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view 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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<?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 #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 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</help> </tool>