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comparison InclusionExclusionListCreator.xml @ 4:6ead64a594bd draft default tip

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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
comparison
equal deleted inserted replaced
3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="InclusionExclusionListCreator" name="InclusionExclusionListCreator" version="1.12.0"> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <description>Creates inclusion and/or exclusion lists.</description> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <macros> 4 <tool id="InclusionExclusionListCreator" name="InclusionExclusionListCreator" version="2.0.0">
5 <token name="@EXECUTABLE@">InclusionExclusionListCreator</token> 5 <description>Creates inclusion and/or exclusion lists.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">InclusionExclusionListCreator</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>InclusionExclusionListCreator 10 <expand macro="references"/>
11 11 <expand macro="stdio"/>
12 -include ${param_include} 12 <expand macro="requirements"/>
13 -exclude ${param_exclude} 13 <command>InclusionExclusionListCreator
14 -out ${param_out} 14
15 -rt_model ${param_rt_model} 15 #if $param_include:
16 -pt_model ${param_pt_model} 16 -include $param_include
17 -inclusion_charges ${param_inclusion_charges} 17 #end if
18 -inclusion_strategy ${param_inclusion_strategy} 18 #if $param_exclude:
19 -exclusion_charges ${param_exclusion_charges} 19 -exclude $param_exclude
20 -raw_data ${param_raw_data} 20 #end if
21 -threads \${GALAXY_SLOTS:-24} 21 #if $param_out:
22 -algorithm:InclusionExclusionList:missed_cleavages ${param_missed_cleavages} 22 -out $param_out
23 -algorithm:InclusionExclusionList:RT:unit ${param_unit} 23 #end if
24 ${param_use_relative} 24 #if $param_rt_model:
25 -algorithm:InclusionExclusionList:RT:window_relative ${param_window_relative} 25 -rt_model $param_rt_model
26 -algorithm:InclusionExclusionList:RT:window_absolute ${param_window_absolute} 26 #end if
27 -algorithm:InclusionExclusionList:merge:mz_tol ${param_mz_tol} 27 #if $param_pt_model:
28 -algorithm:InclusionExclusionList:merge:mz_tol_unit ${param_mz_tol_unit} 28 -pt_model $param_pt_model
29 -algorithm:InclusionExclusionList:merge:rt_tol ${param_rt_tol} 29 #end if
30 -algorithm:PrecursorSelection:ms2_spectra_per_rt_bin ${param_ms2_spectra_per_rt_bin} 30
31 ${param_exclude_overlapping_peaks} 31 #if $rep_param_inclusion_charges:
32 ${param_use_dynamic_exclusion} 32 -inclusion_charges
33 -algorithm:PrecursorSelection:Exclusion:exclusion_time ${param_exclusion_time} 33 #for token in $rep_param_inclusion_charges:
34 -algorithm:PrecursorSelection:ProteinBasedInclusion:max_list_size ${param_max_list_size} 34 #if &quot; &quot; in str(token):
35 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:min_rt ${param_min_rt} 35 &quot;$token.param_inclusion_charges&quot;
36 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:max_rt ${param_max_rt} 36 #else
37 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_step_size ${param_rt_step_size} 37 $token.param_inclusion_charges
38 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_window_size ${param_rt_window_size} 38 #end if
39 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_protein_id_probability ${param_min_protein_id_probability} 39 #end for
40 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_pt_weight ${param_min_pt_weight} 40 #end if
41 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_mz ${param_min_mz} 41 #if $param_inclusion_strategy:
42 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:max_mz ${param_max_mz} 42 -inclusion_strategy
43 ${param_use_peptide_rule} 43 #if &quot; &quot; in str($param_inclusion_strategy):
44 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_ids ${param_min_peptide_ids} 44 &quot;$param_inclusion_strategy&quot;
45 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_probability ${param_min_peptide_probability} 45 #else
46 ${param_no_intensity_normalization} 46 $param_inclusion_strategy
47 -algorithm:PrecursorSelection:feature_based:max_number_precursors_per_feature ${param_max_number_precursors_per_feature} 47 #end if
48 #end if
49
50 #if $rep_param_exclusion_charges:
51 -exclusion_charges
52 #for token in $rep_param_exclusion_charges:
53 #if &quot; &quot; in str(token):
54 &quot;$token.param_exclusion_charges&quot;
55 #else
56 $token.param_exclusion_charges
57 #end if
58 #end for
59 #end if
60 #if $param_raw_data:
61 -raw_data $param_raw_data
62 #end if
63 -threads \${GALAXY_SLOTS:-24}
64 #if $param_algorithm_InclusionExclusionList_missed_cleavages:
65 -algorithm:InclusionExclusionList:missed_cleavages $param_algorithm_InclusionExclusionList_missed_cleavages
66 #end if
67 #if $param_algorithm_InclusionExclusionList_RT_unit:
68 -algorithm:InclusionExclusionList:RT:unit
69 #if &quot; &quot; in str($param_algorithm_InclusionExclusionList_RT_unit):
70 &quot;$param_algorithm_InclusionExclusionList_RT_unit&quot;
71 #else
72 $param_algorithm_InclusionExclusionList_RT_unit
73 #end if
74 #end if
75 #if $param_algorithm_InclusionExclusionList_RT_use_relative:
76 -algorithm:InclusionExclusionList:RT:use_relative
77 #end if
78 #if $param_algorithm_InclusionExclusionList_RT_window_relative:
79 -algorithm:InclusionExclusionList:RT:window_relative $param_algorithm_InclusionExclusionList_RT_window_relative
80 #end if
81 #if $param_algorithm_InclusionExclusionList_RT_window_absolute:
82 -algorithm:InclusionExclusionList:RT:window_absolute $param_algorithm_InclusionExclusionList_RT_window_absolute
83 #end if
84 #if $param_algorithm_InclusionExclusionList_merge_mz_tol:
85 -algorithm:InclusionExclusionList:merge:mz_tol $param_algorithm_InclusionExclusionList_merge_mz_tol
86 #end if
87 #if $param_algorithm_InclusionExclusionList_merge_mz_tol_unit:
88 -algorithm:InclusionExclusionList:merge:mz_tol_unit
89 #if &quot; &quot; in str($param_algorithm_InclusionExclusionList_merge_mz_tol_unit):
90 &quot;$param_algorithm_InclusionExclusionList_merge_mz_tol_unit&quot;
91 #else
92 $param_algorithm_InclusionExclusionList_merge_mz_tol_unit
93 #end if
94 #end if
95 #if $param_algorithm_InclusionExclusionList_merge_rt_tol:
96 -algorithm:InclusionExclusionList:merge:rt_tol $param_algorithm_InclusionExclusionList_merge_rt_tol
97 #end if
98 #if $param_algorithm_PrecursorSelection_ms2_spectra_per_rt_bin:
99 -algorithm:PrecursorSelection:ms2_spectra_per_rt_bin $param_algorithm_PrecursorSelection_ms2_spectra_per_rt_bin
100 #end if
101 #if $param_algorithm_PrecursorSelection_exclude_overlapping_peaks:
102 -algorithm:PrecursorSelection:exclude_overlapping_peaks
103 #end if
104 #if $param_algorithm_PrecursorSelection_Exclusion_use_dynamic_exclusion:
105 -algorithm:PrecursorSelection:Exclusion:use_dynamic_exclusion
106 #end if
107 #if $param_algorithm_PrecursorSelection_Exclusion_exclusion_time:
108 -algorithm:PrecursorSelection:Exclusion:exclusion_time $param_algorithm_PrecursorSelection_Exclusion_exclusion_time
109 #end if
110 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_max_list_size:
111 -algorithm:PrecursorSelection:ProteinBasedInclusion:max_list_size $param_algorithm_PrecursorSelection_ProteinBasedInclusion_max_list_size
112 #end if
113 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_min_rt:
114 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:min_rt $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_min_rt
115 #end if
116 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_max_rt:
117 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:max_rt $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_max_rt
118 #end if
119 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_step_size:
120 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_step_size $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_step_size
121 #end if
122 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_window_size:
123 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_window_size $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_window_size
124 #end if
125 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_protein_id_probability:
126 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_protein_id_probability $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_protein_id_probability
127 #end if
128 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_pt_weight:
129 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_pt_weight $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_pt_weight
130 #end if
131 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_mz:
132 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_mz $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_mz
133 #end if
134 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_max_mz:
135 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:max_mz $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_max_mz
136 #end if
137 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_use_peptide_rule:
138 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:use_peptide_rule
139 #end if
140 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_ids:
141 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_ids $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_ids
142 #end if
143 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_probability:
144 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_probability $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_probability
145 #end if
146 #if $param_algorithm_PrecursorSelection_feature_based_no_intensity_normalization:
147 -algorithm:PrecursorSelection:feature_based:no_intensity_normalization
148 #end if
149 #if $param_algorithm_PrecursorSelection_feature_based_max_number_precursors_per_feature:
150 -algorithm:PrecursorSelection:feature_based:max_number_precursors_per_feature $param_algorithm_PrecursorSelection_feature_based_max_number_precursors_per_feature
151 #end if
152 #if $adv_opts.adv_opts_selector=='advanced':
153 #if $adv_opts.param_force:
154 -force
155 #end if
156 #end if
48 </command> 157 </command>
49 <inputs> 158 <inputs>
50 <param name="param_include" type="data" format="featureXML,fasta" optional="True" label="Inclusion list input file in FASTA or featureXML format." help="(-include)"/> 159 <param format="xml,fasta" help="(-include) " label="Inclusion list input file in FASTA or featureXML format" name="param_include" optional="True" type="data"/>
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)"/> 160 <param format="xml,fasta" help="(-exclude) " label="Exclusion list input file in featureXML, idXML or FASTA format" name="param_exclude" optional="True" type="data"/>
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)"/> 161 <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"/>
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)"/> 162 <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"/>
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)"/> 163 <repeat min="0" name="rep_param_inclusion_charges" title="param_inclusion_charges">
55 <param name="param_inclusion_strategy" type="select" optional="True" value="ALL" label="strategy to be used for selection" help="(-inclusion_strategy)"> 164 <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">
56 <option value="FeatureBased_LP">FeatureBased_LP</option> 165 <sanitizer>
57 <option value="ProteinBased_LP">ProteinBased_LP</option> 166 <valid initial="string.printable">
58 <option value="ALL">ALL</option> 167 <remove value="'"/>
59 </param> 168 <remove value="&quot;"/>
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)"/> 169 </valid>
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)"/> 170 </sanitizer>
62 <param name="param_missed_cleavages" type="integer" value="0" label="Number of missed cleavages used for protein digestion.#br#" help="(-missed_cleavages)"/> 171 </param>
63 <param name="param_unit" type="select" optional="True" value="minutes" label="Create lists with units as seconds instead of minutes" help="(-unit)"> 172 </repeat>
64 <option value="minutes">minutes</option> 173 <param help="(-inclusion_strategy) " label="strategy to be used for selection" name="param_inclusion_strategy" optional="True" type="select" value="ALL">
65 <option value="seconds">seconds</option> 174 <option value="FeatureBased_LP">FeatureBased_LP</option>
66 </param> 175 <option value="ProteinBased_LP">ProteinBased_LP</option>
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)"/> 176 <option value="ALL">ALL</option>
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)"/> 177 </param>
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)"/> 178 <repeat min="0" name="rep_param_exclusion_charges" title="param_exclusion_charges">
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)"/> 179 <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">
71 <param name="param_mz_tol_unit" type="select" optional="True" value="ppm" label="Unit of 'mz_tol'" help="(-mz_tol_unit)"> 180 <sanitizer>
72 <option value="ppm">ppm</option> 181 <valid initial="string.printable">
73 <option value="Da">Da</option> 182 <remove value="'"/>
74 </param> 183 <remove value="&quot;"/>
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)"/> 184 </valid>
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)"/> 185 </sanitizer>
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)"/> 186 </param>
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)"/> 187 </repeat>
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)"/> 188 <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"/>
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)"/> 189 <param help="(-missed_cleavages) &lt;br&gt;" label="Number of missed cleavages used for protein digestion" name="param_algorithm_InclusionExclusionList_missed_cleavages" type="integer" value="0"/>
81 <param name="param_min_rt" type="float" min="0.0" optional="True" value="960.0" label="Minimal rt in seconds." help="(-min_rt)"/> 190 <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">
82 <param name="param_max_rt" type="float" min="0.0" optional="True" value="3840.0" label="Maximal rt in seconds." help="(-max_rt)"/> 191 <option value="minutes">minutes</option>
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)"/> 192 <option value="seconds">seconds</option>
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)"/> 193 </param>
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)"/> 194 <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"/>
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)"/> 195 <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"/>
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)"/> 196 <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"/>
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)"/> 197 <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"/>
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)"/> 198 <param help="(-mz_tol_unit) " label="Unit of 'mz_tol'" name="param_algorithm_InclusionExclusionList_merge_mz_tol_unit" optional="True" type="select" value="ppm">
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)"/> 199 <option value="ppm">ppm</option>
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)"/> 200 <option value="Da">Da</option>
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)"/> 201 </param>
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)"/> 202 <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"/>
94 </inputs> 203 <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"/>
95 <outputs> 204 <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"/>
96 <data name="param_out" label="Output file (tab delimited csv file)." format="tabular"/> 205 <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"/>
97 </outputs> 206 <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"/>
98 <help>**What it does** 207 <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"/>
99 208 <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"/>
100 Creates inclusion and/or exclusion lists. 209 <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"/>
101 210 <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"/>
102 211 <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"/>
103 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InclusionExclusionListCreator.html 212 <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"/>
104 213 <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"/>
105 @REFERENCES@ 214 <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"/>
106 </help> 215 <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"/>
107 </tool> 216 <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"/>
217 <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"/>
218 <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"/>
219 <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"/>
220 <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"/>
221 <expand macro="advanced_options">
222 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
223 </expand>
224 </inputs>
225 <outputs>
226 <data format="tabular" name="param_out"/>
227 </outputs>
228 <help>Creates inclusion and/or exclusion lists.
229
230
231 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InclusionExclusionListCreator.html</help>
232 </tool>