:
+-algorithm:MSSim:Labeling:SILAC:medium_channel:modification_lysine     &quot;$param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_lysine&quot;
+#end if
+#if $param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_arginine:
+-algorithm:MSSim:Labeling:SILAC:medium_channel:modification_arginine     &quot;$param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_arginine&quot;
+#end if
+#if $param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_lysine:
+-algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_lysine     &quot;$param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_lysine&quot;
+#end if
+#if $param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine:
+-algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_arginine     &quot;$param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine&quot;
+#end if
+#if $param_algorithm_MSSim_Labeling_itraq_iTRAQ:
+-algorithm:MSSim:Labeling:itraq:iTRAQ
+#if &quot; &quot; in str($param_algorithm_MSSim_Labeling_itraq_iTRAQ):
+&quot;$param_algorithm_MSSim_Labeling_itraq_iTRAQ&quot;
+#else
+$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 $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_4plex:
+#if &quot; &quot; in str(token):
+&quot;$token.param_algorithm_MSSim_Labeling_itraq_channel_active_4plex&quot;
+#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 $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_8plex:
+#if &quot; &quot; in str(token):
+&quot;$token.param_algorithm_MSSim_Labeling_itraq_channel_active_8plex&quot;
+#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 $param_algorithm_RandomNumberGenerators_biological:
+-algorithm:RandomNumberGenerators:biological
+#if &quot; &quot; in str($param_algorithm_RandomNumberGenerators_biological):
+&quot;$param_algorithm_RandomNumberGenerators_biological&quot;
+#else
+$param_algorithm_RandomNumberGenerators_biological
+#end if
+#end if
+#if $param_algorithm_RandomNumberGenerators_technical:
+-algorithm:RandomNumberGenerators:technical
+#if &quot; &quot; in str($param_algorithm_RandomNumberGenerators_technical):
+&quot;$param_algorithm_RandomNumberGenerators_technical&quot;
+#else
+$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}
+#if $adv_opts.param_force:
--algorithm:MSSim:Labeling:ICPL:ICPL_light_channel_label ${adv_opts.param_ICPL_light_channel_label}
+-force
--algorithm:MSSim:Labeling:ICPL:ICPL_medium_channel_label ${adv_opts.param_ICPL_medium_channel_label}
+#end if
--algorithm:MSSim:Labeling:ICPL:ICPL_heavy_channel_label ${adv_opts.param_ICPL_heavy_channel_label}
+#if $adv_opts.param_algorithm_MSSim_Ionization_esi_max_impurity_set_size:
--algorithm:MSSim:Labeling:itraq:isotope_correction_values_4plex ${adv_opts.param_isotope_correction_values_4plex}
+-algorithm:MSSim:Ionization:esi:max_impurity_set_size $adv_opts.param_algorithm_MSSim_Ionization_esi_max_impurity_set_size
--algorithm:MSSim:Labeling:itraq:isotope_correction_values_8plex ${adv_opts.param_isotope_correction_values_8plex}
+#end if
+#if $adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_light_channel_label:
+-algorithm:MSSim:Labeling:ICPL:ICPL_light_channel_label     &quot;$adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_light_channel_label&quot;
+#end if
+#if $adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_medium_channel_label:
+-algorithm:MSSim:Labeling:ICPL:ICPL_medium_channel_label     &quot;$adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_medium_channel_label&quot;
+#end if
+#if $adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_heavy_channel_label:
+-algorithm:MSSim:Labeling:ICPL:ICPL_heavy_channel_label     &quot;$adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_heavy_channel_label&quot;
+#end if
+#if $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex:
+-algorithm:MSSim:Labeling:itraq:isotope_correction_values_4plex
+#for token in $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex:
+#if &quot; &quot; in str(token):
+&quot;$token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex&quot;
+#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 $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex:
+#if &quot; &quot; in str(token):
+&quot;$token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex&quot;
+#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 format="fasta" help="(-in) " label="Input protein sequences" multiple="true" name="param_in" optional="False" size="30" type="data">
-<param name="param_enzyme" type="select" optional="True" value="Trypsin" label="Enzyme to use for digestion (select 'none' to skip digestion)" help="(-enzyme)">
+<sanitizer>
-<option value="Trypsin">Trypsin</option>
+<valid initial="string.printable">
-<option value="none">none</option>
+<remove value="'"/>
-</param>
+<remove value="&quot;"/>
-<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)">
+</valid>
-<option value="trained">trained</option>
+</sanitizer>
-<option value="naive">naive</option>
+</param>
-</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">
-<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)"/>
+<option value="no cleavage">no cleavage</option>
-<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)"/>
+<option value="V8-E">V8-E</option>
-<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)"/>
+<option value="Trypsin/P">Trypsin/P</option>
-<param name="param_rt_column" type="select" optional="True" value="HPLC" label="Modelling of an RT or CE column" help="(-rt_column)">
+<option value="Lys-C/P">Lys-C/P</option>
-<option value="none">none</option>
+<option value="unspecific cleavage">unspecific cleavage</option>
-<option value="HPLC">HPLC</option>
+<option value="leukocyte elastase">leukocyte elastase</option>
-<option value="CE">CE</option>
+<option value="proline endopeptidase">proline endopeptidase</option>
-</param>
+<option value="V8-DE">V8-DE</option>
-<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)"/>
+<option value="Chymotrypsin">Chymotrypsin</option>
-<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)"/>
+<option value="Asp-N">Asp-N</option>
-<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)"/>
+<option value="2-iodobenzoate">2-iodobenzoate</option>
-<param name="param_min" type="float" min="0.0" optional="True" value="500.0" label="Start of RT Scan Window [s]" help="(-min)"/>
+<option value="Arg-C">Arg-C</option>
-<param name="param_max" type="float" min="1.0" optional="True" value="1500.0" label="End of RT Scan Window [s]" help="(-max)"/>
+<option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-<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)"/>
+<option value="TrypChymo">TrypChymo</option>
-<param name="param_affine_offset" type="integer" value="0" label="Global offset in retention time [s] from predicted model" help="(-affine_offset)"/>
+<option value="Trypsin">Trypsin</option>
-<param name="param_affine_scale" type="integer" value="1" label="Global scaling in retention time from predicted model" help="(-affine_scale)"/>
+<option value="Formic_acid">Formic_acid</option>
-<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 &gt;4." help="(-distortion)"/>
+<option value="CNBr">CNBr</option>
-<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)"/>
+<option value="Asp-N_ambic">Asp-N_ambic</option>
-<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 &gt;= 0)." help="(-variance)"/>
+<option value="PepsinA">PepsinA</option>
-<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)"/>
+<option value="Lys-C">Lys-C</option>
-<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 &gt; 0)." help="(-variance)"/>
+</param>
-<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 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">
-<param name="param_pH" type="float" min="0.0" max="14.0" optional="True" value="3.0" label="pH of buffer" help="(-pH)"/>
+<option value="trained">trained</option>
-<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)"/>
+<option value="naive">naive</option>
-<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>
-<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 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 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 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 name="param_voltage" type="float" min="0.0" optional="True" value="1000.0" label="Voltage applied to capillary" help="(-voltage)"/>
+<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 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 help="(-rt_column) " label="Modelling of an RT or CE column" name="param_algorithm_MSSim_RT_rt_column" optional="True" type="select" value="HPLC">
-<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)"/>
+<option value="none">none</option>
-<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)"/>
+<option value="HPLC">HPLC</option>
-<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="CE">CE</option>
-<option value="Ala">Ala</option>
+</param>
-<option value="Cys">Cys</option>
+<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"/>
-<option value="Asp">Asp</option>
+<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"/>
-<option value="Glu">Glu</option>
+<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"/>
-<option value="Phe">Phe</option>
+<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"/>
-<option value="Gly">Gly</option>
+<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"/>
-<option value="His">His</option>
+<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"/>
-<option value="Ile">Ile</option>
+<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"/>
-<option value="Lys">Lys</option>
+<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"/>
-<option value="Leu">Leu</option>
+<param help="(-distortion) e.g. Orbitrap) distortion should be &gt;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"/>
-<option value="Met">Met</option>
+<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"/>
-<option value="Asn">Asn</option>
+<param help="(-variance) scale parameter for the lorentzian variation of the variance (Note: The scale parameter has to be &gt;= 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"/>
-<option value="Pro">Pro</option>
+<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"/>
-<option value="Gln">Gln</option>
+<param help="(-variance) scale parameter for the lorentzian variation of the time constant (Note: The scale parameter has to be &gt; 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"/>
-<option value="Arg">Arg</option>
+<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">
-<option value="Sec">Sec</option>
+<sanitizer>
-<option value="Ser">Ser</option>
+<valid initial="string.printable">
-<option value="Thr">Thr</option>
+<remove value="'"/>
-<option value="Val">Val</option>
+<remove value="&quot;"/>
-<option value="Trp">Trp</option>
+</valid>
-<option value="Tyr">Tyr</option>
+</sanitizer>
 </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 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 name="param_ionization_probability" type="float" value="0.8" label="Probability for the binomial distribution of the ESI charge states" help="(-ionization_probability)"/>
+<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 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 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 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 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 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 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 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 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 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)">
+<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"/>
-<option value="Gaussian">Gaussian</option>
+<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"/>
-<option value="Lorentzian">Lorentzian</option>
+<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">
-</param>
+<sanitizer>
-<param name="param_value" type="integer" value="50000" label="Instrument resolution at 400 Th." help="(-value)"/>
+<valid initial="string.printable">
-<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)">
+<remove value="'"/>
-<option value="constant">constant</option>
+<remove value="&quot;"/>
-<option value="linear">linear</option>
+</valid>
-<option value="sqrt">sqrt</option>
+</sanitizer>
 </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)"/>
+<repeat max="1" min="0" name="rep_param_algorithm_MSSim_Ionization_esi_ionized_residues" title="param_algorithm_MSSim_Ionization_esi_ionized_residues">
-<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 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">
-<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)"/>
+<option value="Ala">Ala</option>
-<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)"/>
+<option value="Cys">Cys</option>
-<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)"/>
+<option value="Asp">Asp</option>
-<param name="param_error_mean" type="float" value="0.0" label="Average systematic m/z error (Da)" help="(-error_mean)"/>
+<option value="Glu">Glu</option>
-<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)"/>
+<option value="Phe">Phe</option>
-<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)"/>
+<option value="Gly">Gly</option>
-<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)"/>
+<option value="His">His</option>
-<param name="param_intensity-mean" type="float" value="1.0" label="Shot noise intensity mean (exponentially distributed with given mean)." help="(-intensity-mean)"/>
+<option value="Ile">Ile</option>
-<param name="param_mean" type="float" value="0.0" label="Mean value of white noise being added to each measured signal." help="(-mean)"/>
+<option value="Lys">Lys</option>
-<param name="param_stddev" type="float" value="0.0" label="Standard deviation of white noise being added to each measured signal." help="(-stddev)"/>
+<option value="Leu">Leu</option>
-<param name="param_mean" type="float" value="0.0" label="Mean value of the detector noise being added to the complete measurement." help="(-mean)"/>
+<option value="Met">Met</option>
-<param name="param_stddev" type="float" value="0.0" label="Standard deviation of the detector noise being added to the complete measurement." help="(-stddev)"/>
+<option value="Asn">Asn</option>
-<param name="param_status" type="select" optional="True" value="disabled" label="Create Tandem-MS scans?" help="(-status)">
+<option value="Pro">Pro</option>
-<option value="disabled">disabled</option>
+<option value="Gln">Gln</option>
-<option value="precursor">precursor</option>
+<option value="Arg">Arg</option>
-<option value="MS^E">MS^E</option>
+<option value="Sec">Sec</option>
-</param>
+<option value="Ser">Ser</option>
-<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)"/>
+<option value="Thr">Thr</option>
-<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)"/>
+<option value="Val">Val</option>
-<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)"/>
+<option value="Trp">Trp</option>
-<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)"/>
+<option value="Tyr">Tyr</option>
-<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>
-<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)"/>
+</repeat>
-<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)"/>
+<repeat max="1" min="0" name="rep_param_algorithm_MSSim_Ionization_esi_charge_impurity" title="param_algorithm_MSSim_Ionization_esi_charge_impurity">
-<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 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">
-<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)"/>
+<sanitizer>
-<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)"/>
+<valid initial="string.printable">
-<param name="param_min_rt" type="float" min="0.0" optional="True" value="960.0" label="Minimal rt in seconds." help="(-min_rt)"/>
+<remove value="'"/>
-<param name="param_max_rt" type="float" min="0.0" optional="True" value="3840.0" label="Maximal rt in seconds." help="(-max_rt)"/>
+<remove value="&quot;"/>
-<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)"/>
+</valid>
-<param name="param_rt_window_size" type="integer" min="1" optional="True" value="100" label="rt window size in seconds." help="(-rt_window_size)"/>
+</sanitizer>
-<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>
-<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)"/>
+</repeat>
-<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 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"/>
-<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)"/>
+<repeat max="1" min="0" name="rep_param_algorithm_MSSim_Ionization_maldi_ionization_probabilities" title="param_algorithm_MSSim_Ionization_maldi_ionization_probabilities">
-<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 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">
-<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)"/>
+<sanitizer>
-<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)"/>
+<valid initial="string.printable">
-<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)"/>
+<remove value="'"/>
-<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)"/>
+<remove value="&quot;"/>
-<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)"/>
+</valid>
-<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)"/>
+</sanitizer>
-<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>
-<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)"/>
+</repeat>
-<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 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 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 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 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 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 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 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">
-<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)"/>
+<option value="Gaussian">Gaussian</option>
-<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)"/>
+<option value="Lorentzian">Lorentzian</option>
-<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>
-<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 help="(-value) " label="Instrument resolution at 400 Th" name="param_algorithm_MSSim_RawSignal_resolution_value" type="integer" value="50000"/>
-<param name="param_y_intensity" type="float" value="1.0" label="Intensity of the y-ions" help="(-y_intensity)"/>
+<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">
-<param name="param_b_intensity" type="float" value="1.0" label="Intensity of the b-ions" help="(-b_intensity)"/>
+<option value="constant">constant</option>
-<param name="param_a_intensity" type="float" value="1.0" label="Intensity of the a-ions" help="(-a_intensity)"/>
+<option value="linear">linear</option>
-<param name="param_c_intensity" type="float" value="1.0" label="Intensity of the c-ions" help="(-c_intensity)"/>
+<option value="sqrt">sqrt</option>
-<param name="param_x_intensity" type="float" value="1.0" label="Intensity of the x-ions" help="(-x_intensity)"/>
+</param>
-<param name="param_z_intensity" type="float" value="1.0" label="Intensity of the z-ions" help="(-z_intensity)"/>
+<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 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 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 name="param_precursor_intensity" type="float" value="1.0" label="Intensity of the precursor peak" help="(-precursor_intensity)"/>
+<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 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 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">
-<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)"/>
+<sanitizer>
-<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)"/>
+<valid initial="string.printable">
-<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)"/>
+<remove value="'"/>
-<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)"/>
+<remove value="&quot;"/>
-<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)"/>
+</valid>
-<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)"/>
+</sanitizer>
-<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>
-<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 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 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 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 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 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 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 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 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 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 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 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 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 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 name="param_y_intensity" type="float" value="1.0" label="Intensity of the y-ions" help="(-y_intensity)"/>
+<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 name="param_b_intensity" type="float" value="1.0" label="Intensity of the b-ions" help="(-b_intensity)"/>
+<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 name="param_a_intensity" type="float" value="1.0" label="Intensity of the a-ions" help="(-a_intensity)"/>
+<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 name="param_c_intensity" type="float" value="1.0" label="Intensity of the c-ions" help="(-c_intensity)"/>
+<param help="(-status) " label="Create Tandem-MS scans?" name="param_algorithm_MSSim_RawTandemSignal_status" optional="True" type="select" value="disabled">
-<param name="param_x_intensity" type="float" value="1.0" label="Intensity of the x-ions" help="(-x_intensity)"/>
+<option value="disabled">disabled</option>
-<param name="param_z_intensity" type="float" value="1.0" label="Intensity of the z-ions" help="(-z_intensity)"/>
+<option value="precursor">precursor</option>
-<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)"/>
+<option value="MS^E">MS^E</option>
-<param name="param_ionization_type" type="select" optional="True" value="ESI" label="Type of Ionization (MALDI or ESI)" help="(-ionization_type)">
+</param>
-<option value="MALDI">MALDI</option>
+<param help="(-tandem_mode) 0 - fixed intensities, 1 - SVC prediction (abundant/missing), 2 - SVR prediction of peak intensity  &lt;br&gt;" 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"/>
-<option value="ESI">ESI</option>
+<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">
-</param>
+<sanitizer>
-<param name="param_type" type="select" optional="True" value="labelfree" label="Select the labeling type you want for your experiment" help="(-type)">
+<valid initial="string.printable">
-<option value="ICPL">ICPL</option>
+<remove value="'"/>
-<option value="SILAC">SILAC</option>
+<remove value="&quot;"/>
-<option value="itraq">itraq</option>
+</valid>
-<option value="labelfree">labelfree</option>
+</sanitizer>
-<option value="o18">o18</option>
+</param>
-</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 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 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 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 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 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 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"/>
-<param name="param_modification_lysine" type="text" size="20" value="UniMod:481" label="Modification of Lysine in the medium SILAC channel" help="(-modification_lysine)"/>
+<repeat max="1" min="0" name="rep_param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter" title="param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter">
-<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 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">
-<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)"/>
+<sanitizer>
-<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)"/>
+<valid initial="string.printable">
-<param name="param_iTRAQ" type="select" optional="True" value="4plex" label="4plex or 8plex iTRAQ?" help="(-iTRAQ)">
+<remove value="'"/>
-<option value="4plex">4plex</option>
+<remove value="&quot;"/>
-<option value="8plex">8plex</option>
+</valid>
-</param>
+</sanitizer>
-<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>
-<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 &lt;channel&gt;:&lt;name&gt;, e.g. &quot;114:myref&quot;,&quot;115:liver&quot;." help="(-channel_active_4plex)"/>
+</repeat>
-<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 &lt;channel&gt;:&lt;name&gt;, e.g. &quot;113:myref&quot;,&quot;115:liver&quot;,&quot;118:lung&quot;." help="(-channel_active_8plex)"/>
+<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 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 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 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 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 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)">
+<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"/>
-<option value="reproducible">reproducible</option>
+<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"/>
-<option value="random">random</option>
+<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>
+<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 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)">
+<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"/>
-<option value="reproducible">reproducible</option>
+<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"/>
-<option value="random">random</option>
+<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>
+<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"/>
-<expand macro="advanced_options">
+<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 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 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 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 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 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 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 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 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 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: &lt;channel&gt;:&lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ; e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2' " help="(-isotope_correction_values_4plex)"/>
+<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 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: &lt;channel&gt;:&lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ; e.g. '113:0/0.3/4/0' , '116:0.1/0.3/3/0.2' " help="(-isotope_correction_values_8plex)"/>
+<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"/>
-</expand>
+<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"/>
-</inputs>
+<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"/>
-<outputs>
+<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"/>
-<data name="param_out" label="output: simulated MS raw (profile) data" format="mzML"/>
+<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"/>
-<data name="param_out_pm" label="output: ground-truth picked (centroided) MS data" format="mzML"/>
+<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"/>
-<data name="param_out_fm" label="output: ground-truth features" format="featureXML"/>
+<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"/>
-<data name="param_out_cm" label="output: ground-truth features, grouping ESI charge variants of each parent peptide" format="consensusXML"/>
+<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"/>
-<data name="param_out_lcm" label="output: ground-truth features, grouping labeled variants" format="consensusXML"/>
+<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"/>
-<data name="param_out_cntm" label="output: ground-truth features caused by contaminants" format="featureXML"/>
+<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"/>
-<data name="param_out_id" label="output: ground-truth MS2 peptide identifications" format="idXML"/>
+<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"/>
-</outputs>
+<param help="(-y_intensity) " label="Intensity of the y-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_y_intensity" type="float" value="1.0"/>
-<help>**What it does**
+<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"/>
-A highly configurable simulator for mass spectrometry experiments.
+<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="&quot;"/>
+</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="&quot;"/>
+</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="&quot;"/>
+</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="&quot;"/>
+</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. &quot;114:myref&quot;,&quot;115:liver&quot;" label="Four-plex only: Each channel that was used in the experiment and its description (114-117) in format &lt;channel&gt;:&lt;name&gt;," 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="&quot;"/>
+</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. &quot;113:myref&quot;,&quot;115:liver&quot;,&quot;118:lung&quot;" label="Eight-plex only: Each channel that was used in the experiment and its description (113-121) in format &lt;channel&gt;:&lt;name&gt;," 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="&quot;"/>
+</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="&quot;"/>
+</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="&quot;"/>
+</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="&quot;"/>
+</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: &lt;channel&gt;:&lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ;" 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="&quot;"/>
+</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: &lt;channel&gt;:&lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ;" 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="&quot;"/>
+</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
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MSSimulator.html</help>
+</tool>
-@REFERENCES@
-</help>
-</tool>

Mercurial > repos > bgruening > openms

comparison MSSimulator.xml @ 4:6ead64a594bd draft default tip