Mercurial > repos > galaxyp > openms_precursorionselector
diff PrecursorIonSelector.xml @ 9:faac17171cc2 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
| author | galaxyp |
|---|---|
| date | Thu, 03 Sep 2020 16:17:23 +0000 |
| parents | de49246e559a |
| children | fa7a58de2977 |
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--- a/PrecursorIonSelector.xml Fri May 17 10:00:07 2019 -0400 +++ b/PrecursorIonSelector.xml Thu Sep 03 16:17:23 2020 +0000 @@ -1,356 +1,239 @@ <?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 CTDConverter.--> <!--Proposed Tool Section: [Targeted Experiments]--> -<tool id="PrecursorIonSelector" name="PrecursorIonSelector" version="2.3.0"> +<tool id="PrecursorIonSelector" name="PrecursorIonSelector" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>PrecursorIonSelector</description> <macros> <token name="@EXECUTABLE@">PrecursorIonSelector</token> <import>macros.xml</import> + <import>macros_autotest.xml</import> + <import>macros_test.xml</import> </macros> - <expand macro="references"/> - <expand macro="stdio"/> <expand macro="requirements"/> - <command detect_errors="aggressive"><![CDATA[PrecursorIonSelector + <expand macro="stdio"/> + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re -#if $param_in: - -in $param_in +## Preprocessing +mkdir in && +ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + mkdir out && +#end if +#if "next_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + mkdir next_feat && #end if -#if $param_out: - -out $param_out +mkdir ids && +ln -s '$ids' 'ids/${re.sub("[^\w\-_]", "_", $ids.element_identifier)}.$gxy2omsext($ids.ext)' && +#if $raw_data: + mkdir raw_data && + ln -s '$raw_data' 'raw_data/${re.sub("[^\w\-_]", "_", $raw_data.element_identifier)}.$gxy2omsext($raw_data.ext)' && #end if -#if $param_next_feat: - -next_feat $param_next_feat +#if "sim_results_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + mkdir sim_results && #end if -#if $param_ids: - -ids $param_ids +#if $db_path: + mkdir db_path && + ln -s '$db_path' 'db_path/${re.sub("[^\w\-_]", "_", $db_path.element_identifier)}.$gxy2omsext($db_path.ext)' && #end if -#if $param_num_precursors: - -num_precursors $param_num_precursors +#if $rt_model: + mkdir rt_model && + ln -s '$rt_model' 'rt_model/${re.sub("[^\w\-_]", "_", $rt_model.element_identifier)}.$gxy2omsext($rt_model.ext)' && +#end if +#if $dt_model: + mkdir dt_model && + ln -s '$dt_model' 'dt_model/${re.sub("[^\w\-_]", "_", $dt_model.element_identifier)}.$gxy2omsext($dt_model.ext)' && #end if -#if $param_raw_data: - -raw_data $param_raw_data -#end if -#if $param_load_preprocessing: - -load_preprocessing + +## Main program call + +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && +@EXECUTABLE@ -ini @EXECUTABLE@.ctd +-in +'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' +#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + -out + 'out/output.${gxy2omsext("featurexml")}' #end if -#if $param_store_preprocessing: - -store_preprocessing -#end if -#if $param_simulation: - -simulation +#if "next_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + -next_feat + 'next_feat/output.${gxy2omsext("featurexml")}' #end if -#if $param_sim_results: - -sim_results "$param_sim_results" +-ids +'ids/${re.sub("[^\w\-_]", "_", $ids.element_identifier)}.$gxy2omsext($ids.ext)' +#if $raw_data: + -raw_data + 'raw_data/${re.sub("[^\w\-_]", "_", $raw_data.element_identifier)}.$gxy2omsext($raw_data.ext)' #end if -#if $param_db_path: - -db_path $param_db_path +#if "sim_results_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + -sim_results + 'sim_results/output.${gxy2omsext("txt")}' #end if -#if $param_rt_model: - -rt_model "$param_rt_model" +#if $db_path: + -db_path + 'db_path/${re.sub("[^\w\-_]", "_", $db_path.element_identifier)}.$gxy2omsext($db_path.ext)' #end if -#if $param_dt_model: - -dt_model "$param_dt_model" +#if $rt_model: + -rt_model + 'rt_model/${re.sub("[^\w\-_]", "_", $rt_model.element_identifier)}.$gxy2omsext($rt_model.ext)' +#end if +#if $dt_model: + -dt_model + 'dt_model/${re.sub("[^\w\-_]", "_", $dt_model.element_identifier)}.$gxy2omsext($dt_model.ext)' +#end if +#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 + | tee '$stdout' #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 -#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 $param_algorithm_MIPFormulation_combined_ilp_k1 +## Postprocessing +#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + && mv 'out/output.${gxy2omsext("featurexml")}' '$out' #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 $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs: - -algorithm:MIPFormulation:combined_ilp:scale_matching_probs - #if " " in str($param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs): - "$param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs" - #else - $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs - #end if -#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" +#if "next_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + && mv 'next_feat/output.${gxy2omsext("featurexml")}' '$next_feat' #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 $param_algorithm_Preprocessing_rt_settings_gauss_sigma +#if "sim_results_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + && mv 'sim_results/output.${gxy2omsext("txt")}' '$sim_results' #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> +#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS + && mv '@EXECUTABLE@.ctd' '$ctd_out' +#end if]]></command> + <configfiles> + <inputs name="args_json" data_style="paths"/> + <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> + </configfiles> <inputs> - <param name="param_in" type="data" format="featurexml" optional="False" label="Input feature map file (featureXML)" help="(-in) "/> - <param name="param_ids" type="data" format="idxml" optional="False" label="file containing results of identification" 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" display="radio" type="boolean" truevalue="-load_preprocessing" falsevalue="" checked="false" optional="True" label="The preprocessed db is loaded from file, not calculated" help="(-load_preprocessing) "/> - <param name="param_store_preprocessing" display="radio" type="boolean" truevalue="-store_preprocessing" falsevalue="" checked="false" optional="True" label="The preprocessed db is stored" help="(-store_preprocessing) "/> - <param name="param_simulation" display="radio" type="boolean" truevalue="-simulation" falsevalue="" checked="false" optional="True" label="Simulate the whole LC-MS/MS run" help="(-simulation) "/> - <param name="param_sim_results" type="text" size="30" label="File containing the results of the simulation run" help="(-sim_results) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <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="30" label="SVM Model for RTPredict" help="(-rt_model) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_dt_model" type="text" size="30" label="SVM Model for PTPredict" help="(-dt_model) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <repeat name="rep_param_fixed_modifications" min="0" title="param_fixed_modifications"> - <param name="param_fixed_modifications" type="text" size="30" label="the modifications i.e. Carboxymethyl (C)" help="(-fixed_modifications) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - </repeat> - <param name="param_algorithm_type" type="select" optional="False" value="IPS" label="Strategy for precursor ion selection" help="(-type) "> - <option value="ILP_IPS">ILP_IPS</option> - <option value="IPS" selected="true">IPS</option> - <option value="SPS">SPS</option> - <option value="Upshift">Upshift</option> - <option value="Downshift">Downshift</option> - <option value="DEX">DEX</option> + <param name="in" argument="-in" type="data" format="featurexml" optional="false" label="Input feature map file (featureXML)" help=" select featurexml data sets(s)"/> + <param name="ids" argument="-ids" type="data" format="idxml" optional="false" label="file containing results of identification" help=" select idxml data sets(s)"/> + <param name="num_precursors" argument="-num_precursors" type="integer" optional="true" value="1" label="number of precursors to be selected" help=""/> + <param name="raw_data" argument="-raw_data" type="data" format="mzml" optional="true" label="Input profile data" help=" select mzml data sets(s)"/> + <param name="load_preprocessing" argument="-load_preprocessing" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The preprocessed db is loaded from file, not calculated" help=""/> + <param name="store_preprocessing" argument="-store_preprocessing" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The preprocessed db is stored" help=""/> + <param name="simulation" argument="-simulation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Simulate the whole LC-MS/MS run" help=""/> + <param name="db_path" argument="-db_path" type="data" format="fasta" optional="true" label="db file" help=" select fasta data sets(s)"/> + <param name="rt_model" argument="-rt_model" type="data" format="txt" optional="true" label="SVM Model for RTPredict" help=" select txt data sets(s)"/> + <param name="dt_model" argument="-dt_model" type="data" format="txt" optional="true" label="SVM Model for PTPredict" help=" select txt data sets(s)"/> + <param name="fixed_modifications" argument="-fixed_modifications" type="text" optional="true" value="" label="the modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <expand macro="list_string_val"/> + <expand macro="list_string_san"/> </param> - <param name="param_algorithm_max_iteration" type="integer" min="1" optional="True" value="100" label="Maximal number of iterations" help="(-max_iteration) "/> - <param name="param_algorithm_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_algorithm_step_size" type="integer" min="1" optional="True" value="1" label="Maximal number of precursors per iteration" help="(-step_size) "/> - <param name="param_algorithm_peptide_min_prob" type="float" value="0.2" label="Minimal peptide probability" help="(-peptide_min_prob) "/> - <param name="param_algorithm_sequential_spectrum_order" display="radio" type="boolean" truevalue="-algorithm:sequential_spectrum_order" falsevalue="" checked="false" optional="True" label="If true, precursors are selected sequentially with respect to their RT" help="(-sequential_spectrum_order) "/> - <param name="param_algorithm_MIPFormulation_thresholds_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_algorithm_MIPFormulation_thresholds_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_algorithm_MIPFormulation_thresholds_min_pt_weight" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal pt weight of a precurso" help="(-min_pt_weight) "/> - <param name="param_algorithm_MIPFormulation_thresholds_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_algorithm_MIPFormulation_thresholds_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_algorithm_MIPFormulation_thresholds_min_pred_pep_prob" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal predicted peptide probability of a precurso" help="(-min_pred_pep_prob) "/> - <param name="param_algorithm_MIPFormulation_thresholds_min_rt_weight" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal rt weight of a precurso" help="(-min_rt_weight) "/> - <param name="param_algorithm_MIPFormulation_thresholds_use_peptide_rule" display="radio" type="boolean" truevalue="-algorithm:MIPFormulation:thresholds:use_peptide_rule" falsevalue="" checked="false" optional="True" label="Use peptide rule instead of minimal protein id probability" help="(-use_peptide_rule) "/> - <param name="param_algorithm_MIPFormulation_thresholds_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_algorithm_MIPFormulation_thresholds_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_algorithm_MIPFormulation_combined_ilp_k1" type="float" min="0.0" optional="True" value="0.2" label="combined ilp: weight for z_i" help="(-k1) "/> - <param name="param_algorithm_MIPFormulation_combined_ilp_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_algorithm_MIPFormulation_combined_ilp_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_algorithm_MIPFormulation_combined_ilp_scale_matching_probs" display="radio" type="select" optional="False" value="true" label="flag if detectability * rt_weight shall be scaled to cover all [0,1]" help="(-scale_matching_probs) "> - <option value="true" selected="true">true</option> - <option value="false">false</option> - </param> - <param name="param_algorithm_MIPFormulation_feature_based_no_intensity_normalization" display="radio" type="boolean" truevalue="-algorithm:MIPFormulation:feature_based:no_intensity_normalization" falsevalue="" checked="false" optional="True" label="Flag indicating if intensities shall be scaled to be in [0,1]" 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"/> - <param name="param_algorithm_MIPFormulation_feature_based_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_algorithm_Preprocessing_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_algorithm_Preprocessing_precursor_mass_tolerance_unit" display="radio" type="select" optional="False" value="ppm" label="Precursor mass tolerance unit" help="(-precursor_mass_tolerance_unit) "> - <option value="ppm" selected="true">ppm</option> - <option value="Da">Da</option> - </param> - <param name="param_algorithm_Preprocessing_preprocessed_db_path" type="text" size="30" label="Path where the preprocessed database should be stored" help="(-preprocessed_db_path) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_algorithm_Preprocessing_preprocessed_db_pred_rt_path" type="text" size="30" label="Path where the predicted rts of the preprocessed database should be stored" help="(-preprocessed_db_pred_rt_path) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_algorithm_Preprocessing_preprocessed_db_pred_dt_path" type="text" size="30" label="Path where the predicted rts of the preprocessed database should be stored" help="(-preprocessed_db_pred_dt_path) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_algorithm_Preprocessing_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_algorithm_Preprocessing_missed_cleavages" type="integer" min="0" optional="True" value="1" label="Number of allowed missed cleavages" help="(-missed_cleavages) "/> - <param name="param_algorithm_Preprocessing_taxonomy" type="text" size="30" label="Taxonomy" help="(-taxonomy) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_algorithm_Preprocessing_tmp_dir" type="text" size="30" label="Absolute path to tmp data directory used to store files needed for rt and dt prediction" help="(-tmp_dir) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_algorithm_Preprocessing_store_peptide_sequences" type="text" size="30" value="false" label="Flag if peptide sequences should be stored" help="(-store_peptide_sequences) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_algorithm_Preprocessing_rt_settings_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_algorithm_Preprocessing_rt_settings_max_rt" type="float" value="3840.0" label="Maximal RT in the experiment (in seconds)" help="(-max_rt) "/> - <param name="param_algorithm_Preprocessing_rt_settings_rt_step_size" type="float" value="30.0" label="Time between two consecutive spectra (in seconds)" help="(-rt_step_size) "/> - <param name="param_algorithm_Preprocessing_rt_settings_gauss_mean" type="float" value="-1.0" label="mean of the gauss curve" help="(-gauss_mean) "/> - <param name="param_algorithm_Preprocessing_rt_settings_gauss_sigma" type="float" value="3.0" label="std of the gauss curve" help="(-gauss_sigma) "/> - <expand macro="advanced_options"> - <param name="param_solver" display="radio" type="select" optional="False" value="GLPK" label="LP solver type" help="(-solver) "> + <section name="algorithm" title="Settings for the compound list creation and rescoring" help="" expanded="false"> + <param name="type" argument="-algorithm:type" type="select" optional="false" label="Strategy for precursor ion selection" help=""> + <option value="ILP_IPS">ILP_IPS</option> + <option value="IPS" selected="true">IPS</option> + <option value="SPS">SPS</option> + <option value="Upshift">Upshift</option> + <option value="Downshift">Downshift</option> + <option value="DEX">DEX</option> + <expand macro="list_string_san"/> + </param> + <param name="max_iteration" argument="-algorithm:max_iteration" type="integer" optional="true" min="1" value="100" label="Maximal number of iterations" help=""/> + <param name="rt_bin_capacity" argument="-algorithm:rt_bin_capacity" type="integer" optional="true" min="1" value="10" label="Maximal number of precursors per rt bin" help=""/> + <param name="step_size" argument="-algorithm:step_size" type="integer" optional="true" min="1" value="1" label="Maximal number of precursors per iteration" help=""/> + <param name="peptide_min_prob" argument="-algorithm:peptide_min_prob" type="float" optional="true" value="0.2" label="Minimal peptide probability" help=""/> + <param name="sequential_spectrum_order" argument="-algorithm:sequential_spectrum_order" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, precursors are selected sequentially with respect to their RT" help=""/> + <section name="MIPFormulation" title="" help="" expanded="false"> + <section name="thresholds" title="" help="" expanded="false"> + <param name="min_protein_probability" argument="-algorithm:MIPFormulation:thresholds:min_protein_probability" type="float" optional="true" min="0.0" max="1.0" value="0.2" label="Minimal protein probability for a protein to be considered in the ILP" help=""/> + <param name="min_protein_id_probability" argument="-algorithm:MIPFormulation:thresholds:min_protein_id_probability" type="float" optional="true" min="0.0" max="1.0" value="0.95" label="Minimal protein probability for a protein to be considered identified" help=""/> + <param name="min_pt_weight" argument="-algorithm:MIPFormulation:thresholds:min_pt_weight" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Minimal pt weight of a precurso" help=""/> + <param name="min_mz" argument="-algorithm:MIPFormulation:thresholds:min_mz" type="float" optional="true" min="0.0" value="500.0" label="Minimal mz to be considered in protein based LP formulation" help=""/> + <param name="max_mz" argument="-algorithm:MIPFormulation:thresholds:max_mz" type="float" optional="true" min="0.0" value="5000.0" label="Minimal mz to be considered in protein based LP formulation" help=""/> + <param name="min_pred_pep_prob" argument="-algorithm:MIPFormulation:thresholds:min_pred_pep_prob" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Minimal predicted peptide probability of a precurso" help=""/> + <param name="min_rt_weight" argument="-algorithm:MIPFormulation:thresholds:min_rt_weight" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Minimal rt weight of a precurso" help=""/> + <param name="use_peptide_rule" argument="-algorithm:MIPFormulation:thresholds:use_peptide_rule" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use peptide rule instead of minimal protein id probability" help=""/> + <param name="min_peptide_ids" argument="-algorithm:MIPFormulation:thresholds:min_peptide_ids" type="integer" optional="true" min="1" value="2" label="If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id" help=""/> + <param name="min_peptide_probability" argument="-algorithm:MIPFormulation:thresholds:min_peptide_probability" type="float" optional="true" min="0.0" max="1.0" value="0.95" label="If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified" help=""/> + </section> + <section name="combined_ilp" title="" help="" expanded="false"> + <param name="k1" argument="-algorithm:MIPFormulation:combined_ilp:k1" type="float" optional="true" min="0.0" value="0.2" label="combined ilp: weight for z_i" help=""/> + <param name="k2" argument="-algorithm:MIPFormulation:combined_ilp:k2" type="float" optional="true" min="0.0" value="0.2" label="combined ilp: weight for x_j,s*int_j,s" help=""/> + <param name="k3" argument="-algorithm:MIPFormulation:combined_ilp:k3" type="float" optional="true" min="0.0" value="0.4" label="combined ilp: weight for -x_j,s*w_j,s" help=""/> + <param name="scale_matching_probs" argument="-algorithm:MIPFormulation:combined_ilp:scale_matching_probs" type="boolean" truevalue="true" falsevalue="false" checked="true" label="flag if detectability * rt_weight shall be scaled to cover all [0,1]" help=""/> + </section> + <section name="feature_based" title="" help="" expanded="false"> + <param name="no_intensity_normalization" argument="-algorithm:MIPFormulation:feature_based:no_intensity_normalization" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Flag indicating if intensities shall be scaled to be in [0,1]" help="This is done for each feature separately, so that the feature's maximal intensity in a spectrum is set to 1"/> + <param name="max_number_precursors_per_feature" argument="-algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature" type="integer" optional="true" min="1" value="1" label="The maximal number of precursors per feature" help=""/> + </section> + </section> + <section name="Preprocessing" title="" help="" expanded="false"> + <param name="precursor_mass_tolerance" argument="-algorithm:Preprocessing:precursor_mass_tolerance" type="float" optional="true" min="0.0" value="10.0" label="Precursor mass tolerance which is used to query the peptide database for peptides" help=""/> + <param name="precursor_mass_tolerance_unit" argument="-algorithm:Preprocessing:precursor_mass_tolerance_unit" display="radio" type="select" optional="false" label="Precursor mass tolerance unit" help=""> + <option value="ppm" selected="true">ppm</option> + <option value="Da">Da</option> + <expand macro="list_string_san"/> + </param> + <param name="preprocessed_db_path" argument="-algorithm:Preprocessing:preprocessed_db_path" type="text" optional="true" value="" label="Path where the preprocessed database should be stored" help=""> + <expand macro="list_string_san"/> + </param> + <param name="preprocessed_db_pred_rt_path" argument="-algorithm:Preprocessing:preprocessed_db_pred_rt_path" type="text" optional="true" value="" label="Path where the predicted rts of the preprocessed database should be stored" help=""> + <expand macro="list_string_san"/> + </param> + <param name="preprocessed_db_pred_dt_path" argument="-algorithm:Preprocessing:preprocessed_db_pred_dt_path" type="text" optional="true" value="" label="Path where the predicted rts of the preprocessed database should be stored" help=""> + <expand macro="list_string_san"/> + </param> + <param name="max_peptides_per_run" argument="-algorithm:Preprocessing:max_peptides_per_run" type="integer" optional="true" min="1" value="100000" label="Number of peptides for that the pt and rt are parallely predicted" help=""/> + <param name="missed_cleavages" argument="-algorithm:Preprocessing:missed_cleavages" type="integer" optional="true" min="0" value="1" label="Number of allowed missed cleavages" help=""/> + <param name="taxonomy" argument="-algorithm:Preprocessing:taxonomy" type="text" optional="true" value="" label="Taxonomy" help=""> + <expand macro="list_string_san"/> + </param> + <param name="store_peptide_sequences" argument="-algorithm:Preprocessing:store_peptide_sequences" type="text" optional="true" value="false" label="Flag if peptide sequences should be stored" help=""> + <expand macro="list_string_san"/> + </param> + <section name="rt_settings" title="" help="" expanded="false"> + <param name="min_rt" argument="-algorithm:Preprocessing:rt_settings:min_rt" type="float" optional="true" min="1.0" value="960.0" label="Minimal RT in the experiment (in seconds)" help=""/> + <param name="max_rt" argument="-algorithm:Preprocessing:rt_settings:max_rt" type="float" optional="true" value="3840.0" label="Maximal RT in the experiment (in seconds)" help=""/> + <param name="rt_step_size" argument="-algorithm:Preprocessing:rt_settings:rt_step_size" type="float" optional="true" value="30.0" label="Time between two consecutive spectra (in seconds)" help=""/> + <param name="gauss_mean" argument="-algorithm:Preprocessing:rt_settings:gauss_mean" type="float" optional="true" value="-1.0" label="mean of the gauss curve" help=""/> + <param name="gauss_sigma" argument="-algorithm:Preprocessing:rt_settings:gauss_sigma" type="float" optional="true" value="3.0" label="std of the gauss curve" help=""/> + </section> + </section> + </section> + <expand macro="adv_opts_macro"> + <param name="solver" argument="-solver" display="radio" type="select" optional="false" label="LP solver type" help=""> <option value="GLPK" selected="true">GLPK</option> <option value="COINOR">COINOR</option> + <expand macro="list_string_san"/> </param> - <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> + <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> + <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <expand macro="list_string_san"/> + </param> </expand> + <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false"> + <option value="out_FLAG">out (std of the gauss curve)</option> + <option value="next_feat_FLAG">next_feat (std of the gauss curve)</option> + <option value="sim_results_FLAG">sim_results (std of the gauss curve)</option> + <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> + </param> </inputs> <outputs> - <data name="param_out" format="featurexml"/> - <data name="param_next_feat" format="featurexml"/> + <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"> + <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> + <data name="next_feat" label="${tool.name} on ${on_string}: next_feat" format="featurexml"> + <filter>OPTIONAL_OUTPUTS is not None and "next_feat_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> + <data name="sim_results" label="${tool.name} on ${on_string}: sim_results" format="txt"> + <filter>OPTIONAL_OUTPUTS is not None and "sim_results_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> + <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout"> + <filter>OPTIONAL_OUTPUTS is None</filter> + </data> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>PrecursorIonSelector + <tests> + <expand macro="autotest_PrecursorIonSelector"/> + <expand macro="manutest_PrecursorIonSelector"/> + </tests> + <help><![CDATA[PrecursorIonSelector -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_PrecursorIonSelector.html</help> +For more information, visit http://www.openms.de/documentation/TOPP_PrecursorIonSelector.html]]></help> + <expand macro="references"/> </tool>