Mercurial > repos > bgruening > openms
diff InclusionExclusionListCreator.xml @ 4:6ead64a594bd draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
| author | bgruening |
|---|---|
| date | Wed, 27 Jan 2016 10:06:49 -0500 |
| parents | 3d84209d3178 |
| children |
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--- a/InclusionExclusionListCreator.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/InclusionExclusionListCreator.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,107 +1,232 @@ -<?xml version='1.0' encoding='UTF-8'?> -<tool id="InclusionExclusionListCreator" name="InclusionExclusionListCreator" version="1.12.0"> - <description>Creates inclusion and/or exclusion lists.</description> - <macros> - <token name="@EXECUTABLE@">InclusionExclusionListCreator</token> - <import>macros.xml</import> - </macros> - <expand macro="stdio"/> - <expand macro="requirements"/> - <command>InclusionExclusionListCreator +<?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="InclusionExclusionListCreator" name="InclusionExclusionListCreator" version="2.0.0"> + <description>Creates inclusion and/or exclusion lists.</description> + <macros> + <token name="@EXECUTABLE@">InclusionExclusionListCreator</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>InclusionExclusionListCreator + +#if $param_include: + -include $param_include +#end if +#if $param_exclude: + -exclude $param_exclude +#end if +#if $param_out: + -out $param_out +#end if +#if $param_rt_model: + -rt_model $param_rt_model +#end if +#if $param_pt_model: + -pt_model $param_pt_model +#end if + +#if $rep_param_inclusion_charges: +-inclusion_charges + #for token in $rep_param_inclusion_charges: + #if " " in str(token): + "$token.param_inclusion_charges" + #else + $token.param_inclusion_charges + #end if + #end for +#end if +#if $param_inclusion_strategy: + -inclusion_strategy + #if " " in str($param_inclusion_strategy): + "$param_inclusion_strategy" + #else + $param_inclusion_strategy + #end if +#end if --include ${param_include} --exclude ${param_exclude} --out ${param_out} --rt_model ${param_rt_model} --pt_model ${param_pt_model} --inclusion_charges ${param_inclusion_charges} --inclusion_strategy ${param_inclusion_strategy} --exclusion_charges ${param_exclusion_charges} --raw_data ${param_raw_data} --threads \${GALAXY_SLOTS:-24} --algorithm:InclusionExclusionList:missed_cleavages ${param_missed_cleavages} --algorithm:InclusionExclusionList:RT:unit ${param_unit} -${param_use_relative} --algorithm:InclusionExclusionList:RT:window_relative ${param_window_relative} --algorithm:InclusionExclusionList:RT:window_absolute ${param_window_absolute} --algorithm:InclusionExclusionList:merge:mz_tol ${param_mz_tol} --algorithm:InclusionExclusionList:merge:mz_tol_unit ${param_mz_tol_unit} --algorithm:InclusionExclusionList:merge:rt_tol ${param_rt_tol} --algorithm:PrecursorSelection:ms2_spectra_per_rt_bin ${param_ms2_spectra_per_rt_bin} -${param_exclude_overlapping_peaks} -${param_use_dynamic_exclusion} --algorithm:PrecursorSelection:Exclusion:exclusion_time ${param_exclusion_time} --algorithm:PrecursorSelection:ProteinBasedInclusion:max_list_size ${param_max_list_size} --algorithm:PrecursorSelection:ProteinBasedInclusion:rt:min_rt ${param_min_rt} --algorithm:PrecursorSelection:ProteinBasedInclusion:rt:max_rt ${param_max_rt} --algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_step_size ${param_rt_step_size} --algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_window_size ${param_rt_window_size} --algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_protein_id_probability ${param_min_protein_id_probability} --algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_pt_weight ${param_min_pt_weight} --algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_mz ${param_min_mz} --algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:max_mz ${param_max_mz} -${param_use_peptide_rule} --algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_ids ${param_min_peptide_ids} --algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_probability ${param_min_peptide_probability} -${param_no_intensity_normalization} --algorithm:PrecursorSelection:feature_based:max_number_precursors_per_feature ${param_max_number_precursors_per_feature} +#if $rep_param_exclusion_charges: +-exclusion_charges + #for token in $rep_param_exclusion_charges: + #if " " in str(token): + "$token.param_exclusion_charges" + #else + $token.param_exclusion_charges + #end if + #end for +#end if +#if $param_raw_data: + -raw_data $param_raw_data +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_InclusionExclusionList_missed_cleavages: + -algorithm:InclusionExclusionList:missed_cleavages $param_algorithm_InclusionExclusionList_missed_cleavages +#end if +#if $param_algorithm_InclusionExclusionList_RT_unit: + -algorithm:InclusionExclusionList:RT:unit + #if " " in str($param_algorithm_InclusionExclusionList_RT_unit): + "$param_algorithm_InclusionExclusionList_RT_unit" + #else + $param_algorithm_InclusionExclusionList_RT_unit + #end if +#end if +#if $param_algorithm_InclusionExclusionList_RT_use_relative: + -algorithm:InclusionExclusionList:RT:use_relative +#end if +#if $param_algorithm_InclusionExclusionList_RT_window_relative: + -algorithm:InclusionExclusionList:RT:window_relative $param_algorithm_InclusionExclusionList_RT_window_relative +#end if +#if $param_algorithm_InclusionExclusionList_RT_window_absolute: + -algorithm:InclusionExclusionList:RT:window_absolute $param_algorithm_InclusionExclusionList_RT_window_absolute +#end if +#if $param_algorithm_InclusionExclusionList_merge_mz_tol: + -algorithm:InclusionExclusionList:merge:mz_tol $param_algorithm_InclusionExclusionList_merge_mz_tol +#end if +#if $param_algorithm_InclusionExclusionList_merge_mz_tol_unit: + -algorithm:InclusionExclusionList:merge:mz_tol_unit + #if " " in str($param_algorithm_InclusionExclusionList_merge_mz_tol_unit): + "$param_algorithm_InclusionExclusionList_merge_mz_tol_unit" + #else + $param_algorithm_InclusionExclusionList_merge_mz_tol_unit + #end if +#end if +#if $param_algorithm_InclusionExclusionList_merge_rt_tol: + -algorithm:InclusionExclusionList:merge:rt_tol $param_algorithm_InclusionExclusionList_merge_rt_tol +#end if +#if $param_algorithm_PrecursorSelection_ms2_spectra_per_rt_bin: + -algorithm:PrecursorSelection:ms2_spectra_per_rt_bin $param_algorithm_PrecursorSelection_ms2_spectra_per_rt_bin +#end if +#if $param_algorithm_PrecursorSelection_exclude_overlapping_peaks: + -algorithm:PrecursorSelection:exclude_overlapping_peaks +#end if +#if $param_algorithm_PrecursorSelection_Exclusion_use_dynamic_exclusion: + -algorithm:PrecursorSelection:Exclusion:use_dynamic_exclusion +#end if +#if $param_algorithm_PrecursorSelection_Exclusion_exclusion_time: + -algorithm:PrecursorSelection:Exclusion:exclusion_time $param_algorithm_PrecursorSelection_Exclusion_exclusion_time +#end if +#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_max_list_size: + -algorithm:PrecursorSelection:ProteinBasedInclusion:max_list_size $param_algorithm_PrecursorSelection_ProteinBasedInclusion_max_list_size +#end if +#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_min_rt: + -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:min_rt $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_min_rt +#end if +#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_max_rt: + -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:max_rt $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_max_rt +#end if +#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_step_size: + -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_step_size $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_step_size +#end if +#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_window_size: + -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_window_size $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_window_size +#end if +#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_protein_id_probability: + -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_protein_id_probability $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_protein_id_probability +#end if +#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_pt_weight: + -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_pt_weight $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_pt_weight +#end if +#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_mz: + -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_mz $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_mz +#end if +#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_max_mz: + -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:max_mz $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_max_mz +#end if +#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_use_peptide_rule: + -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:use_peptide_rule +#end if +#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_ids: + -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_ids $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_ids +#end if +#if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_probability: + -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_probability $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_probability +#end if +#if $param_algorithm_PrecursorSelection_feature_based_no_intensity_normalization: + -algorithm:PrecursorSelection:feature_based:no_intensity_normalization +#end if +#if $param_algorithm_PrecursorSelection_feature_based_max_number_precursors_per_feature: + -algorithm:PrecursorSelection:feature_based:max_number_precursors_per_feature $param_algorithm_PrecursorSelection_feature_based_max_number_precursors_per_feature +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if </command> - <inputs> - <param name="param_include" type="data" format="featureXML,fasta" optional="True" label="Inclusion list input file in FASTA or featureXML format." help="(-include)"/> - <param name="param_exclude" type="data" format="featureXML,idXML,fasta" optional="True" label="Exclusion list input file in featureXML, idXML or FASTA format." help="(-exclude)"/> - <param name="param_rt_model" type="data" format="txt" optional="True" label="RTModel file used for the rt prediction of peptides in FASTA files." help="(-rt_model)"/> - <param name="param_pt_model" type="data" format="txt" optional="True" label="PTModel file used for the pt prediction of peptides in FASTA files (only needed for inclusion_strategy PreotinBased_LP)." help="(-pt_model)"/> - <param name="param_inclusion_charges" type="text" min="1" optional="True" size="20" value="1" label="List containing the charge states to be considered for the inclusion list compounds, space separated." help="(-inclusion_charges)"/> - <param name="param_inclusion_strategy" type="select" optional="True" value="ALL" label="strategy to be used for selection" help="(-inclusion_strategy)"> - <option value="FeatureBased_LP">FeatureBased_LP</option> - <option value="ProteinBased_LP">ProteinBased_LP</option> - <option value="ALL">ALL</option> - </param> - <param name="param_exclusion_charges" type="text" min="1" optional="True" size="20" value="1" label="List containing the charge states to be considered for the exclusion list compounds (for idXML and FASTA input), space separated." help="(-exclusion_charges)"/> - <param name="param_raw_data" type="data" format="mzML" optional="True" label="File containing the raw data (only needed for FeatureBased_LP)." help="(-raw_data)"/> - <param name="param_missed_cleavages" type="integer" value="0" label="Number of missed cleavages used for protein digestion.#br#" help="(-missed_cleavages)"/> - <param name="param_unit" type="select" optional="True" value="minutes" label="Create lists with units as seconds instead of minutes" help="(-unit)"> - <option value="minutes">minutes</option> - <option value="seconds">seconds</option> - </param> - <param name="param_use_relative" type="boolean" truevalue="-algorithm:InclusionExclusionList:RT:use_relative true" falsevalue="-algorithm:InclusionExclusionList:RT:use_relative false" checked="true" optional="True" label="Use relative RT window, which depends on RT of precursor." help="(-use_relative)"/> - <param name="param_window_relative" type="float" min="0.0" max="10.0" optional="True" value="0.05" label="[for RT:use_relative == true] The relative factor X for the RT exclusion window, e.g. the window is calculated as [rt - rt*X, rt + rt*X]." help="(-window_relative)"/> - <param name="param_window_absolute" type="float" min="0.0" optional="True" value="90.0" label="[for RT:use_relative == false] The absolute value X for the RT exclusion window in [sec], e.g. the window is calculated as [rt - X, rt + X]." help="(-window_absolute)"/> - <param name="param_mz_tol" type="float" min="0.0" optional="True" value="10.0" label="Two inclusion/exclusion windows are merged when they (almost) overlap in RT (see 'rt_tol') and are close in m/z by this tolerance. Unit of this is defined in 'mz_tol_unit'." help="(-mz_tol)"/> - <param name="param_mz_tol_unit" type="select" optional="True" value="ppm" label="Unit of 'mz_tol'" help="(-mz_tol_unit)"> - <option value="ppm">ppm</option> - <option value="Da">Da</option> - </param> - <param name="param_rt_tol" type="float" min="0.0" optional="True" value="1.1" label="Maximal RT delta (in seconds) which would allow two windows in RT to overlap (which causes merging the windows). Two inclusion/exclusion windows are merged when they (almost) overlap in RT and are close in m/z by this tolerance (see 'mz_tol'). Unit of this param is [seconds]." help="(-rt_tol)"/> - <param name="param_ms2_spectra_per_rt_bin" type="integer" min="1" optional="True" value="5" label="Number of allowed MS/MS spectra in a retention time bin." help="(-ms2_spectra_per_rt_bin)"/> - <param name="param_exclude_overlapping_peaks" type="boolean" truevalue="-algorithm:PrecursorSelection:exclude_overlapping_peaks true" falsevalue="-algorithm:PrecursorSelection:exclude_overlapping_peaks false" checked="false" optional="True" label="If true overlapping or nearby peaks (within min_peak_distance) are excluded for selection." help="(-exclude_overlapping_peaks)"/> - <param name="param_use_dynamic_exclusion" type="boolean" truevalue="-algorithm:PrecursorSelection:Exclusion:use_dynamic_exclusion true" falsevalue="-algorithm:PrecursorSelection:Exclusion:use_dynamic_exclusion false" checked="false" optional="True" label="If true dynamic exclusion is applied." help="(-use_dynamic_exclusion)"/> - <param name="param_exclusion_time" type="float" min="0.0" optional="True" value="100.0" label="The time (in seconds) a feature is excluded." help="(-exclusion_time)"/> - <param name="param_max_list_size" type="integer" min="1" optional="True" value="1000" label="The maximal number of precursors in the inclusion list." help="(-max_list_size)"/> - <param name="param_min_rt" type="float" min="0.0" optional="True" value="960.0" label="Minimal rt in seconds." help="(-min_rt)"/> - <param name="param_max_rt" type="float" min="0.0" optional="True" value="3840.0" label="Maximal rt in seconds." help="(-max_rt)"/> - <param name="param_rt_step_size" type="float" min="1.0" optional="True" value="30.0" label="rt step size in seconds." help="(-rt_step_size)"/> - <param name="param_rt_window_size" type="integer" min="1" optional="True" value="100" label="rt window size in seconds." help="(-rt_window_size)"/> - <param name="param_min_protein_id_probability" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="Minimal protein probability for a protein to be considered identified." help="(-min_protein_id_probability)"/> - <param name="param_min_pt_weight" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal pt weight of a precursor" help="(-min_pt_weight)"/> - <param name="param_min_mz" type="float" min="0.0" optional="True" value="500.0" label="Minimal mz to be considered in protein based LP formulation." help="(-min_mz)"/> - <param name="param_max_mz" type="float" min="0.0" optional="True" value="5000.0" label="Minimal mz to be considered in protein based LP formulation." help="(-max_mz)"/> - <param name="param_use_peptide_rule" type="boolean" truevalue="-algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:use_peptide_rule true" falsevalue="-algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:use_peptide_rule false" checked="false" optional="True" label="Use peptide rule instead of minimal protein id probability" help="(-use_peptide_rule)"/> - <param name="param_min_peptide_ids" type="integer" min="1" optional="True" value="2" label="If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id" help="(-min_peptide_ids)"/> - <param name="param_min_peptide_probability" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified" help="(-min_peptide_probability)"/> - <param name="param_no_intensity_normalization" type="boolean" truevalue="-algorithm:PrecursorSelection:feature_based:no_intensity_normalization true" falsevalue="-algorithm:PrecursorSelection: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)"/> - </inputs> - <outputs> - <data name="param_out" label="Output file (tab delimited csv file)." format="tabular"/> - </outputs> - <help>**What it does** - -Creates inclusion and/or exclusion lists. + <inputs> + <param format="xml,fasta" help="(-include) " label="Inclusion list input file in FASTA or featureXML format" name="param_include" optional="True" type="data"/> + <param format="xml,fasta" help="(-exclude) " label="Exclusion list input file in featureXML, idXML or FASTA format" name="param_exclude" optional="True" type="data"/> + <param format="txt" help="(-rt_model) " label="RTModel file used for the rt prediction of peptides in FASTA files" name="param_rt_model" optional="True" type="data"/> + <param format="txt" help="(-pt_model) " label="PTModel file used for the pt prediction of peptides in FASTA files (only needed for inclusion_strategy PreotinBased_LP)" name="param_pt_model" optional="True" type="data"/> + <repeat min="0" name="rep_param_inclusion_charges" title="param_inclusion_charges"> + <param help="(-inclusion_charges) " label="List containing the charge states to be considered for the inclusion list compounds, space separated" min="1" name="param_inclusion_charges" optional="True" size="30" type="text" value="1"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <param help="(-inclusion_strategy) " label="strategy to be used for selection" name="param_inclusion_strategy" optional="True" type="select" value="ALL"> + <option value="FeatureBased_LP">FeatureBased_LP</option> + <option value="ProteinBased_LP">ProteinBased_LP</option> + <option value="ALL">ALL</option> + </param> + <repeat min="0" name="rep_param_exclusion_charges" title="param_exclusion_charges"> + <param help="(-exclusion_charges) " label="List containing the charge states to be considered for the exclusion list compounds (for idXML and FASTA input), space separated" min="1" name="param_exclusion_charges" optional="True" size="30" type="text" value="1"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <param format="mzml" help="(-raw_data) " label="File containing the raw data (only needed for FeatureBased_LP)" name="param_raw_data" optional="True" type="data"/> + <param help="(-missed_cleavages) <br>" label="Number of missed cleavages used for protein digestion" name="param_algorithm_InclusionExclusionList_missed_cleavages" type="integer" value="0"/> + <param help="(-unit) " label="Create lists with units as seconds instead of minutes" name="param_algorithm_InclusionExclusionList_RT_unit" optional="True" type="select" value="minutes"> + <option value="minutes">minutes</option> + <option value="seconds">seconds</option> + </param> + <param checked="true" falsevalue="" help="(-use_relative) " label="Use relative RT window, which depends on RT of precurso" name="param_algorithm_InclusionExclusionList_RT_use_relative" optional="True" truevalue="-algorithm:InclusionExclusionList:RT:use_relative" type="boolean"/> + <param help="(-window_relative) e.g. the window is calculated as [rt - rt*X, rt + rt*X]" label="[for RT:use_relative == true] The relative factor X for the RT exclusion window," max="10.0" min="0.0" name="param_algorithm_InclusionExclusionList_RT_window_relative" optional="True" type="float" value="0.05"/> + <param help="(-window_absolute) e.g. the window is calculated as [rt - X, rt + X]" label="[for RT:use_relative == false] The absolute value X for the RT exclusion window in [sec]," min="0.0" name="param_algorithm_InclusionExclusionList_RT_window_absolute" optional="True" type="float" value="90.0"/> + <param help="(-mz_tol) Unit of this is defined in 'mz_tol_unit'" label="Two inclusion/exclusion windows are merged when they (almost) overlap in RT (see 'rt_tol') and are close in m/z by this tolerance" min="0.0" name="param_algorithm_InclusionExclusionList_merge_mz_tol" optional="True" type="float" value="10.0"/> + <param help="(-mz_tol_unit) " label="Unit of 'mz_tol'" name="param_algorithm_InclusionExclusionList_merge_mz_tol_unit" optional="True" type="select" value="ppm"> + <option value="ppm">ppm</option> + <option value="Da">Da</option> + </param> + <param help="(-rt_tol) Two inclusion/exclusion windows are merged when they (almost) overlap in RT and are close in m/z by this tolerance (see 'mz_tol'). Unit of this param is [seconds]" label="Maximal RT delta (in seconds) which would allow two windows in RT to overlap (which causes merging the windows)" min="0.0" name="param_algorithm_InclusionExclusionList_merge_rt_tol" optional="True" type="float" value="1.1"/> + <param help="(-ms2_spectra_per_rt_bin) " label="Number of allowed MS/MS spectra in a retention time bin" min="1" name="param_algorithm_PrecursorSelection_ms2_spectra_per_rt_bin" optional="True" type="integer" value="5"/> + <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_PrecursorSelection_exclude_overlapping_peaks" optional="True" truevalue="-algorithm:PrecursorSelection:exclude_overlapping_peaks" type="boolean"/> + <param checked="false" falsevalue="" help="(-use_dynamic_exclusion) " label="If true dynamic exclusion is applied" name="param_algorithm_PrecursorSelection_Exclusion_use_dynamic_exclusion" optional="True" truevalue="-algorithm:PrecursorSelection:Exclusion:use_dynamic_exclusion" type="boolean"/> + <param help="(-exclusion_time) " label="The time (in seconds) a feature is excluded" min="0.0" name="param_algorithm_PrecursorSelection_Exclusion_exclusion_time" optional="True" type="float" value="100.0"/> + <param help="(-max_list_size) " label="The maximal number of precursors in the inclusion list" min="1" name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_max_list_size" optional="True" type="integer" value="1000"/> + <param help="(-min_rt) " label="Minimal rt in seconds" min="0.0" name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_min_rt" optional="True" type="float" value="960.0"/> + <param help="(-max_rt) " label="Maximal rt in seconds" min="0.0" name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_max_rt" optional="True" type="float" value="3840.0"/> + <param help="(-rt_step_size) " label="rt step size in seconds" min="1.0" name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_step_size" optional="True" type="float" value="30.0"/> + <param help="(-rt_window_size) " label="rt window size in seconds" min="1" name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_window_size" optional="True" type="integer" value="100"/> + <param help="(-min_protein_id_probability) " label="Minimal protein probability for a protein to be considered identified" max="1.0" min="0.0" name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_protein_id_probability" optional="True" type="float" value="0.95"/> + <param help="(-min_pt_weight) " label="Minimal pt weight of a precurso" max="1.0" min="0.0" name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_pt_weight" optional="True" type="float" value="0.5"/> + <param help="(-min_mz) " label="Minimal mz to be considered in protein based LP formulation" min="0.0" name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_mz" optional="True" type="float" value="500.0"/> + <param help="(-max_mz) " label="Minimal mz to be considered in protein based LP formulation" min="0.0" name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_max_mz" optional="True" type="float" value="5000.0"/> + <param checked="false" falsevalue="" help="(-use_peptide_rule) " label="Use peptide rule instead of minimal protein id probability" name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_use_peptide_rule" optional="True" truevalue="-algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:use_peptide_rule" type="boolean"/> + <param help="(-min_peptide_ids) " label="If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id" min="1" name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_ids" optional="True" type="integer" value="2"/> + <param help="(-min_peptide_probability) " label="If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified" max="1.0" min="0.0" name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_probability" optional="True" type="float" value="0.95"/> + <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_PrecursorSelection_feature_based_no_intensity_normalization" optional="True" truevalue="-algorithm:PrecursorSelection: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_PrecursorSelection_feature_based_max_number_precursors_per_feature" optional="True" type="integer" value="1"/> + <expand macro="advanced_options"> + <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="tabular" name="param_out"/> + </outputs> + <help>Creates inclusion and/or exclusion lists. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InclusionExclusionListCreator.html - -@REFERENCES@ -</help> -</tool> +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InclusionExclusionListCreator.html</help> + </tool>