Mercurial > repos > bgruening > openms
diff PrecursorIonSelector.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 |
line wrap: on
line diff
--- a/PrecursorIonSelector.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/PrecursorIonSelector.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,148 +1,349 @@ -<?xml version='1.0' encoding='UTF-8'?> -<tool id="PrecursorIonSelector" name="PrecursorIonSelector" version="1.12.0"> - <description>PrecursorIonSelector</description> - <macros> - <token name="@EXECUTABLE@">PrecursorIonSelector</token> - <import>macros.xml</import> - </macros> - <expand macro="stdio"/> - <expand macro="requirements"/> - <command>PrecursorIonSelector +<?xml version="1.0" encoding="UTF-8"?> + <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> + <!--Proposed Tool Section: [Targeted Experiments]--> + <tool id="PrecursorIonSelector" name="PrecursorIonSelector" version="2.0.0"> + <description>PrecursorIonSelector</description> + <macros> + <token name="@EXECUTABLE@">PrecursorIonSelector</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>PrecursorIonSelector + +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_next_feat: + -next_feat $param_next_feat +#end if +#if $param_ids: + -ids $param_ids +#end if +#if $param_num_precursors: + -num_precursors $param_num_precursors +#end if +#if $param_raw_data: + -raw_data $param_raw_data +#end if +#if $param_load_preprocessing: + -load_preprocessing +#end if +#if $param_store_preprocessing: + -store_preprocessing +#end if +#if $param_simulation: + -simulation +#end if +#if $param_sim_results: + -sim_results "$param_sim_results" +#end if +#if $param_db_path: + -db_path $param_db_path +#end if +#if $param_rt_model: + -rt_model "$param_rt_model" +#end if +#if $param_dt_model: + -dt_model "$param_dt_model" +#end if --in ${param_in} --out ${param_out} --next_feat ${param_next_feat} --ids ${param_ids} --num_precursors ${param_num_precursors} --raw_data ${param_raw_data} -${param_load_preprocessing} -${param_store_preprocessing} -${param_simulation} --sim_results ${param_sim_results} --db_path ${param_db_path} --rt_model ${param_rt_model} --dt_model ${param_dt_model} --fixed_modifications ${param_fixed_modifications} --threads \${GALAXY_SLOTS:-24} --algorithm:type ${param_type} --algorithm:max_iteration ${param_max_iteration} --algorithm:rt_bin_capacity ${param_rt_bin_capacity} --algorithm:step_size ${param_step_size} --algorithm:peptide_min_prob ${param_peptide_min_prob} -${param_sequential_spectrum_order} --algorithm:MIPFormulation:thresholds:min_protein_probability ${param_min_protein_probability} --algorithm:MIPFormulation:thresholds:min_protein_id_probability ${param_min_protein_id_probability} --algorithm:MIPFormulation:thresholds:min_pt_weight ${param_min_pt_weight} --algorithm:MIPFormulation:thresholds:min_mz ${param_min_mz} --algorithm:MIPFormulation:thresholds:max_mz ${param_max_mz} --algorithm:MIPFormulation:thresholds:min_pred_pep_prob ${param_min_pred_pep_prob} --algorithm:MIPFormulation:thresholds:min_rt_weight ${param_min_rt_weight} -${param_use_peptide_rule} --algorithm:MIPFormulation:thresholds:min_peptide_ids ${param_min_peptide_ids} --algorithm:MIPFormulation:thresholds:min_peptide_probability ${param_min_peptide_probability} --algorithm:MIPFormulation:combined_ilp:k1 ${param_k1} --algorithm:MIPFormulation:combined_ilp:k2 ${param_k2} --algorithm:MIPFormulation:combined_ilp:k3 ${param_k3} -${param_scale_matching_probs} -${param_no_intensity_normalization} --algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature ${param_max_number_precursors_per_feature} --algorithm:Preprocessing:precursor_mass_tolerance ${param_precursor_mass_tolerance} --algorithm:Preprocessing:precursor_mass_tolerance_unit ${param_precursor_mass_tolerance_unit} --algorithm:Preprocessing:preprocessed_db_path ${param_preprocessed_db_path} --algorithm:Preprocessing:preprocessed_db_pred_rt_path ${param_preprocessed_db_pred_rt_path} --algorithm:Preprocessing:preprocessed_db_pred_dt_path ${param_preprocessed_db_pred_dt_path} --algorithm:Preprocessing:max_peptides_per_run ${param_max_peptides_per_run} --algorithm:Preprocessing:missed_cleavages ${param_missed_cleavages} --algorithm:Preprocessing:taxonomy ${param_taxonomy} --algorithm:Preprocessing:tmp_dir ${param_tmp_dir} --algorithm:Preprocessing:store_peptide_sequences ${param_store_peptide_sequences} --algorithm:Preprocessing:rt_settings:min_rt ${param_min_rt} --algorithm:Preprocessing:rt_settings:max_rt ${param_max_rt} --algorithm:Preprocessing:rt_settings:rt_step_size ${param_rt_step_size} --algorithm:Preprocessing:rt_settings:gauss_mean ${param_gauss_mean} --algorithm:Preprocessing:rt_settings:gauss_sigma ${param_gauss_sigma} +#if $rep_param_fixed_modifications: +-fixed_modifications + #for token in $rep_param_fixed_modifications: + #if " " in str(token): + "$token.param_fixed_modifications" + #else + $token.param_fixed_modifications + #end if + #end for +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_type: + -algorithm:type + #if " " in str($param_algorithm_type): + "$param_algorithm_type" + #else + $param_algorithm_type + #end if +#end if +#if $param_algorithm_max_iteration: + -algorithm:max_iteration $param_algorithm_max_iteration +#end if +#if $param_algorithm_rt_bin_capacity: + -algorithm:rt_bin_capacity $param_algorithm_rt_bin_capacity +#end if +#if $param_algorithm_step_size: + -algorithm:step_size $param_algorithm_step_size +#end if +#if $param_algorithm_peptide_min_prob: + -algorithm:peptide_min_prob $param_algorithm_peptide_min_prob +#end if +#if $param_algorithm_sequential_spectrum_order: + -algorithm:sequential_spectrum_order +#end if +#if $param_algorithm_MIPFormulation_thresholds_min_protein_probability: + -algorithm:MIPFormulation:thresholds:min_protein_probability $param_algorithm_MIPFormulation_thresholds_min_protein_probability +#end if +#if $param_algorithm_MIPFormulation_thresholds_min_protein_id_probability: + -algorithm:MIPFormulation:thresholds:min_protein_id_probability $param_algorithm_MIPFormulation_thresholds_min_protein_id_probability +#end if +#if $param_algorithm_MIPFormulation_thresholds_min_pt_weight: + -algorithm:MIPFormulation:thresholds:min_pt_weight $param_algorithm_MIPFormulation_thresholds_min_pt_weight +#end if +#if $param_algorithm_MIPFormulation_thresholds_min_mz: + -algorithm:MIPFormulation:thresholds:min_mz $param_algorithm_MIPFormulation_thresholds_min_mz +#end if +#if $param_algorithm_MIPFormulation_thresholds_max_mz: + -algorithm:MIPFormulation:thresholds:max_mz $param_algorithm_MIPFormulation_thresholds_max_mz +#end if +#if $param_algorithm_MIPFormulation_thresholds_min_pred_pep_prob: + -algorithm:MIPFormulation:thresholds:min_pred_pep_prob $param_algorithm_MIPFormulation_thresholds_min_pred_pep_prob +#end if +#if $param_algorithm_MIPFormulation_thresholds_min_rt_weight: + -algorithm:MIPFormulation:thresholds:min_rt_weight $param_algorithm_MIPFormulation_thresholds_min_rt_weight +#end if +#if $param_algorithm_MIPFormulation_thresholds_use_peptide_rule: + -algorithm:MIPFormulation:thresholds:use_peptide_rule +#end if +#if $param_algorithm_MIPFormulation_thresholds_min_peptide_ids: + -algorithm:MIPFormulation:thresholds:min_peptide_ids $param_algorithm_MIPFormulation_thresholds_min_peptide_ids +#end if +#if $param_algorithm_MIPFormulation_thresholds_min_peptide_probability: + -algorithm:MIPFormulation:thresholds:min_peptide_probability $param_algorithm_MIPFormulation_thresholds_min_peptide_probability +#end if +#if $param_algorithm_MIPFormulation_combined_ilp_k1: + -algorithm:MIPFormulation:combined_ilp:k1 $param_algorithm_MIPFormulation_combined_ilp_k1 +#end if +#if $param_algorithm_MIPFormulation_combined_ilp_k2: + -algorithm:MIPFormulation:combined_ilp:k2 $param_algorithm_MIPFormulation_combined_ilp_k2 +#end if +#if $param_algorithm_MIPFormulation_combined_ilp_k3: + -algorithm:MIPFormulation:combined_ilp:k3 $param_algorithm_MIPFormulation_combined_ilp_k3 +#end if +#if $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs: + -algorithm:MIPFormulation:combined_ilp:scale_matching_probs +#end if +#if $param_algorithm_MIPFormulation_feature_based_no_intensity_normalization: + -algorithm:MIPFormulation:feature_based:no_intensity_normalization +#end if +#if $param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature: + -algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature $param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature +#end if +#if $param_algorithm_Preprocessing_precursor_mass_tolerance: + -algorithm:Preprocessing:precursor_mass_tolerance $param_algorithm_Preprocessing_precursor_mass_tolerance +#end if +#if $param_algorithm_Preprocessing_precursor_mass_tolerance_unit: + -algorithm:Preprocessing:precursor_mass_tolerance_unit + #if " " in str($param_algorithm_Preprocessing_precursor_mass_tolerance_unit): + "$param_algorithm_Preprocessing_precursor_mass_tolerance_unit" + #else + $param_algorithm_Preprocessing_precursor_mass_tolerance_unit + #end if +#end if +#if $param_algorithm_Preprocessing_preprocessed_db_path: + -algorithm:Preprocessing:preprocessed_db_path "$param_algorithm_Preprocessing_preprocessed_db_path" +#end if +#if $param_algorithm_Preprocessing_preprocessed_db_pred_rt_path: + -algorithm:Preprocessing:preprocessed_db_pred_rt_path "$param_algorithm_Preprocessing_preprocessed_db_pred_rt_path" +#end if +#if $param_algorithm_Preprocessing_preprocessed_db_pred_dt_path: + -algorithm:Preprocessing:preprocessed_db_pred_dt_path "$param_algorithm_Preprocessing_preprocessed_db_pred_dt_path" +#end if +#if $param_algorithm_Preprocessing_max_peptides_per_run: + -algorithm:Preprocessing:max_peptides_per_run $param_algorithm_Preprocessing_max_peptides_per_run +#end if +#if $param_algorithm_Preprocessing_missed_cleavages: + -algorithm:Preprocessing:missed_cleavages $param_algorithm_Preprocessing_missed_cleavages +#end if +#if $param_algorithm_Preprocessing_taxonomy: + -algorithm:Preprocessing:taxonomy "$param_algorithm_Preprocessing_taxonomy" +#end if +#if $param_algorithm_Preprocessing_tmp_dir: + -algorithm:Preprocessing:tmp_dir "$param_algorithm_Preprocessing_tmp_dir" +#end if +#if $param_algorithm_Preprocessing_store_peptide_sequences: + -algorithm:Preprocessing:store_peptide_sequences "$param_algorithm_Preprocessing_store_peptide_sequences" +#end if +#if $param_algorithm_Preprocessing_rt_settings_min_rt: + -algorithm:Preprocessing:rt_settings:min_rt $param_algorithm_Preprocessing_rt_settings_min_rt +#end if +#if $param_algorithm_Preprocessing_rt_settings_max_rt: + -algorithm:Preprocessing:rt_settings:max_rt $param_algorithm_Preprocessing_rt_settings_max_rt +#end if +#if $param_algorithm_Preprocessing_rt_settings_rt_step_size: + -algorithm:Preprocessing:rt_settings:rt_step_size $param_algorithm_Preprocessing_rt_settings_rt_step_size +#end if +#if $param_algorithm_Preprocessing_rt_settings_gauss_mean: + -algorithm:Preprocessing:rt_settings:gauss_mean $param_algorithm_Preprocessing_rt_settings_gauss_mean +#end if +#if $param_algorithm_Preprocessing_rt_settings_gauss_sigma: + -algorithm:Preprocessing:rt_settings:gauss_sigma $param_algorithm_Preprocessing_rt_settings_gauss_sigma +#end if #if $adv_opts.adv_opts_selector=='advanced': - -solver ${adv_opts.param_solver} + #if $adv_opts.param_solver: + -solver + #if " " in str($adv_opts.param_solver): + "$adv_opts.param_solver" + #else + $adv_opts.param_solver + #end if +#end if + #if $adv_opts.param_force: + -force +#end if #end if </command> - <inputs> - <param name="param_in" type="data" format="featureXML" optional="False" label="Input feature map file (featureXML)" help="(-in)"/> - <param name="param_ids" type="text" size="20" label="file containing results of identification (idXML)" help="(-ids)"/> - <param name="param_num_precursors" type="integer" value="1" label="number of precursors to be selected" help="(-num_precursors)"/> - <param name="param_raw_data" type="data" format="mzML" optional="True" label="Input profile data." help="(-raw_data)"/> - <param name="param_load_preprocessing" type="boolean" truevalue="-load_preprocessing true" falsevalue="-load_preprocessing false" checked="false" optional="True" label="The preprocessed db is loaded from file, not calculated." help="(-load_preprocessing)"/> - <param name="param_store_preprocessing" type="boolean" truevalue="-store_preprocessing true" falsevalue="-store_preprocessing false" checked="false" optional="True" label="The preprocessed db is stored." help="(-store_preprocessing)"/> - <param name="param_simulation" type="boolean" truevalue="-simulation true" falsevalue="-simulation false" checked="false" optional="True" label="Simulate the whole LC-MS/MS run." help="(-simulation)"/> - <param name="param_sim_results" type="text" size="20" label="File containing the results of the simulation run" help="(-sim_results)"/> - <param name="param_db_path" type="data" format="fasta" optional="True" label="db file" help="(-db_path)"/> - <param name="param_rt_model" type="text" size="20" label="SVM Model for RTPredict" help="(-rt_model)"/> - <param name="param_dt_model" type="text" size="20" label="SVM Model for PTPredict" help="(-dt_model)"/> - <param name="param_fixed_modifications" type="text" size="20" label="the modifications i.e. Carboxymethyl (C)" help="(-fixed_modifications)"/> - <param name="param_type" type="select" optional="True" value="IPS" label="Strategy for precursor ion selection." help="(-type)"> - <option value="ILP_IPS">ILP_IPS</option> - <option value="IPS">IPS</option> - <option value="SPS">SPS</option> - <option value="Upshift">Upshift</option> - <option value="Downshift">Downshift</option> - <option value="DEX">DEX</option> - </param> - <param name="param_max_iteration" type="integer" min="1" optional="True" value="100" label="Maximal number of iterations." help="(-max_iteration)"/> - <param name="param_rt_bin_capacity" type="integer" min="1" optional="True" value="10" label="Maximal number of precursors per rt bin." help="(-rt_bin_capacity)"/> - <param name="param_step_size" type="integer" min="1" optional="True" value="1" label="Maximal number of precursors per iteration." help="(-step_size)"/> - <param name="param_peptide_min_prob" type="float" value="0.2" label="Minimal peptide probability." help="(-peptide_min_prob)"/> - <param name="param_sequential_spectrum_order" type="boolean" truevalue="-algorithm:sequential_spectrum_order true" falsevalue="-algorithm:sequential_spectrum_order false" checked="false" optional="True" label="If true, precursors are selected sequentially with respect to their RT." help="(-sequential_spectrum_order)"/> - <param name="param_min_protein_probability" type="float" min="0.0" max="1.0" optional="True" value="0.2" label="Minimal protein probability for a protein to be considered in the ILP" help="(-min_protein_probability)"/> - <param name="param_min_protein_id_probability" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="Minimal protein probability for a protein to be considered identified." help="(-min_protein_id_probability)"/> - <param name="param_min_pt_weight" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal pt weight of a precursor" help="(-min_pt_weight)"/> - <param name="param_min_mz" type="float" min="0.0" optional="True" value="500.0" label="Minimal mz to be considered in protein based LP formulation." help="(-min_mz)"/> - <param name="param_max_mz" type="float" min="0.0" optional="True" value="5000.0" label="Minimal mz to be considered in protein based LP formulation." help="(-max_mz)"/> - <param name="param_min_pred_pep_prob" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal predicted peptide probability of a precursor" help="(-min_pred_pep_prob)"/> - <param name="param_min_rt_weight" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal rt weight of a precursor" help="(-min_rt_weight)"/> - <param name="param_use_peptide_rule" type="boolean" truevalue="-algorithm:MIPFormulation:thresholds:use_peptide_rule true" falsevalue="-algorithm:MIPFormulation:thresholds:use_peptide_rule false" checked="false" optional="True" label="Use peptide rule instead of minimal protein id probability" help="(-use_peptide_rule)"/> - <param name="param_min_peptide_ids" type="integer" min="1" optional="True" value="2" label="If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id" help="(-min_peptide_ids)"/> - <param name="param_min_peptide_probability" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified" help="(-min_peptide_probability)"/> - <param name="param_k1" type="float" min="0.0" optional="True" value="0.2" label="combined ilp: weight for z_i" help="(-k1)"/> - <param name="param_k2" type="float" min="0.0" optional="True" value="0.2" label="combined ilp: weight for x_j,s*int_j,s" help="(-k2)"/> - <param name="param_k3" type="float" min="0.0" optional="True" value="0.4" label="combined ilp: weight for -x_j,s*w_j,s" help="(-k3)"/> - <param name="param_scale_matching_probs" type="boolean" truevalue="-algorithm:MIPFormulation:combined_ilp:scale_matching_probs true" falsevalue="-algorithm:MIPFormulation:combined_ilp:scale_matching_probs false" checked="true" optional="True" label="flag if detectability * rt_weight shall be scaled to cover all [0,1]" help="(-scale_matching_probs)"/> - <param name="param_no_intensity_normalization" type="boolean" truevalue="-algorithm:MIPFormulation:feature_based:no_intensity_normalization true" falsevalue="-algorithm:MIPFormulation:feature_based:no_intensity_normalization false" checked="false" optional="True" label="Flag indicating if intensities shall be scaled to be in [0,1]. This is done for each feature separately, so that the feature's maximal intensity in a spectrum is set to 1." help="(-no_intensity_normalization)"/> - <param name="param_max_number_precursors_per_feature" type="integer" min="1" optional="True" value="1" label="The maximal number of precursors per feature." help="(-max_number_precursors_per_feature)"/> - <param name="param_precursor_mass_tolerance" type="float" min="0.0" optional="True" value="10.0" label="Precursor mass tolerance which is used to query the peptide database for peptides" help="(-precursor_mass_tolerance)"/> - <param name="param_precursor_mass_tolerance_unit" type="select" optional="True" value="ppm" label="Precursor mass tolerance unit." help="(-precursor_mass_tolerance_unit)"> - <option value="ppm">ppm</option> - <option value="Da">Da</option> - </param> - <param name="param_preprocessed_db_path" type="text" size="20" label="Path where the preprocessed database should be stored" help="(-preprocessed_db_path)"/> - <param name="param_preprocessed_db_pred_rt_path" type="text" size="20" label="Path where the predicted rts of the preprocessed database should be stored" help="(-preprocessed_db_pred_rt_path)"/> - <param name="param_preprocessed_db_pred_dt_path" type="text" size="20" label="Path where the predicted rts of the preprocessed database should be stored" help="(-preprocessed_db_pred_dt_path)"/> - <param name="param_max_peptides_per_run" type="integer" min="1" optional="True" value="100000" label="Number of peptides for that the pt and rt are parallely predicted." help="(-max_peptides_per_run)"/> - <param name="param_missed_cleavages" type="integer" min="0" optional="True" value="1" label="Number of allowed missed cleavages." help="(-missed_cleavages)"/> - <param name="param_taxonomy" type="text" size="20" label="Taxonomy" help="(-taxonomy)"/> - <param name="param_tmp_dir" type="text" size="20" label="Absolute path to tmp data directory used to store files needed for rt and dt prediction." help="(-tmp_dir)"/> - <param name="param_store_peptide_sequences" type="text" size="20" value="false" label="Flag if peptide sequences should be stored." help="(-store_peptide_sequences)"/> - <param name="param_min_rt" type="float" min="1.0" optional="True" value="960.0" label="Minimal RT in the experiment (in seconds)" help="(-min_rt)"/> - <param name="param_max_rt" type="float" value="3840.0" label="Maximal RT in the experiment (in seconds)" help="(-max_rt)"/> - <param name="param_rt_step_size" type="float" value="30.0" label="Time between two consecutive spectra (in seconds)" help="(-rt_step_size)"/> - <param name="param_gauss_mean" type="float" value="-1.0" label="mean of the gauss curve" help="(-gauss_mean)"/> - <param name="param_gauss_sigma" type="float" value="3.0" label="std of the gauss curve" help="(-gauss_sigma)"/> - <expand macro="advanced_options"> - <param name="param_solver" type="select" optional="True" value="GLPK" label="LP solver type" help="(-solver)"> - <option value="GLPK">GLPK</option> - <option value="COINOR">COINOR</option> + <inputs> + <param format="xml" help="(-in) " label="Input feature map file (featureXML)" name="param_in" optional="False" type="data"/> + <param format="xml" help="(-ids) " label="file containing results of identification" name="param_ids" optional="False" type="data"/> + <param help="(-num_precursors) " label="number of precursors to be selected" name="param_num_precursors" type="integer" value="1"/> + <param format="mzml" help="(-raw_data) " label="Input profile data" name="param_raw_data" optional="True" type="data"/> + <param checked="false" falsevalue="" help="(-load_preprocessing) " label="The preprocessed db is loaded from file, not calculated" name="param_load_preprocessing" optional="True" truevalue="-load_preprocessing" type="boolean"/> + <param checked="false" falsevalue="" help="(-store_preprocessing) " label="The preprocessed db is stored" name="param_store_preprocessing" optional="True" truevalue="-store_preprocessing" type="boolean"/> + <param checked="false" falsevalue="" help="(-simulation) " label="Simulate the whole LC-MS/MS run" name="param_simulation" optional="True" truevalue="-simulation" type="boolean"/> + <param help="(-sim_results) " label="File containing the results of the simulation run" name="param_sim_results" size="30" type="text"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param format="fasta" help="(-db_path) " label="db file" name="param_db_path" optional="True" type="data"/> + <param help="(-rt_model) " label="SVM Model for RTPredict" name="param_rt_model" size="30" type="text"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param help="(-dt_model) " label="SVM Model for PTPredict" name="param_dt_model" size="30" type="text"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <repeat min="0" name="rep_param_fixed_modifications" title="param_fixed_modifications"> + <param help="(-fixed_modifications) " label="the modifications i.e. Carboxymethyl (C)" name="param_fixed_modifications" size="30" type="text"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <param help="(-type) " label="Strategy for precursor ion selection" name="param_algorithm_type" optional="True" type="select" value="IPS"> + <option value="ILP_IPS">ILP_IPS</option> + <option value="IPS">IPS</option> + <option value="SPS">SPS</option> + <option value="Upshift">Upshift</option> + <option value="Downshift">Downshift</option> + <option value="DEX">DEX</option> </param> - </expand> - </inputs> - <outputs> - <data name="param_out" label="modified feature map" format="featureXML"/> - <data name="param_next_feat" label="feature map (featureXML) file with the selected precursors" format="featureXML"/> - </outputs> - <help>**What it does** - -PrecursorIonSelector + <param help="(-max_iteration) " label="Maximal number of iterations" min="1" name="param_algorithm_max_iteration" optional="True" type="integer" value="100"/> + <param help="(-rt_bin_capacity) " label="Maximal number of precursors per rt bin" min="1" name="param_algorithm_rt_bin_capacity" optional="True" type="integer" value="10"/> + <param help="(-step_size) " label="Maximal number of precursors per iteration" min="1" name="param_algorithm_step_size" optional="True" type="integer" value="1"/> + <param help="(-peptide_min_prob) " label="Minimal peptide probability" name="param_algorithm_peptide_min_prob" type="float" value="0.2"/> + <param checked="false" falsevalue="" help="(-sequential_spectrum_order) " label="If true, precursors are selected sequentially with respect to their RT" name="param_algorithm_sequential_spectrum_order" optional="True" truevalue="-algorithm:sequential_spectrum_order" type="boolean"/> + <param help="(-min_protein_probability) " label="Minimal protein probability for a protein to be considered in the ILP" max="1.0" min="0.0" name="param_algorithm_MIPFormulation_thresholds_min_protein_probability" optional="True" type="float" value="0.2"/> + <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_MIPFormulation_thresholds_min_protein_id_probability" optional="True" type="float" value="0.95"/> + <param help="(-min_pt_weight) " label="Minimal pt weight of a precurso" max="1.0" min="0.0" name="param_algorithm_MIPFormulation_thresholds_min_pt_weight" optional="True" type="float" value="0.5"/> + <param help="(-min_mz) " label="Minimal mz to be considered in protein based LP formulation" min="0.0" name="param_algorithm_MIPFormulation_thresholds_min_mz" optional="True" type="float" value="500.0"/> + <param help="(-max_mz) " label="Minimal mz to be considered in protein based LP formulation" min="0.0" name="param_algorithm_MIPFormulation_thresholds_max_mz" optional="True" type="float" value="5000.0"/> + <param help="(-min_pred_pep_prob) " label="Minimal predicted peptide probability of a precurso" max="1.0" min="0.0" name="param_algorithm_MIPFormulation_thresholds_min_pred_pep_prob" optional="True" type="float" value="0.5"/> + <param help="(-min_rt_weight) " label="Minimal rt weight of a precurso" max="1.0" min="0.0" name="param_algorithm_MIPFormulation_thresholds_min_rt_weight" optional="True" type="float" value="0.5"/> + <param checked="false" falsevalue="" help="(-use_peptide_rule) " label="Use peptide rule instead of minimal protein id probability" name="param_algorithm_MIPFormulation_thresholds_use_peptide_rule" optional="True" truevalue="-algorithm:MIPFormulation:thresholds:use_peptide_rule" type="boolean"/> + <param help="(-min_peptide_ids) " label="If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id" min="1" name="param_algorithm_MIPFormulation_thresholds_min_peptide_ids" optional="True" type="integer" value="2"/> + <param help="(-min_peptide_probability) " label="If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified" max="1.0" min="0.0" name="param_algorithm_MIPFormulation_thresholds_min_peptide_probability" optional="True" type="float" value="0.95"/> + <param help="(-k1) " label="combined ilp: weight for z_i" min="0.0" name="param_algorithm_MIPFormulation_combined_ilp_k1" optional="True" type="float" value="0.2"/> + <param help="(-k2) " label="combined ilp: weight for x_j,s*int_j,s" min="0.0" name="param_algorithm_MIPFormulation_combined_ilp_k2" optional="True" type="float" value="0.2"/> + <param help="(-k3) " label="combined ilp: weight for -x_j,s*w_j,s" min="0.0" name="param_algorithm_MIPFormulation_combined_ilp_k3" optional="True" type="float" value="0.4"/> + <param checked="true" falsevalue="" help="(-scale_matching_probs) " label="flag if detectability * rt_weight shall be scaled to cover all [0,1]" name="param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs" optional="True" truevalue="-algorithm:MIPFormulation:combined_ilp:scale_matching_probs" type="boolean"/> + <param checked="false" falsevalue="" help="(-no_intensity_normalization) This is done for each feature separately, so that the feature's maximal intensity in a spectrum is set to 1" label="Flag indicating if intensities shall be scaled to be in [0,1]" name="param_algorithm_MIPFormulation_feature_based_no_intensity_normalization" optional="True" truevalue="-algorithm:MIPFormulation:feature_based:no_intensity_normalization" type="boolean"/> + <param help="(-max_number_precursors_per_feature) " label="The maximal number of precursors per feature" min="1" name="param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature" optional="True" type="integer" value="1"/> + <param help="(-precursor_mass_tolerance) " label="Precursor mass tolerance which is used to query the peptide database for peptides" min="0.0" name="param_algorithm_Preprocessing_precursor_mass_tolerance" optional="True" type="float" value="10.0"/> + <param help="(-precursor_mass_tolerance_unit) " label="Precursor mass tolerance unit" name="param_algorithm_Preprocessing_precursor_mass_tolerance_unit" optional="True" type="select" value="ppm"> + <option value="ppm">ppm</option> + <option value="Da">Da</option> + </param> + <param help="(-preprocessed_db_path) " label="Path where the preprocessed database should be stored" name="param_algorithm_Preprocessing_preprocessed_db_path" size="30" type="text"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param help="(-preprocessed_db_pred_rt_path) " label="Path where the predicted rts of the preprocessed database should be stored" name="param_algorithm_Preprocessing_preprocessed_db_pred_rt_path" size="30" type="text"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param help="(-preprocessed_db_pred_dt_path) " label="Path where the predicted rts of the preprocessed database should be stored" name="param_algorithm_Preprocessing_preprocessed_db_pred_dt_path" size="30" type="text"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param help="(-max_peptides_per_run) " label="Number of peptides for that the pt and rt are parallely predicted" min="1" name="param_algorithm_Preprocessing_max_peptides_per_run" optional="True" type="integer" value="100000"/> + <param help="(-missed_cleavages) " label="Number of allowed missed cleavages" min="0" name="param_algorithm_Preprocessing_missed_cleavages" optional="True" type="integer" value="1"/> + <param help="(-taxonomy) " label="Taxonomy" name="param_algorithm_Preprocessing_taxonomy" size="30" type="text"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param help="(-tmp_dir) " label="Absolute path to tmp data directory used to store files needed for rt and dt prediction" name="param_algorithm_Preprocessing_tmp_dir" size="30" type="text"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param help="(-store_peptide_sequences) " label="Flag if peptide sequences should be stored" name="param_algorithm_Preprocessing_store_peptide_sequences" size="30" type="text" value="false"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param help="(-min_rt) " label="Minimal RT in the experiment (in seconds)" min="1.0" name="param_algorithm_Preprocessing_rt_settings_min_rt" optional="True" type="float" value="960.0"/> + <param help="(-max_rt) " label="Maximal RT in the experiment (in seconds)" name="param_algorithm_Preprocessing_rt_settings_max_rt" type="float" value="3840.0"/> + <param help="(-rt_step_size) " label="Time between two consecutive spectra (in seconds)" name="param_algorithm_Preprocessing_rt_settings_rt_step_size" type="float" value="30.0"/> + <param help="(-gauss_mean) " label="mean of the gauss curve" name="param_algorithm_Preprocessing_rt_settings_gauss_mean" type="float" value="-1.0"/> + <param help="(-gauss_sigma) " label="std of the gauss curve" name="param_algorithm_Preprocessing_rt_settings_gauss_sigma" type="float" value="3.0"/> + <expand macro="advanced_options"> + <param help="(-solver) " label="LP solver type" name="param_solver" optional="True" type="select" value="GLPK"> + <option value="GLPK">GLPK</option> + <option value="COINOR">COINOR</option> + </param> + <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/> + </expand> + </inputs> + <outputs> + <data format="xml" name="param_out"/> + <data format="xml" name="param_next_feat"/> + </outputs> + <help>PrecursorIonSelector -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PrecursorIonSelector.html - -@REFERENCES@ -</help> -</tool> +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PrecursorIonSelector.html</help> + </tool>