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comparison PrecursorIonSelector.xml @ 9:faac17171cc2 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 03 Sep 2020 16:17:23 +0000
parents de49246e559a
children fa7a58de2977
comparison
equal deleted inserted replaced
8:2faa1a2401c5 9:faac17171cc2
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Targeted Experiments]--> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="PrecursorIonSelector" name="PrecursorIonSelector" version="2.3.0"> 4 <tool id="PrecursorIonSelector" name="PrecursorIonSelector" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>PrecursorIonSelector</description> 5 <description>PrecursorIonSelector</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">PrecursorIonSelector</token> 7 <token name="@EXECUTABLE@">PrecursorIonSelector</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[PrecursorIonSelector 15 @EXT_FOO@
14 16 #import re
15 #if $param_in: 17
16 -in $param_in 18 ## Preprocessing
17 #end if 19 mkdir in &&
18 #if $param_out: 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 -out $param_out 21 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
20 #end if 22 mkdir out &&
21 #if $param_next_feat: 23 #end if
22 -next_feat $param_next_feat 24 #if "next_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
23 #end if 25 mkdir next_feat &&
24 #if $param_ids: 26 #end if
25 -ids $param_ids 27 mkdir ids &&
26 #end if 28 ln -s '$ids' 'ids/${re.sub("[^\w\-_]", "_", $ids.element_identifier)}.$gxy2omsext($ids.ext)' &&
27 #if $param_num_precursors: 29 #if $raw_data:
28 -num_precursors $param_num_precursors 30 mkdir raw_data &&
29 #end if 31 ln -s '$raw_data' 'raw_data/${re.sub("[^\w\-_]", "_", $raw_data.element_identifier)}.$gxy2omsext($raw_data.ext)' &&
30 #if $param_raw_data: 32 #end if
31 -raw_data $param_raw_data 33 #if "sim_results_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
32 #end if 34 mkdir sim_results &&
33 #if $param_load_preprocessing: 35 #end if
34 -load_preprocessing 36 #if $db_path:
35 #end if 37 mkdir db_path &&
36 #if $param_store_preprocessing: 38 ln -s '$db_path' 'db_path/${re.sub("[^\w\-_]", "_", $db_path.element_identifier)}.$gxy2omsext($db_path.ext)' &&
37 -store_preprocessing 39 #end if
38 #end if 40 #if $rt_model:
39 #if $param_simulation: 41 mkdir rt_model &&
40 -simulation 42 ln -s '$rt_model' 'rt_model/${re.sub("[^\w\-_]", "_", $rt_model.element_identifier)}.$gxy2omsext($rt_model.ext)' &&
41 #end if 43 #end if
42 #if $param_sim_results: 44 #if $dt_model:
43 -sim_results "$param_sim_results" 45 mkdir dt_model &&
44 #end if 46 ln -s '$dt_model' 'dt_model/${re.sub("[^\w\-_]", "_", $dt_model.element_identifier)}.$gxy2omsext($dt_model.ext)' &&
45 #if $param_db_path: 47 #end if
46 -db_path $param_db_path 48
47 #end if 49 ## Main program call
48 #if $param_rt_model: 50
49 -rt_model "$param_rt_model" 51 set -o pipefail &&
50 #end if 52 @EXECUTABLE@ -write_ctd ./ &&
51 #if $param_dt_model: 53 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
52 -dt_model "$param_dt_model" 54 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
53 #end if 55 -in
54 56 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
55 #if $rep_param_fixed_modifications: 57 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
56 -fixed_modifications 58 -out
57 #for token in $rep_param_fixed_modifications: 59 'out/output.${gxy2omsext("featurexml")}'
58 #if " " in str(token): 60 #end if
59 "$token.param_fixed_modifications" 61 #if "next_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
60 #else 62 -next_feat
61 $token.param_fixed_modifications 63 'next_feat/output.${gxy2omsext("featurexml")}'
62 #end if 64 #end if
63 #end for 65 -ids
64 #end if 66 'ids/${re.sub("[^\w\-_]", "_", $ids.element_identifier)}.$gxy2omsext($ids.ext)'
65 #if $param_algorithm_type: 67 #if $raw_data:
66 -algorithm:type 68 -raw_data
67 #if " " in str($param_algorithm_type): 69 'raw_data/${re.sub("[^\w\-_]", "_", $raw_data.element_identifier)}.$gxy2omsext($raw_data.ext)'
68 "$param_algorithm_type" 70 #end if
69 #else 71 #if "sim_results_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
70 $param_algorithm_type 72 -sim_results
71 #end if 73 'sim_results/output.${gxy2omsext("txt")}'
72 #end if 74 #end if
73 #if $param_algorithm_max_iteration: 75 #if $db_path:
74 -algorithm:max_iteration $param_algorithm_max_iteration 76 -db_path
75 #end if 77 'db_path/${re.sub("[^\w\-_]", "_", $db_path.element_identifier)}.$gxy2omsext($db_path.ext)'
76 #if $param_algorithm_rt_bin_capacity: 78 #end if
77 -algorithm:rt_bin_capacity $param_algorithm_rt_bin_capacity 79 #if $rt_model:
78 #end if 80 -rt_model
79 #if $param_algorithm_step_size: 81 'rt_model/${re.sub("[^\w\-_]", "_", $rt_model.element_identifier)}.$gxy2omsext($rt_model.ext)'
80 -algorithm:step_size $param_algorithm_step_size 82 #end if
81 #end if 83 #if $dt_model:
82 #if $param_algorithm_peptide_min_prob: 84 -dt_model
83 -algorithm:peptide_min_prob $param_algorithm_peptide_min_prob 85 'dt_model/${re.sub("[^\w\-_]", "_", $dt_model.element_identifier)}.$gxy2omsext($dt_model.ext)'
84 #end if 86 #end if
85 #if $param_algorithm_sequential_spectrum_order: 87 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
86 -algorithm:sequential_spectrum_order 88 | tee '$stdout'
87 #end if 89 #end if
88 #if $param_algorithm_MIPFormulation_thresholds_min_protein_probability: 90
89 -algorithm:MIPFormulation:thresholds:min_protein_probability $param_algorithm_MIPFormulation_thresholds_min_protein_probability 91 ## Postprocessing
90 #end if 92 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
91 #if $param_algorithm_MIPFormulation_thresholds_min_protein_id_probability: 93 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
92 -algorithm:MIPFormulation:thresholds:min_protein_id_probability $param_algorithm_MIPFormulation_thresholds_min_protein_id_probability 94 #end if
93 #end if 95 #if "next_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
94 #if $param_algorithm_MIPFormulation_thresholds_min_pt_weight: 96 && mv 'next_feat/output.${gxy2omsext("featurexml")}' '$next_feat'
95 -algorithm:MIPFormulation:thresholds:min_pt_weight $param_algorithm_MIPFormulation_thresholds_min_pt_weight 97 #end if
96 #end if 98 #if "sim_results_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
97 #if $param_algorithm_MIPFormulation_thresholds_min_mz: 99 && mv 'sim_results/output.${gxy2omsext("txt")}' '$sim_results'
98 -algorithm:MIPFormulation:thresholds:min_mz $param_algorithm_MIPFormulation_thresholds_min_mz 100 #end if
99 #end if 101 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
100 #if $param_algorithm_MIPFormulation_thresholds_max_mz: 102 && mv '@EXECUTABLE@.ctd' '$ctd_out'
101 -algorithm:MIPFormulation:thresholds:max_mz $param_algorithm_MIPFormulation_thresholds_max_mz 103 #end if]]></command>
102 #end if 104 <configfiles>
103 #if $param_algorithm_MIPFormulation_thresholds_min_pred_pep_prob: 105 <inputs name="args_json" data_style="paths"/>
104 -algorithm:MIPFormulation:thresholds:min_pred_pep_prob $param_algorithm_MIPFormulation_thresholds_min_pred_pep_prob 106 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
105 #end if 107 </configfiles>
106 #if $param_algorithm_MIPFormulation_thresholds_min_rt_weight:
107 -algorithm:MIPFormulation:thresholds:min_rt_weight $param_algorithm_MIPFormulation_thresholds_min_rt_weight
108 #end if
109 #if $param_algorithm_MIPFormulation_thresholds_use_peptide_rule:
110 -algorithm:MIPFormulation:thresholds:use_peptide_rule
111 #end if
112 #if $param_algorithm_MIPFormulation_thresholds_min_peptide_ids:
113 -algorithm:MIPFormulation:thresholds:min_peptide_ids $param_algorithm_MIPFormulation_thresholds_min_peptide_ids
114 #end if
115 #if $param_algorithm_MIPFormulation_thresholds_min_peptide_probability:
116 -algorithm:MIPFormulation:thresholds:min_peptide_probability $param_algorithm_MIPFormulation_thresholds_min_peptide_probability
117 #end if
118 #if $param_algorithm_MIPFormulation_combined_ilp_k1:
119 -algorithm:MIPFormulation:combined_ilp:k1 $param_algorithm_MIPFormulation_combined_ilp_k1
120 #end if
121 #if $param_algorithm_MIPFormulation_combined_ilp_k2:
122 -algorithm:MIPFormulation:combined_ilp:k2 $param_algorithm_MIPFormulation_combined_ilp_k2
123 #end if
124 #if $param_algorithm_MIPFormulation_combined_ilp_k3:
125 -algorithm:MIPFormulation:combined_ilp:k3 $param_algorithm_MIPFormulation_combined_ilp_k3
126 #end if
127 #if $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs:
128 -algorithm:MIPFormulation:combined_ilp:scale_matching_probs
129 #if " " in str($param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs):
130 "$param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs"
131 #else
132 $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs
133 #end if
134 #end if
135 #if $param_algorithm_MIPFormulation_feature_based_no_intensity_normalization:
136 -algorithm:MIPFormulation:feature_based:no_intensity_normalization
137 #end if
138 #if $param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature:
139 -algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature $param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature
140 #end if
141 #if $param_algorithm_Preprocessing_precursor_mass_tolerance:
142 -algorithm:Preprocessing:precursor_mass_tolerance $param_algorithm_Preprocessing_precursor_mass_tolerance
143 #end if
144 #if $param_algorithm_Preprocessing_precursor_mass_tolerance_unit:
145 -algorithm:Preprocessing:precursor_mass_tolerance_unit
146 #if " " in str($param_algorithm_Preprocessing_precursor_mass_tolerance_unit):
147 "$param_algorithm_Preprocessing_precursor_mass_tolerance_unit"
148 #else
149 $param_algorithm_Preprocessing_precursor_mass_tolerance_unit
150 #end if
151 #end if
152 #if $param_algorithm_Preprocessing_preprocessed_db_path:
153 -algorithm:Preprocessing:preprocessed_db_path "$param_algorithm_Preprocessing_preprocessed_db_path"
154 #end if
155 #if $param_algorithm_Preprocessing_preprocessed_db_pred_rt_path:
156 -algorithm:Preprocessing:preprocessed_db_pred_rt_path "$param_algorithm_Preprocessing_preprocessed_db_pred_rt_path"
157 #end if
158 #if $param_algorithm_Preprocessing_preprocessed_db_pred_dt_path:
159 -algorithm:Preprocessing:preprocessed_db_pred_dt_path "$param_algorithm_Preprocessing_preprocessed_db_pred_dt_path"
160 #end if
161 #if $param_algorithm_Preprocessing_max_peptides_per_run:
162 -algorithm:Preprocessing:max_peptides_per_run $param_algorithm_Preprocessing_max_peptides_per_run
163 #end if
164 #if $param_algorithm_Preprocessing_missed_cleavages:
165 -algorithm:Preprocessing:missed_cleavages $param_algorithm_Preprocessing_missed_cleavages
166 #end if
167 #if $param_algorithm_Preprocessing_taxonomy:
168 -algorithm:Preprocessing:taxonomy "$param_algorithm_Preprocessing_taxonomy"
169 #end if
170 #if $param_algorithm_Preprocessing_tmp_dir:
171 -algorithm:Preprocessing:tmp_dir "$param_algorithm_Preprocessing_tmp_dir"
172 #end if
173 #if $param_algorithm_Preprocessing_store_peptide_sequences:
174 -algorithm:Preprocessing:store_peptide_sequences "$param_algorithm_Preprocessing_store_peptide_sequences"
175 #end if
176 #if $param_algorithm_Preprocessing_rt_settings_min_rt:
177 -algorithm:Preprocessing:rt_settings:min_rt $param_algorithm_Preprocessing_rt_settings_min_rt
178 #end if
179 #if $param_algorithm_Preprocessing_rt_settings_max_rt:
180 -algorithm:Preprocessing:rt_settings:max_rt $param_algorithm_Preprocessing_rt_settings_max_rt
181 #end if
182 #if $param_algorithm_Preprocessing_rt_settings_rt_step_size:
183 -algorithm:Preprocessing:rt_settings:rt_step_size $param_algorithm_Preprocessing_rt_settings_rt_step_size
184 #end if
185 #if $param_algorithm_Preprocessing_rt_settings_gauss_mean:
186 -algorithm:Preprocessing:rt_settings:gauss_mean $param_algorithm_Preprocessing_rt_settings_gauss_mean
187 #end if
188 #if $param_algorithm_Preprocessing_rt_settings_gauss_sigma:
189 -algorithm:Preprocessing:rt_settings:gauss_sigma $param_algorithm_Preprocessing_rt_settings_gauss_sigma
190 #end if
191 #if $adv_opts.adv_opts_selector=='advanced':
192 #if $adv_opts.param_solver:
193 -solver
194 #if " " in str($adv_opts.param_solver):
195 "$adv_opts.param_solver"
196 #else
197 $adv_opts.param_solver
198 #end if
199 #end if
200 #if $adv_opts.param_force:
201 -force
202 #end if
203 #end if
204 ]]></command>
205 <inputs> 108 <inputs>
206 <param name="param_in" type="data" format="featurexml" optional="False" label="Input feature map file (featureXML)" help="(-in) "/> 109 <param name="in" argument="-in" type="data" format="featurexml" optional="false" label="Input feature map file (featureXML)" help=" select featurexml data sets(s)"/>
207 <param name="param_ids" type="data" format="idxml" optional="False" label="file containing results of identification" help="(-ids) "/> 110 <param name="ids" argument="-ids" type="data" format="idxml" optional="false" label="file containing results of identification" help=" select idxml data sets(s)"/>
208 <param name="param_num_precursors" type="integer" value="1" label="number of precursors to be selected" help="(-num_precursors) "/> 111 <param name="num_precursors" argument="-num_precursors" type="integer" optional="true" value="1" label="number of precursors to be selected" help=""/>
209 <param name="param_raw_data" type="data" format="mzml" optional="True" label="Input profile data" help="(-raw_data) "/> 112 <param name="raw_data" argument="-raw_data" type="data" format="mzml" optional="true" label="Input profile data" help=" select mzml data sets(s)"/>
210 <param name="param_load_preprocessing" display="radio" type="boolean" truevalue="-load_preprocessing" falsevalue="" checked="false" optional="True" label="The preprocessed db is loaded from file, not calculated" help="(-load_preprocessing) "/> 113 <param name="load_preprocessing" argument="-load_preprocessing" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The preprocessed db is loaded from file, not calculated" help=""/>
211 <param name="param_store_preprocessing" display="radio" type="boolean" truevalue="-store_preprocessing" falsevalue="" checked="false" optional="True" label="The preprocessed db is stored" help="(-store_preprocessing) "/> 114 <param name="store_preprocessing" argument="-store_preprocessing" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The preprocessed db is stored" help=""/>
212 <param name="param_simulation" display="radio" type="boolean" truevalue="-simulation" falsevalue="" checked="false" optional="True" label="Simulate the whole LC-MS/MS run" help="(-simulation) "/> 115 <param name="simulation" argument="-simulation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Simulate the whole LC-MS/MS run" help=""/>
213 <param name="param_sim_results" type="text" size="30" label="File containing the results of the simulation run" help="(-sim_results) "> 116 <param name="db_path" argument="-db_path" type="data" format="fasta" optional="true" label="db file" help=" select fasta data sets(s)"/>
214 <sanitizer> 117 <param name="rt_model" argument="-rt_model" type="data" format="txt" optional="true" label="SVM Model for RTPredict" help=" select txt data sets(s)"/>
215 <valid initial="string.printable"> 118 <param name="dt_model" argument="-dt_model" type="data" format="txt" optional="true" label="SVM Model for PTPredict" help=" select txt data sets(s)"/>
216 <remove value="'"/> 119 <param name="fixed_modifications" argument="-fixed_modifications" type="text" optional="true" value="" label="the modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
217 <remove value="&quot;"/> 120 <expand macro="list_string_val"/>
218 </valid> 121 <expand macro="list_string_san"/>
219 </sanitizer>
220 </param> 122 </param>
221 <param name="param_db_path" type="data" format="fasta" optional="True" label="db file" help="(-db_path) "/> 123 <section name="algorithm" title="Settings for the compound list creation and rescoring" help="" expanded="false">
222 <param name="param_rt_model" type="text" size="30" label="SVM Model for RTPredict" help="(-rt_model) "> 124 <param name="type" argument="-algorithm:type" type="select" optional="false" label="Strategy for precursor ion selection" help="">
223 <sanitizer> 125 <option value="ILP_IPS">ILP_IPS</option>
224 <valid initial="string.printable"> 126 <option value="IPS" selected="true">IPS</option>
225 <remove value="'"/> 127 <option value="SPS">SPS</option>
226 <remove value="&quot;"/> 128 <option value="Upshift">Upshift</option>
227 </valid> 129 <option value="Downshift">Downshift</option>
228 </sanitizer> 130 <option value="DEX">DEX</option>
229 </param> 131 <expand macro="list_string_san"/>
230 <param name="param_dt_model" type="text" size="30" label="SVM Model for PTPredict" help="(-dt_model) ">
231 <sanitizer>
232 <valid initial="string.printable">
233 <remove value="'"/>
234 <remove value="&quot;"/>
235 </valid>
236 </sanitizer>
237 </param>
238 <repeat name="rep_param_fixed_modifications" min="0" title="param_fixed_modifications">
239 <param name="param_fixed_modifications" type="text" size="30" label="the modifications i.e. Carboxymethyl (C)" help="(-fixed_modifications) ">
240 <sanitizer>
241 <valid initial="string.printable">
242 <remove value="'"/>
243 <remove value="&quot;"/>
244 </valid>
245 </sanitizer>
246 </param> 132 </param>
247 </repeat> 133 <param name="max_iteration" argument="-algorithm:max_iteration" type="integer" optional="true" min="1" value="100" label="Maximal number of iterations" help=""/>
248 <param name="param_algorithm_type" type="select" optional="False" value="IPS" label="Strategy for precursor ion selection" help="(-type) "> 134 <param name="rt_bin_capacity" argument="-algorithm:rt_bin_capacity" type="integer" optional="true" min="1" value="10" label="Maximal number of precursors per rt bin" help=""/>
249 <option value="ILP_IPS">ILP_IPS</option> 135 <param name="step_size" argument="-algorithm:step_size" type="integer" optional="true" min="1" value="1" label="Maximal number of precursors per iteration" help=""/>
250 <option value="IPS" selected="true">IPS</option> 136 <param name="peptide_min_prob" argument="-algorithm:peptide_min_prob" type="float" optional="true" value="0.2" label="Minimal peptide probability" help=""/>
251 <option value="SPS">SPS</option> 137 <param name="sequential_spectrum_order" argument="-algorithm:sequential_spectrum_order" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, precursors are selected sequentially with respect to their RT" help=""/>
252 <option value="Upshift">Upshift</option> 138 <section name="MIPFormulation" title="" help="" expanded="false">
253 <option value="Downshift">Downshift</option> 139 <section name="thresholds" title="" help="" expanded="false">
254 <option value="DEX">DEX</option> 140 <param name="min_protein_probability" argument="-algorithm:MIPFormulation:thresholds:min_protein_probability" type="float" optional="true" min="0.0" max="1.0" value="0.2" label="Minimal protein probability for a protein to be considered in the ILP" help=""/>
255 </param> 141 <param name="min_protein_id_probability" argument="-algorithm:MIPFormulation:thresholds:min_protein_id_probability" type="float" optional="true" min="0.0" max="1.0" value="0.95" label="Minimal protein probability for a protein to be considered identified" help=""/>
256 <param name="param_algorithm_max_iteration" type="integer" min="1" optional="True" value="100" label="Maximal number of iterations" help="(-max_iteration) "/> 142 <param name="min_pt_weight" argument="-algorithm:MIPFormulation:thresholds:min_pt_weight" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Minimal pt weight of a precurso" help=""/>
257 <param name="param_algorithm_rt_bin_capacity" type="integer" min="1" optional="True" value="10" label="Maximal number of precursors per rt bin" help="(-rt_bin_capacity) "/> 143 <param name="min_mz" argument="-algorithm:MIPFormulation:thresholds:min_mz" type="float" optional="true" min="0.0" value="500.0" label="Minimal mz to be considered in protein based LP formulation" help=""/>
258 <param name="param_algorithm_step_size" type="integer" min="1" optional="True" value="1" label="Maximal number of precursors per iteration" help="(-step_size) "/> 144 <param name="max_mz" argument="-algorithm:MIPFormulation:thresholds:max_mz" type="float" optional="true" min="0.0" value="5000.0" label="Minimal mz to be considered in protein based LP formulation" help=""/>
259 <param name="param_algorithm_peptide_min_prob" type="float" value="0.2" label="Minimal peptide probability" help="(-peptide_min_prob) "/> 145 <param name="min_pred_pep_prob" argument="-algorithm:MIPFormulation:thresholds:min_pred_pep_prob" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Minimal predicted peptide probability of a precurso" help=""/>
260 <param name="param_algorithm_sequential_spectrum_order" display="radio" type="boolean" truevalue="-algorithm:sequential_spectrum_order" falsevalue="" checked="false" optional="True" label="If true, precursors are selected sequentially with respect to their RT" help="(-sequential_spectrum_order) "/> 146 <param name="min_rt_weight" argument="-algorithm:MIPFormulation:thresholds:min_rt_weight" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Minimal rt weight of a precurso" help=""/>
261 <param name="param_algorithm_MIPFormulation_thresholds_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) "/> 147 <param name="use_peptide_rule" argument="-algorithm:MIPFormulation:thresholds:use_peptide_rule" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use peptide rule instead of minimal protein id probability" help=""/>
262 <param name="param_algorithm_MIPFormulation_thresholds_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) "/> 148 <param name="min_peptide_ids" argument="-algorithm:MIPFormulation:thresholds:min_peptide_ids" type="integer" optional="true" min="1" value="2" label="If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id" help=""/>
263 <param name="param_algorithm_MIPFormulation_thresholds_min_pt_weight" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal pt weight of a precurso" help="(-min_pt_weight) "/> 149 <param name="min_peptide_probability" argument="-algorithm:MIPFormulation:thresholds:min_peptide_probability" type="float" optional="true" min="0.0" max="1.0" value="0.95" label="If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified" help=""/>
264 <param name="param_algorithm_MIPFormulation_thresholds_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) "/> 150 </section>
265 <param name="param_algorithm_MIPFormulation_thresholds_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) "/> 151 <section name="combined_ilp" title="" help="" expanded="false">
266 <param name="param_algorithm_MIPFormulation_thresholds_min_pred_pep_prob" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal predicted peptide probability of a precurso" help="(-min_pred_pep_prob) "/> 152 <param name="k1" argument="-algorithm:MIPFormulation:combined_ilp:k1" type="float" optional="true" min="0.0" value="0.2" label="combined ilp: weight for z_i" help=""/>
267 <param name="param_algorithm_MIPFormulation_thresholds_min_rt_weight" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal rt weight of a precurso" help="(-min_rt_weight) "/> 153 <param name="k2" argument="-algorithm:MIPFormulation:combined_ilp:k2" type="float" optional="true" min="0.0" value="0.2" label="combined ilp: weight for x_j,s*int_j,s" help=""/>
268 <param name="param_algorithm_MIPFormulation_thresholds_use_peptide_rule" display="radio" type="boolean" truevalue="-algorithm:MIPFormulation:thresholds:use_peptide_rule" falsevalue="" checked="false" optional="True" label="Use peptide rule instead of minimal protein id probability" help="(-use_peptide_rule) "/> 154 <param name="k3" argument="-algorithm:MIPFormulation:combined_ilp:k3" type="float" optional="true" min="0.0" value="0.4" label="combined ilp: weight for -x_j,s*w_j,s" help=""/>
269 <param name="param_algorithm_MIPFormulation_thresholds_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) "/> 155 <param name="scale_matching_probs" argument="-algorithm:MIPFormulation:combined_ilp:scale_matching_probs" type="boolean" truevalue="true" falsevalue="false" checked="true" label="flag if detectability * rt_weight shall be scaled to cover all [0,1]" help=""/>
270 <param name="param_algorithm_MIPFormulation_thresholds_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) "/> 156 </section>
271 <param name="param_algorithm_MIPFormulation_combined_ilp_k1" type="float" min="0.0" optional="True" value="0.2" label="combined ilp: weight for z_i" help="(-k1) "/> 157 <section name="feature_based" title="" help="" expanded="false">
272 <param name="param_algorithm_MIPFormulation_combined_ilp_k2" type="float" min="0.0" optional="True" value="0.2" label="combined ilp: weight for x_j,s*int_j,s" help="(-k2) "/> 158 <param name="no_intensity_normalization" argument="-algorithm:MIPFormulation:feature_based:no_intensity_normalization" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Flag indicating if intensities shall be scaled to be in [0,1]" help="This is done for each feature separately, so that the feature's maximal intensity in a spectrum is set to 1"/>
273 <param name="param_algorithm_MIPFormulation_combined_ilp_k3" type="float" min="0.0" optional="True" value="0.4" label="combined ilp: weight for -x_j,s*w_j,s" help="(-k3) "/> 159 <param name="max_number_precursors_per_feature" argument="-algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature" type="integer" optional="true" min="1" value="1" label="The maximal number of precursors per feature" help=""/>
274 <param name="param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs" display="radio" type="select" optional="False" value="true" label="flag if detectability * rt_weight shall be scaled to cover all [0,1]" help="(-scale_matching_probs) "> 160 </section>
275 <option value="true" selected="true">true</option> 161 </section>
276 <option value="false">false</option> 162 <section name="Preprocessing" title="" help="" expanded="false">
277 </param> 163 <param name="precursor_mass_tolerance" argument="-algorithm:Preprocessing:precursor_mass_tolerance" type="float" optional="true" min="0.0" value="10.0" label="Precursor mass tolerance which is used to query the peptide database for peptides" help=""/>
278 <param name="param_algorithm_MIPFormulation_feature_based_no_intensity_normalization" display="radio" type="boolean" truevalue="-algorithm:MIPFormulation:feature_based:no_intensity_normalization" falsevalue="" checked="false" optional="True" label="Flag indicating if intensities shall be scaled to be in [0,1]" 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"/> 164 <param name="precursor_mass_tolerance_unit" argument="-algorithm:Preprocessing:precursor_mass_tolerance_unit" display="radio" type="select" optional="false" label="Precursor mass tolerance unit" help="">
279 <param name="param_algorithm_MIPFormulation_feature_based_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) "/> 165 <option value="ppm" selected="true">ppm</option>
280 <param name="param_algorithm_Preprocessing_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) "/> 166 <option value="Da">Da</option>
281 <param name="param_algorithm_Preprocessing_precursor_mass_tolerance_unit" display="radio" type="select" optional="False" value="ppm" label="Precursor mass tolerance unit" help="(-precursor_mass_tolerance_unit) "> 167 <expand macro="list_string_san"/>
282 <option value="ppm" selected="true">ppm</option> 168 </param>
283 <option value="Da">Da</option> 169 <param name="preprocessed_db_path" argument="-algorithm:Preprocessing:preprocessed_db_path" type="text" optional="true" value="" label="Path where the preprocessed database should be stored" help="">
284 </param> 170 <expand macro="list_string_san"/>
285 <param name="param_algorithm_Preprocessing_preprocessed_db_path" type="text" size="30" label="Path where the preprocessed database should be stored" help="(-preprocessed_db_path) "> 171 </param>
286 <sanitizer> 172 <param name="preprocessed_db_pred_rt_path" argument="-algorithm:Preprocessing:preprocessed_db_pred_rt_path" type="text" optional="true" value="" label="Path where the predicted rts of the preprocessed database should be stored" help="">
287 <valid initial="string.printable"> 173 <expand macro="list_string_san"/>
288 <remove value="'"/> 174 </param>
289 <remove value="&quot;"/> 175 <param name="preprocessed_db_pred_dt_path" argument="-algorithm:Preprocessing:preprocessed_db_pred_dt_path" type="text" optional="true" value="" label="Path where the predicted rts of the preprocessed database should be stored" help="">
290 </valid> 176 <expand macro="list_string_san"/>
291 </sanitizer> 177 </param>
292 </param> 178 <param name="max_peptides_per_run" argument="-algorithm:Preprocessing:max_peptides_per_run" type="integer" optional="true" min="1" value="100000" label="Number of peptides for that the pt and rt are parallely predicted" help=""/>
293 <param name="param_algorithm_Preprocessing_preprocessed_db_pred_rt_path" type="text" size="30" label="Path where the predicted rts of the preprocessed database should be stored" help="(-preprocessed_db_pred_rt_path) "> 179 <param name="missed_cleavages" argument="-algorithm:Preprocessing:missed_cleavages" type="integer" optional="true" min="0" value="1" label="Number of allowed missed cleavages" help=""/>
294 <sanitizer> 180 <param name="taxonomy" argument="-algorithm:Preprocessing:taxonomy" type="text" optional="true" value="" label="Taxonomy" help="">
295 <valid initial="string.printable"> 181 <expand macro="list_string_san"/>
296 <remove value="'"/> 182 </param>
297 <remove value="&quot;"/> 183 <param name="store_peptide_sequences" argument="-algorithm:Preprocessing:store_peptide_sequences" type="text" optional="true" value="false" label="Flag if peptide sequences should be stored" help="">
298 </valid> 184 <expand macro="list_string_san"/>
299 </sanitizer> 185 </param>
300 </param> 186 <section name="rt_settings" title="" help="" expanded="false">
301 <param name="param_algorithm_Preprocessing_preprocessed_db_pred_dt_path" type="text" size="30" label="Path where the predicted rts of the preprocessed database should be stored" help="(-preprocessed_db_pred_dt_path) "> 187 <param name="min_rt" argument="-algorithm:Preprocessing:rt_settings:min_rt" type="float" optional="true" min="1.0" value="960.0" label="Minimal RT in the experiment (in seconds)" help=""/>
302 <sanitizer> 188 <param name="max_rt" argument="-algorithm:Preprocessing:rt_settings:max_rt" type="float" optional="true" value="3840.0" label="Maximal RT in the experiment (in seconds)" help=""/>
303 <valid initial="string.printable"> 189 <param name="rt_step_size" argument="-algorithm:Preprocessing:rt_settings:rt_step_size" type="float" optional="true" value="30.0" label="Time between two consecutive spectra (in seconds)" help=""/>
304 <remove value="'"/> 190 <param name="gauss_mean" argument="-algorithm:Preprocessing:rt_settings:gauss_mean" type="float" optional="true" value="-1.0" label="mean of the gauss curve" help=""/>
305 <remove value="&quot;"/> 191 <param name="gauss_sigma" argument="-algorithm:Preprocessing:rt_settings:gauss_sigma" type="float" optional="true" value="3.0" label="std of the gauss curve" help=""/>
306 </valid> 192 </section>
307 </sanitizer> 193 </section>
308 </param> 194 </section>
309 <param name="param_algorithm_Preprocessing_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) "/> 195 <expand macro="adv_opts_macro">
310 <param name="param_algorithm_Preprocessing_missed_cleavages" type="integer" min="0" optional="True" value="1" label="Number of allowed missed cleavages" help="(-missed_cleavages) "/> 196 <param name="solver" argument="-solver" display="radio" type="select" optional="false" label="LP solver type" help="">
311 <param name="param_algorithm_Preprocessing_taxonomy" type="text" size="30" label="Taxonomy" help="(-taxonomy) ">
312 <sanitizer>
313 <valid initial="string.printable">
314 <remove value="'"/>
315 <remove value="&quot;"/>
316 </valid>
317 </sanitizer>
318 </param>
319 <param name="param_algorithm_Preprocessing_tmp_dir" type="text" size="30" label="Absolute path to tmp data directory used to store files needed for rt and dt prediction" help="(-tmp_dir) ">
320 <sanitizer>
321 <valid initial="string.printable">
322 <remove value="'"/>
323 <remove value="&quot;"/>
324 </valid>
325 </sanitizer>
326 </param>
327 <param name="param_algorithm_Preprocessing_store_peptide_sequences" type="text" size="30" value="false" label="Flag if peptide sequences should be stored" help="(-store_peptide_sequences) ">
328 <sanitizer>
329 <valid initial="string.printable">
330 <remove value="'"/>
331 <remove value="&quot;"/>
332 </valid>
333 </sanitizer>
334 </param>
335 <param name="param_algorithm_Preprocessing_rt_settings_min_rt" type="float" min="1.0" optional="True" value="960.0" label="Minimal RT in the experiment (in seconds)" help="(-min_rt) "/>
336 <param name="param_algorithm_Preprocessing_rt_settings_max_rt" type="float" value="3840.0" label="Maximal RT in the experiment (in seconds)" help="(-max_rt) "/>
337 <param name="param_algorithm_Preprocessing_rt_settings_rt_step_size" type="float" value="30.0" label="Time between two consecutive spectra (in seconds)" help="(-rt_step_size) "/>
338 <param name="param_algorithm_Preprocessing_rt_settings_gauss_mean" type="float" value="-1.0" label="mean of the gauss curve" help="(-gauss_mean) "/>
339 <param name="param_algorithm_Preprocessing_rt_settings_gauss_sigma" type="float" value="3.0" label="std of the gauss curve" help="(-gauss_sigma) "/>
340 <expand macro="advanced_options">
341 <param name="param_solver" display="radio" type="select" optional="False" value="GLPK" label="LP solver type" help="(-solver) ">
342 <option value="GLPK" selected="true">GLPK</option> 197 <option value="GLPK" selected="true">GLPK</option>
343 <option value="COINOR">COINOR</option> 198 <option value="COINOR">COINOR</option>
199 <expand macro="list_string_san"/>
344 </param> 200 </param>
345 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 201 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
202 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
203 <expand macro="list_string_san"/>
204 </param>
346 </expand> 205 </expand>
206 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false">
207 <option value="out_FLAG">out (std of the gauss curve)</option>
208 <option value="next_feat_FLAG">next_feat (std of the gauss curve)</option>
209 <option value="sim_results_FLAG">sim_results (std of the gauss curve)</option>
210 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
211 </param>
347 </inputs> 212 </inputs>
348 <outputs> 213 <outputs>
349 <data name="param_out" format="featurexml"/> 214 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml">
350 <data name="param_next_feat" format="featurexml"/> 215 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
216 </data>
217 <data name="next_feat" label="${tool.name} on ${on_string}: next_feat" format="featurexml">
218 <filter>OPTIONAL_OUTPUTS is not None and "next_feat_FLAG" in OPTIONAL_OUTPUTS</filter>
219 </data>
220 <data name="sim_results" label="${tool.name} on ${on_string}: sim_results" format="txt">
221 <filter>OPTIONAL_OUTPUTS is not None and "sim_results_FLAG" in OPTIONAL_OUTPUTS</filter>
222 </data>
223 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
224 <filter>OPTIONAL_OUTPUTS is None</filter>
225 </data>
226 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
227 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
228 </data>
351 </outputs> 229 </outputs>
352 <help>PrecursorIonSelector 230 <tests>
353 231 <expand macro="autotest_PrecursorIonSelector"/>
354 232 <expand macro="manutest_PrecursorIonSelector"/>
355 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_PrecursorIonSelector.html</help> 233 </tests>
234 <help><![CDATA[PrecursorIonSelector
235
236
237 For more information, visit http://www.openms.de/documentation/TOPP_PrecursorIonSelector.html]]></help>
238 <expand macro="references"/>
356 </tool> 239 </tool>