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view 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 |
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<?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 #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': #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 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> <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</help> </tool>