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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="InclusionExclusionListCreator" name="InclusionExclusionListCreator" version="1.12.0">
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3 <description>Creates inclusion and/or exclusion lists.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">InclusionExclusionListCreator</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>InclusionExclusionListCreator
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11
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12 -include ${param_include}
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13 -exclude ${param_exclude}
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14 -out ${param_out}
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15 -rt_model ${param_rt_model}
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16 -pt_model ${param_pt_model}
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17 -inclusion_charges ${param_inclusion_charges}
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18 -inclusion_strategy ${param_inclusion_strategy}
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19 -exclusion_charges ${param_exclusion_charges}
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20 -raw_data ${param_raw_data}
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21 -threads \${GALAXY_SLOTS:-24}
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22 -algorithm:InclusionExclusionList:missed_cleavages ${param_missed_cleavages}
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23 -algorithm:InclusionExclusionList:RT:unit ${param_unit}
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24 ${param_use_relative}
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25 -algorithm:InclusionExclusionList:RT:window_relative ${param_window_relative}
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26 -algorithm:InclusionExclusionList:RT:window_absolute ${param_window_absolute}
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27 -algorithm:InclusionExclusionList:merge:mz_tol ${param_mz_tol}
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28 -algorithm:InclusionExclusionList:merge:mz_tol_unit ${param_mz_tol_unit}
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29 -algorithm:InclusionExclusionList:merge:rt_tol ${param_rt_tol}
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30 -algorithm:PrecursorSelection:ms2_spectra_per_rt_bin ${param_ms2_spectra_per_rt_bin}
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31 ${param_exclude_overlapping_peaks}
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32 ${param_use_dynamic_exclusion}
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33 -algorithm:PrecursorSelection:Exclusion:exclusion_time ${param_exclusion_time}
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34 -algorithm:PrecursorSelection:ProteinBasedInclusion:max_list_size ${param_max_list_size}
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35 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:min_rt ${param_min_rt}
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36 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:max_rt ${param_max_rt}
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37 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_step_size ${param_rt_step_size}
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38 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_window_size ${param_rt_window_size}
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39 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_protein_id_probability ${param_min_protein_id_probability}
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40 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_pt_weight ${param_min_pt_weight}
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41 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_mz ${param_min_mz}
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42 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:max_mz ${param_max_mz}
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43 ${param_use_peptide_rule}
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44 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_ids ${param_min_peptide_ids}
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45 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_probability ${param_min_peptide_probability}
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46 ${param_no_intensity_normalization}
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47 -algorithm:PrecursorSelection:feature_based:max_number_precursors_per_feature ${param_max_number_precursors_per_feature}
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48 </command>
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49 <inputs>
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50 <param name="param_include" type="data" format="featureXML,fasta" optional="True" label="Inclusion list input file in FASTA or featureXML format." help="(-include)"/>
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51 <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)"/>
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52 <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)"/>
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53 <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)"/>
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54 <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)"/>
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55 <param name="param_inclusion_strategy" type="select" optional="True" value="ALL" label="strategy to be used for selection" help="(-inclusion_strategy)">
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56 <option value="FeatureBased_LP">FeatureBased_LP</option>
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57 <option value="ProteinBased_LP">ProteinBased_LP</option>
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58 <option value="ALL">ALL</option>
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59 </param>
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60 <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)"/>
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61 <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)"/>
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62 <param name="param_missed_cleavages" type="integer" value="0" label="Number of missed cleavages used for protein digestion.#br#" help="(-missed_cleavages)"/>
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63 <param name="param_unit" type="select" optional="True" value="minutes" label="Create lists with units as seconds instead of minutes" help="(-unit)">
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64 <option value="minutes">minutes</option>
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65 <option value="seconds">seconds</option>
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66 </param>
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67 <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)"/>
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68 <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)"/>
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69 <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)"/>
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70 <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)"/>
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71 <param name="param_mz_tol_unit" type="select" optional="True" value="ppm" label="Unit of 'mz_tol'" help="(-mz_tol_unit)">
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72 <option value="ppm">ppm</option>
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73 <option value="Da">Da</option>
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74 </param>
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75 <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)"/>
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76 <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)"/>
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77 <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)"/>
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78 <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)"/>
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79 <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)"/>
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80 <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)"/>
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81 <param name="param_min_rt" type="float" min="0.0" optional="True" value="960.0" label="Minimal rt in seconds." help="(-min_rt)"/>
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82 <param name="param_max_rt" type="float" min="0.0" optional="True" value="3840.0" label="Maximal rt in seconds." help="(-max_rt)"/>
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83 <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)"/>
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84 <param name="param_rt_window_size" type="integer" min="1" optional="True" value="100" label="rt window size in seconds." help="(-rt_window_size)"/>
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85 <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)"/>
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86 <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)"/>
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87 <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)"/>
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88 <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)"/>
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89 <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)"/>
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90 <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)"/>
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91 <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)"/>
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92 <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)"/>
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93 <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)"/>
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94 </inputs>
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95 <outputs>
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96 <data name="param_out" label="Output file (tab delimited csv file)." format="tabular"/>
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97 </outputs>
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98 <help>**What it does**
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99
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100 Creates inclusion and/or exclusion lists.
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101
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102
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103 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InclusionExclusionListCreator.html
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104
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105 @REFERENCES@
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106 </help>
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107 </tool>
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