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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
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3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="PrecursorIonSelector" name="PrecursorIonSelector" 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>PrecursorIonSelector</description> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <macros> 4 <tool id="PrecursorIonSelector" name="PrecursorIonSelector" version="2.0.0">
5 <token name="@EXECUTABLE@">PrecursorIonSelector</token> 5 <description>PrecursorIonSelector</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">PrecursorIonSelector</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>PrecursorIonSelector 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>PrecursorIonSelector
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 -next_feat ${param_next_feat} 17 #end if
15 -ids ${param_ids} 18 #if $param_out:
16 -num_precursors ${param_num_precursors} 19 -out $param_out
17 -raw_data ${param_raw_data} 20 #end if
18 ${param_load_preprocessing} 21 #if $param_next_feat:
19 ${param_store_preprocessing} 22 -next_feat $param_next_feat
20 ${param_simulation} 23 #end if
21 -sim_results ${param_sim_results} 24 #if $param_ids:
22 -db_path ${param_db_path} 25 -ids $param_ids
23 -rt_model ${param_rt_model} 26 #end if
24 -dt_model ${param_dt_model} 27 #if $param_num_precursors:
25 -fixed_modifications ${param_fixed_modifications} 28 -num_precursors $param_num_precursors
26 -threads \${GALAXY_SLOTS:-24} 29 #end if
27 -algorithm:type ${param_type} 30 #if $param_raw_data:
28 -algorithm:max_iteration ${param_max_iteration} 31 -raw_data $param_raw_data
29 -algorithm:rt_bin_capacity ${param_rt_bin_capacity} 32 #end if
30 -algorithm:step_size ${param_step_size} 33 #if $param_load_preprocessing:
31 -algorithm:peptide_min_prob ${param_peptide_min_prob} 34 -load_preprocessing
32 ${param_sequential_spectrum_order} 35 #end if
33 -algorithm:MIPFormulation:thresholds:min_protein_probability ${param_min_protein_probability} 36 #if $param_store_preprocessing:
34 -algorithm:MIPFormulation:thresholds:min_protein_id_probability ${param_min_protein_id_probability} 37 -store_preprocessing
35 -algorithm:MIPFormulation:thresholds:min_pt_weight ${param_min_pt_weight} 38 #end if
36 -algorithm:MIPFormulation:thresholds:min_mz ${param_min_mz} 39 #if $param_simulation:
37 -algorithm:MIPFormulation:thresholds:max_mz ${param_max_mz} 40 -simulation
38 -algorithm:MIPFormulation:thresholds:min_pred_pep_prob ${param_min_pred_pep_prob} 41 #end if
39 -algorithm:MIPFormulation:thresholds:min_rt_weight ${param_min_rt_weight} 42 #if $param_sim_results:
40 ${param_use_peptide_rule} 43 -sim_results &quot;$param_sim_results&quot;
41 -algorithm:MIPFormulation:thresholds:min_peptide_ids ${param_min_peptide_ids} 44 #end if
42 -algorithm:MIPFormulation:thresholds:min_peptide_probability ${param_min_peptide_probability} 45 #if $param_db_path:
43 -algorithm:MIPFormulation:combined_ilp:k1 ${param_k1} 46 -db_path $param_db_path
44 -algorithm:MIPFormulation:combined_ilp:k2 ${param_k2} 47 #end if
45 -algorithm:MIPFormulation:combined_ilp:k3 ${param_k3} 48 #if $param_rt_model:
46 ${param_scale_matching_probs} 49 -rt_model &quot;$param_rt_model&quot;
47 ${param_no_intensity_normalization} 50 #end if
48 -algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature ${param_max_number_precursors_per_feature} 51 #if $param_dt_model:
49 -algorithm:Preprocessing:precursor_mass_tolerance ${param_precursor_mass_tolerance} 52 -dt_model &quot;$param_dt_model&quot;
50 -algorithm:Preprocessing:precursor_mass_tolerance_unit ${param_precursor_mass_tolerance_unit} 53 #end if
51 -algorithm:Preprocessing:preprocessed_db_path ${param_preprocessed_db_path} 54
52 -algorithm:Preprocessing:preprocessed_db_pred_rt_path ${param_preprocessed_db_pred_rt_path} 55 #if $rep_param_fixed_modifications:
53 -algorithm:Preprocessing:preprocessed_db_pred_dt_path ${param_preprocessed_db_pred_dt_path} 56 -fixed_modifications
54 -algorithm:Preprocessing:max_peptides_per_run ${param_max_peptides_per_run} 57 #for token in $rep_param_fixed_modifications:
55 -algorithm:Preprocessing:missed_cleavages ${param_missed_cleavages} 58 #if &quot; &quot; in str(token):
56 -algorithm:Preprocessing:taxonomy ${param_taxonomy} 59 &quot;$token.param_fixed_modifications&quot;
57 -algorithm:Preprocessing:tmp_dir ${param_tmp_dir} 60 #else
58 -algorithm:Preprocessing:store_peptide_sequences ${param_store_peptide_sequences} 61 $token.param_fixed_modifications
59 -algorithm:Preprocessing:rt_settings:min_rt ${param_min_rt} 62 #end if
60 -algorithm:Preprocessing:rt_settings:max_rt ${param_max_rt} 63 #end for
61 -algorithm:Preprocessing:rt_settings:rt_step_size ${param_rt_step_size} 64 #end if
62 -algorithm:Preprocessing:rt_settings:gauss_mean ${param_gauss_mean} 65 -threads \${GALAXY_SLOTS:-24}
63 -algorithm:Preprocessing:rt_settings:gauss_sigma ${param_gauss_sigma} 66 #if $param_algorithm_type:
67 -algorithm:type
68 #if &quot; &quot; in str($param_algorithm_type):
69 &quot;$param_algorithm_type&quot;
70 #else
71 $param_algorithm_type
72 #end if
73 #end if
74 #if $param_algorithm_max_iteration:
75 -algorithm:max_iteration $param_algorithm_max_iteration
76 #end if
77 #if $param_algorithm_rt_bin_capacity:
78 -algorithm:rt_bin_capacity $param_algorithm_rt_bin_capacity
79 #end if
80 #if $param_algorithm_step_size:
81 -algorithm:step_size $param_algorithm_step_size
82 #end if
83 #if $param_algorithm_peptide_min_prob:
84 -algorithm:peptide_min_prob $param_algorithm_peptide_min_prob
85 #end if
86 #if $param_algorithm_sequential_spectrum_order:
87 -algorithm:sequential_spectrum_order
88 #end if
89 #if $param_algorithm_MIPFormulation_thresholds_min_protein_probability:
90 -algorithm:MIPFormulation:thresholds:min_protein_probability $param_algorithm_MIPFormulation_thresholds_min_protein_probability
91 #end if
92 #if $param_algorithm_MIPFormulation_thresholds_min_protein_id_probability:
93 -algorithm:MIPFormulation:thresholds:min_protein_id_probability $param_algorithm_MIPFormulation_thresholds_min_protein_id_probability
94 #end if
95 #if $param_algorithm_MIPFormulation_thresholds_min_pt_weight:
96 -algorithm:MIPFormulation:thresholds:min_pt_weight $param_algorithm_MIPFormulation_thresholds_min_pt_weight
97 #end if
98 #if $param_algorithm_MIPFormulation_thresholds_min_mz:
99 -algorithm:MIPFormulation:thresholds:min_mz $param_algorithm_MIPFormulation_thresholds_min_mz
100 #end if
101 #if $param_algorithm_MIPFormulation_thresholds_max_mz:
102 -algorithm:MIPFormulation:thresholds:max_mz $param_algorithm_MIPFormulation_thresholds_max_mz
103 #end if
104 #if $param_algorithm_MIPFormulation_thresholds_min_pred_pep_prob:
105 -algorithm:MIPFormulation:thresholds:min_pred_pep_prob $param_algorithm_MIPFormulation_thresholds_min_pred_pep_prob
106 #end if
107 #if $param_algorithm_MIPFormulation_thresholds_min_rt_weight:
108 -algorithm:MIPFormulation:thresholds:min_rt_weight $param_algorithm_MIPFormulation_thresholds_min_rt_weight
109 #end if
110 #if $param_algorithm_MIPFormulation_thresholds_use_peptide_rule:
111 -algorithm:MIPFormulation:thresholds:use_peptide_rule
112 #end if
113 #if $param_algorithm_MIPFormulation_thresholds_min_peptide_ids:
114 -algorithm:MIPFormulation:thresholds:min_peptide_ids $param_algorithm_MIPFormulation_thresholds_min_peptide_ids
115 #end if
116 #if $param_algorithm_MIPFormulation_thresholds_min_peptide_probability:
117 -algorithm:MIPFormulation:thresholds:min_peptide_probability $param_algorithm_MIPFormulation_thresholds_min_peptide_probability
118 #end if
119 #if $param_algorithm_MIPFormulation_combined_ilp_k1:
120 -algorithm:MIPFormulation:combined_ilp:k1 $param_algorithm_MIPFormulation_combined_ilp_k1
121 #end if
122 #if $param_algorithm_MIPFormulation_combined_ilp_k2:
123 -algorithm:MIPFormulation:combined_ilp:k2 $param_algorithm_MIPFormulation_combined_ilp_k2
124 #end if
125 #if $param_algorithm_MIPFormulation_combined_ilp_k3:
126 -algorithm:MIPFormulation:combined_ilp:k3 $param_algorithm_MIPFormulation_combined_ilp_k3
127 #end if
128 #if $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs:
129 -algorithm:MIPFormulation:combined_ilp:scale_matching_probs
130 #end if
131 #if $param_algorithm_MIPFormulation_feature_based_no_intensity_normalization:
132 -algorithm:MIPFormulation:feature_based:no_intensity_normalization
133 #end if
134 #if $param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature:
135 -algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature $param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature
136 #end if
137 #if $param_algorithm_Preprocessing_precursor_mass_tolerance:
138 -algorithm:Preprocessing:precursor_mass_tolerance $param_algorithm_Preprocessing_precursor_mass_tolerance
139 #end if
140 #if $param_algorithm_Preprocessing_precursor_mass_tolerance_unit:
141 -algorithm:Preprocessing:precursor_mass_tolerance_unit
142 #if &quot; &quot; in str($param_algorithm_Preprocessing_precursor_mass_tolerance_unit):
143 &quot;$param_algorithm_Preprocessing_precursor_mass_tolerance_unit&quot;
144 #else
145 $param_algorithm_Preprocessing_precursor_mass_tolerance_unit
146 #end if
147 #end if
148 #if $param_algorithm_Preprocessing_preprocessed_db_path:
149 -algorithm:Preprocessing:preprocessed_db_path &quot;$param_algorithm_Preprocessing_preprocessed_db_path&quot;
150 #end if
151 #if $param_algorithm_Preprocessing_preprocessed_db_pred_rt_path:
152 -algorithm:Preprocessing:preprocessed_db_pred_rt_path &quot;$param_algorithm_Preprocessing_preprocessed_db_pred_rt_path&quot;
153 #end if
154 #if $param_algorithm_Preprocessing_preprocessed_db_pred_dt_path:
155 -algorithm:Preprocessing:preprocessed_db_pred_dt_path &quot;$param_algorithm_Preprocessing_preprocessed_db_pred_dt_path&quot;
156 #end if
157 #if $param_algorithm_Preprocessing_max_peptides_per_run:
158 -algorithm:Preprocessing:max_peptides_per_run $param_algorithm_Preprocessing_max_peptides_per_run
159 #end if
160 #if $param_algorithm_Preprocessing_missed_cleavages:
161 -algorithm:Preprocessing:missed_cleavages $param_algorithm_Preprocessing_missed_cleavages
162 #end if
163 #if $param_algorithm_Preprocessing_taxonomy:
164 -algorithm:Preprocessing:taxonomy &quot;$param_algorithm_Preprocessing_taxonomy&quot;
165 #end if
166 #if $param_algorithm_Preprocessing_tmp_dir:
167 -algorithm:Preprocessing:tmp_dir &quot;$param_algorithm_Preprocessing_tmp_dir&quot;
168 #end if
169 #if $param_algorithm_Preprocessing_store_peptide_sequences:
170 -algorithm:Preprocessing:store_peptide_sequences &quot;$param_algorithm_Preprocessing_store_peptide_sequences&quot;
171 #end if
172 #if $param_algorithm_Preprocessing_rt_settings_min_rt:
173 -algorithm:Preprocessing:rt_settings:min_rt $param_algorithm_Preprocessing_rt_settings_min_rt
174 #end if
175 #if $param_algorithm_Preprocessing_rt_settings_max_rt:
176 -algorithm:Preprocessing:rt_settings:max_rt $param_algorithm_Preprocessing_rt_settings_max_rt
177 #end if
178 #if $param_algorithm_Preprocessing_rt_settings_rt_step_size:
179 -algorithm:Preprocessing:rt_settings:rt_step_size $param_algorithm_Preprocessing_rt_settings_rt_step_size
180 #end if
181 #if $param_algorithm_Preprocessing_rt_settings_gauss_mean:
182 -algorithm:Preprocessing:rt_settings:gauss_mean $param_algorithm_Preprocessing_rt_settings_gauss_mean
183 #end if
184 #if $param_algorithm_Preprocessing_rt_settings_gauss_sigma:
185 -algorithm:Preprocessing:rt_settings:gauss_sigma $param_algorithm_Preprocessing_rt_settings_gauss_sigma
186 #end if
64 #if $adv_opts.adv_opts_selector=='advanced': 187 #if $adv_opts.adv_opts_selector=='advanced':
65 -solver ${adv_opts.param_solver} 188 #if $adv_opts.param_solver:
189 -solver
190 #if &quot; &quot; in str($adv_opts.param_solver):
191 &quot;$adv_opts.param_solver&quot;
192 #else
193 $adv_opts.param_solver
194 #end if
195 #end if
196 #if $adv_opts.param_force:
197 -force
198 #end if
66 #end if 199 #end if
67 </command> 200 </command>
68 <inputs> 201 <inputs>
69 <param name="param_in" type="data" format="featureXML" optional="False" label="Input feature map file (featureXML)" help="(-in)"/> 202 <param format="xml" help="(-in) " label="Input feature map file (featureXML)" name="param_in" optional="False" type="data"/>
70 <param name="param_ids" type="text" size="20" label="file containing results of identification (idXML)" help="(-ids)"/> 203 <param format="xml" help="(-ids) " label="file containing results of identification" name="param_ids" optional="False" type="data"/>
71 <param name="param_num_precursors" type="integer" value="1" label="number of precursors to be selected" help="(-num_precursors)"/> 204 <param help="(-num_precursors) " label="number of precursors to be selected" name="param_num_precursors" type="integer" value="1"/>
72 <param name="param_raw_data" type="data" format="mzML" optional="True" label="Input profile data." help="(-raw_data)"/> 205 <param format="mzml" help="(-raw_data) " label="Input profile data" name="param_raw_data" optional="True" type="data"/>
73 <param name="param_load_preprocessing" type="boolean" truevalue="-load_preprocessing true" falsevalue="-load_preprocessing false" checked="false" optional="True" label="The preprocessed db is loaded from file, not calculated." help="(-load_preprocessing)"/> 206 <param checked="false" falsevalue="" help="(-load_preprocessing) " label="The preprocessed db is loaded from file, not calculated" name="param_load_preprocessing" optional="True" truevalue="-load_preprocessing" type="boolean"/>
74 <param name="param_store_preprocessing" type="boolean" truevalue="-store_preprocessing true" falsevalue="-store_preprocessing false" checked="false" optional="True" label="The preprocessed db is stored." help="(-store_preprocessing)"/> 207 <param checked="false" falsevalue="" help="(-store_preprocessing) " label="The preprocessed db is stored" name="param_store_preprocessing" optional="True" truevalue="-store_preprocessing" type="boolean"/>
75 <param name="param_simulation" type="boolean" truevalue="-simulation true" falsevalue="-simulation false" checked="false" optional="True" label="Simulate the whole LC-MS/MS run." help="(-simulation)"/> 208 <param checked="false" falsevalue="" help="(-simulation) " label="Simulate the whole LC-MS/MS run" name="param_simulation" optional="True" truevalue="-simulation" type="boolean"/>
76 <param name="param_sim_results" type="text" size="20" label="File containing the results of the simulation run" help="(-sim_results)"/> 209 <param help="(-sim_results) " label="File containing the results of the simulation run" name="param_sim_results" size="30" type="text">
77 <param name="param_db_path" type="data" format="fasta" optional="True" label="db file" help="(-db_path)"/> 210 <sanitizer>
78 <param name="param_rt_model" type="text" size="20" label="SVM Model for RTPredict" help="(-rt_model)"/> 211 <valid initial="string.printable">
79 <param name="param_dt_model" type="text" size="20" label="SVM Model for PTPredict" help="(-dt_model)"/> 212 <remove value="'"/>
80 <param name="param_fixed_modifications" type="text" size="20" label="the modifications i.e. Carboxymethyl (C)" help="(-fixed_modifications)"/> 213 <remove value="&quot;"/>
81 <param name="param_type" type="select" optional="True" value="IPS" label="Strategy for precursor ion selection." help="(-type)"> 214 </valid>
82 <option value="ILP_IPS">ILP_IPS</option> 215 </sanitizer>
83 <option value="IPS">IPS</option> 216 </param>
84 <option value="SPS">SPS</option> 217 <param format="fasta" help="(-db_path) " label="db file" name="param_db_path" optional="True" type="data"/>
85 <option value="Upshift">Upshift</option> 218 <param help="(-rt_model) " label="SVM Model for RTPredict" name="param_rt_model" size="30" type="text">
86 <option value="Downshift">Downshift</option> 219 <sanitizer>
87 <option value="DEX">DEX</option> 220 <valid initial="string.printable">
88 </param> 221 <remove value="'"/>
89 <param name="param_max_iteration" type="integer" min="1" optional="True" value="100" label="Maximal number of iterations." help="(-max_iteration)"/> 222 <remove value="&quot;"/>
90 <param name="param_rt_bin_capacity" type="integer" min="1" optional="True" value="10" label="Maximal number of precursors per rt bin." help="(-rt_bin_capacity)"/> 223 </valid>
91 <param name="param_step_size" type="integer" min="1" optional="True" value="1" label="Maximal number of precursors per iteration." help="(-step_size)"/> 224 </sanitizer>
92 <param name="param_peptide_min_prob" type="float" value="0.2" label="Minimal peptide probability." help="(-peptide_min_prob)"/> 225 </param>
93 <param name="param_sequential_spectrum_order" type="boolean" truevalue="-algorithm:sequential_spectrum_order true" falsevalue="-algorithm:sequential_spectrum_order false" checked="false" optional="True" label="If true, precursors are selected sequentially with respect to their RT." help="(-sequential_spectrum_order)"/> 226 <param help="(-dt_model) " label="SVM Model for PTPredict" name="param_dt_model" size="30" type="text">
94 <param name="param_min_protein_probability" type="float" min="0.0" max="1.0" optional="True" value="0.2" label="Minimal protein probability for a protein to be considered in the ILP" help="(-min_protein_probability)"/> 227 <sanitizer>
95 <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)"/> 228 <valid initial="string.printable">
96 <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)"/> 229 <remove value="'"/>
97 <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)"/> 230 <remove value="&quot;"/>
98 <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)"/> 231 </valid>
99 <param name="param_min_pred_pep_prob" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal predicted peptide probability of a precursor" help="(-min_pred_pep_prob)"/> 232 </sanitizer>
100 <param name="param_min_rt_weight" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal rt weight of a precursor" help="(-min_rt_weight)"/> 233 </param>
101 <param name="param_use_peptide_rule" type="boolean" truevalue="-algorithm:MIPFormulation:thresholds:use_peptide_rule true" falsevalue="-algorithm:MIPFormulation:thresholds:use_peptide_rule false" checked="false" optional="True" label="Use peptide rule instead of minimal protein id probability" help="(-use_peptide_rule)"/> 234 <repeat min="0" name="rep_param_fixed_modifications" title="param_fixed_modifications">
102 <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)"/> 235 <param help="(-fixed_modifications) " label="the modifications i.e. Carboxymethyl (C)" name="param_fixed_modifications" size="30" type="text">
103 <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)"/> 236 <sanitizer>
104 <param name="param_k1" type="float" min="0.0" optional="True" value="0.2" label="combined ilp: weight for z_i" help="(-k1)"/> 237 <valid initial="string.printable">
105 <param name="param_k2" type="float" min="0.0" optional="True" value="0.2" label="combined ilp: weight for x_j,s*int_j,s" help="(-k2)"/> 238 <remove value="'"/>
106 <param name="param_k3" type="float" min="0.0" optional="True" value="0.4" label="combined ilp: weight for -x_j,s*w_j,s" help="(-k3)"/> 239 <remove value="&quot;"/>
107 <param name="param_scale_matching_probs" type="boolean" truevalue="-algorithm:MIPFormulation:combined_ilp:scale_matching_probs true" falsevalue="-algorithm:MIPFormulation:combined_ilp:scale_matching_probs false" checked="true" optional="True" label="flag if detectability * rt_weight shall be scaled to cover all [0,1]" help="(-scale_matching_probs)"/> 240 </valid>
108 <param name="param_no_intensity_normalization" type="boolean" truevalue="-algorithm:MIPFormulation:feature_based:no_intensity_normalization true" falsevalue="-algorithm:MIPFormulation: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)"/> 241 </sanitizer>
109 <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)"/> 242 </param>
110 <param name="param_precursor_mass_tolerance" type="float" min="0.0" optional="True" value="10.0" label="Precursor mass tolerance which is used to query the peptide database for peptides" help="(-precursor_mass_tolerance)"/> 243 </repeat>
111 <param name="param_precursor_mass_tolerance_unit" type="select" optional="True" value="ppm" label="Precursor mass tolerance unit." help="(-precursor_mass_tolerance_unit)"> 244 <param help="(-type) " label="Strategy for precursor ion selection" name="param_algorithm_type" optional="True" type="select" value="IPS">
112 <option value="ppm">ppm</option> 245 <option value="ILP_IPS">ILP_IPS</option>
113 <option value="Da">Da</option> 246 <option value="IPS">IPS</option>
114 </param> 247 <option value="SPS">SPS</option>
115 <param name="param_preprocessed_db_path" type="text" size="20" label="Path where the preprocessed database should be stored" help="(-preprocessed_db_path)"/> 248 <option value="Upshift">Upshift</option>
116 <param name="param_preprocessed_db_pred_rt_path" type="text" size="20" label="Path where the predicted rts of the preprocessed database should be stored" help="(-preprocessed_db_pred_rt_path)"/> 249 <option value="Downshift">Downshift</option>
117 <param name="param_preprocessed_db_pred_dt_path" type="text" size="20" label="Path where the predicted rts of the preprocessed database should be stored" help="(-preprocessed_db_pred_dt_path)"/> 250 <option value="DEX">DEX</option>
118 <param name="param_max_peptides_per_run" type="integer" min="1" optional="True" value="100000" label="Number of peptides for that the pt and rt are parallely predicted." help="(-max_peptides_per_run)"/> 251 </param>
119 <param name="param_missed_cleavages" type="integer" min="0" optional="True" value="1" label="Number of allowed missed cleavages." help="(-missed_cleavages)"/> 252 <param help="(-max_iteration) " label="Maximal number of iterations" min="1" name="param_algorithm_max_iteration" optional="True" type="integer" value="100"/>
120 <param name="param_taxonomy" type="text" size="20" label="Taxonomy" help="(-taxonomy)"/> 253 <param help="(-rt_bin_capacity) " label="Maximal number of precursors per rt bin" min="1" name="param_algorithm_rt_bin_capacity" optional="True" type="integer" value="10"/>
121 <param name="param_tmp_dir" type="text" size="20" label="Absolute path to tmp data directory used to store files needed for rt and dt prediction." help="(-tmp_dir)"/> 254 <param help="(-step_size) " label="Maximal number of precursors per iteration" min="1" name="param_algorithm_step_size" optional="True" type="integer" value="1"/>
122 <param name="param_store_peptide_sequences" type="text" size="20" value="false" label="Flag if peptide sequences should be stored." help="(-store_peptide_sequences)"/> 255 <param help="(-peptide_min_prob) " label="Minimal peptide probability" name="param_algorithm_peptide_min_prob" type="float" value="0.2"/>
123 <param name="param_min_rt" type="float" min="1.0" optional="True" value="960.0" label="Minimal RT in the experiment (in seconds)" help="(-min_rt)"/> 256 <param checked="false" falsevalue="" help="(-sequential_spectrum_order) " label="If true, precursors are selected sequentially with respect to their RT" name="param_algorithm_sequential_spectrum_order" optional="True" truevalue="-algorithm:sequential_spectrum_order" type="boolean"/>
124 <param name="param_max_rt" type="float" value="3840.0" label="Maximal RT in the experiment (in seconds)" help="(-max_rt)"/> 257 <param help="(-min_protein_probability) " label="Minimal protein probability for a protein to be considered in the ILP" max="1.0" min="0.0" name="param_algorithm_MIPFormulation_thresholds_min_protein_probability" optional="True" type="float" value="0.2"/>
125 <param name="param_rt_step_size" type="float" value="30.0" label="Time between two consecutive spectra (in seconds)" help="(-rt_step_size)"/> 258 <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_MIPFormulation_thresholds_min_protein_id_probability" optional="True" type="float" value="0.95"/>
126 <param name="param_gauss_mean" type="float" value="-1.0" label="mean of the gauss curve" help="(-gauss_mean)"/> 259 <param help="(-min_pt_weight) " label="Minimal pt weight of a precurso" max="1.0" min="0.0" name="param_algorithm_MIPFormulation_thresholds_min_pt_weight" optional="True" type="float" value="0.5"/>
127 <param name="param_gauss_sigma" type="float" value="3.0" label="std of the gauss curve" help="(-gauss_sigma)"/> 260 <param help="(-min_mz) " label="Minimal mz to be considered in protein based LP formulation" min="0.0" name="param_algorithm_MIPFormulation_thresholds_min_mz" optional="True" type="float" value="500.0"/>
128 <expand macro="advanced_options"> 261 <param help="(-max_mz) " label="Minimal mz to be considered in protein based LP formulation" min="0.0" name="param_algorithm_MIPFormulation_thresholds_max_mz" optional="True" type="float" value="5000.0"/>
129 <param name="param_solver" type="select" optional="True" value="GLPK" label="LP solver type" help="(-solver)"> 262 <param help="(-min_pred_pep_prob) " label="Minimal predicted peptide probability of a precurso" max="1.0" min="0.0" name="param_algorithm_MIPFormulation_thresholds_min_pred_pep_prob" optional="True" type="float" value="0.5"/>
130 <option value="GLPK">GLPK</option> 263 <param help="(-min_rt_weight) " label="Minimal rt weight of a precurso" max="1.0" min="0.0" name="param_algorithm_MIPFormulation_thresholds_min_rt_weight" optional="True" type="float" value="0.5"/>
131 <option value="COINOR">COINOR</option> 264 <param checked="false" falsevalue="" help="(-use_peptide_rule) " label="Use peptide rule instead of minimal protein id probability" name="param_algorithm_MIPFormulation_thresholds_use_peptide_rule" optional="True" truevalue="-algorithm:MIPFormulation:thresholds:use_peptide_rule" type="boolean"/>
132 </param> 265 <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_MIPFormulation_thresholds_min_peptide_ids" optional="True" type="integer" value="2"/>
133 </expand> 266 <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_MIPFormulation_thresholds_min_peptide_probability" optional="True" type="float" value="0.95"/>
134 </inputs> 267 <param help="(-k1) " label="combined ilp: weight for z_i" min="0.0" name="param_algorithm_MIPFormulation_combined_ilp_k1" optional="True" type="float" value="0.2"/>
135 <outputs> 268 <param help="(-k2) " label="combined ilp: weight for x_j,s*int_j,s" min="0.0" name="param_algorithm_MIPFormulation_combined_ilp_k2" optional="True" type="float" value="0.2"/>
136 <data name="param_out" label="modified feature map" format="featureXML"/> 269 <param help="(-k3) " label="combined ilp: weight for -x_j,s*w_j,s" min="0.0" name="param_algorithm_MIPFormulation_combined_ilp_k3" optional="True" type="float" value="0.4"/>
137 <data name="param_next_feat" label="feature map (featureXML) file with the selected precursors" format="featureXML"/> 270 <param checked="true" falsevalue="" help="(-scale_matching_probs) " label="flag if detectability * rt_weight shall be scaled to cover all [0,1]" name="param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs" optional="True" truevalue="-algorithm:MIPFormulation:combined_ilp:scale_matching_probs" type="boolean"/>
138 </outputs> 271 <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_MIPFormulation_feature_based_no_intensity_normalization" optional="True" truevalue="-algorithm:MIPFormulation:feature_based:no_intensity_normalization" type="boolean"/>
139 <help>**What it does** 272 <param help="(-max_number_precursors_per_feature) " label="The maximal number of precursors per feature" min="1" name="param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature" optional="True" type="integer" value="1"/>
140 273 <param help="(-precursor_mass_tolerance) " label="Precursor mass tolerance which is used to query the peptide database for peptides" min="0.0" name="param_algorithm_Preprocessing_precursor_mass_tolerance" optional="True" type="float" value="10.0"/>
141 PrecursorIonSelector 274 <param help="(-precursor_mass_tolerance_unit) " label="Precursor mass tolerance unit" name="param_algorithm_Preprocessing_precursor_mass_tolerance_unit" optional="True" type="select" value="ppm">
275 <option value="ppm">ppm</option>
276 <option value="Da">Da</option>
277 </param>
278 <param help="(-preprocessed_db_path) " label="Path where the preprocessed database should be stored" name="param_algorithm_Preprocessing_preprocessed_db_path" size="30" type="text">
279 <sanitizer>
280 <valid initial="string.printable">
281 <remove value="'"/>
282 <remove value="&quot;"/>
283 </valid>
284 </sanitizer>
285 </param>
286 <param help="(-preprocessed_db_pred_rt_path) " label="Path where the predicted rts of the preprocessed database should be stored" name="param_algorithm_Preprocessing_preprocessed_db_pred_rt_path" size="30" type="text">
287 <sanitizer>
288 <valid initial="string.printable">
289 <remove value="'"/>
290 <remove value="&quot;"/>
291 </valid>
292 </sanitizer>
293 </param>
294 <param help="(-preprocessed_db_pred_dt_path) " label="Path where the predicted rts of the preprocessed database should be stored" name="param_algorithm_Preprocessing_preprocessed_db_pred_dt_path" size="30" type="text">
295 <sanitizer>
296 <valid initial="string.printable">
297 <remove value="'"/>
298 <remove value="&quot;"/>
299 </valid>
300 </sanitizer>
301 </param>
302 <param help="(-max_peptides_per_run) " label="Number of peptides for that the pt and rt are parallely predicted" min="1" name="param_algorithm_Preprocessing_max_peptides_per_run" optional="True" type="integer" value="100000"/>
303 <param help="(-missed_cleavages) " label="Number of allowed missed cleavages" min="0" name="param_algorithm_Preprocessing_missed_cleavages" optional="True" type="integer" value="1"/>
304 <param help="(-taxonomy) " label="Taxonomy" name="param_algorithm_Preprocessing_taxonomy" size="30" type="text">
305 <sanitizer>
306 <valid initial="string.printable">
307 <remove value="'"/>
308 <remove value="&quot;"/>
309 </valid>
310 </sanitizer>
311 </param>
312 <param help="(-tmp_dir) " label="Absolute path to tmp data directory used to store files needed for rt and dt prediction" name="param_algorithm_Preprocessing_tmp_dir" size="30" type="text">
313 <sanitizer>
314 <valid initial="string.printable">
315 <remove value="'"/>
316 <remove value="&quot;"/>
317 </valid>
318 </sanitizer>
319 </param>
320 <param help="(-store_peptide_sequences) " label="Flag if peptide sequences should be stored" name="param_algorithm_Preprocessing_store_peptide_sequences" size="30" type="text" value="false">
321 <sanitizer>
322 <valid initial="string.printable">
323 <remove value="'"/>
324 <remove value="&quot;"/>
325 </valid>
326 </sanitizer>
327 </param>
328 <param help="(-min_rt) " label="Minimal RT in the experiment (in seconds)" min="1.0" name="param_algorithm_Preprocessing_rt_settings_min_rt" optional="True" type="float" value="960.0"/>
329 <param help="(-max_rt) " label="Maximal RT in the experiment (in seconds)" name="param_algorithm_Preprocessing_rt_settings_max_rt" type="float" value="3840.0"/>
330 <param help="(-rt_step_size) " label="Time between two consecutive spectra (in seconds)" name="param_algorithm_Preprocessing_rt_settings_rt_step_size" type="float" value="30.0"/>
331 <param help="(-gauss_mean) " label="mean of the gauss curve" name="param_algorithm_Preprocessing_rt_settings_gauss_mean" type="float" value="-1.0"/>
332 <param help="(-gauss_sigma) " label="std of the gauss curve" name="param_algorithm_Preprocessing_rt_settings_gauss_sigma" type="float" value="3.0"/>
333 <expand macro="advanced_options">
334 <param help="(-solver) " label="LP solver type" name="param_solver" optional="True" type="select" value="GLPK">
335 <option value="GLPK">GLPK</option>
336 <option value="COINOR">COINOR</option>
337 </param>
338 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
339 </expand>
340 </inputs>
341 <outputs>
342 <data format="xml" name="param_out"/>
343 <data format="xml" name="param_next_feat"/>
344 </outputs>
345 <help>PrecursorIonSelector
142 346
143 347
144 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PrecursorIonSelector.html 348 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PrecursorIonSelector.html</help>
145 349 </tool>
146 @REFERENCES@
147 </help>
148 </tool>