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comparison PrecursorIonSelector.xml @ 0:45a9649b4891 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:20:14 -0500
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children 828f4c70d584
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-1:000000000000 0:45a9649b4891
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 CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="PrecursorIonSelector" name="PrecursorIonSelector" version="2.1.0">
5 <description>PrecursorIonSelector</description>
6 <macros>
7 <token name="@EXECUTABLE@">PrecursorIonSelector</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>PrecursorIonSelector
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_next_feat:
22 -next_feat $param_next_feat
23 #end if
24 #if $param_ids:
25 -ids $param_ids
26 #end if
27 #if $param_num_precursors:
28 -num_precursors $param_num_precursors
29 #end if
30 #if $param_raw_data:
31 -raw_data $param_raw_data
32 #end if
33 #if $param_load_preprocessing:
34 -load_preprocessing
35 #end if
36 #if $param_store_preprocessing:
37 -store_preprocessing
38 #end if
39 #if $param_simulation:
40 -simulation
41 #end if
42 #if $param_sim_results:
43 -sim_results "$param_sim_results"
44 #end if
45 #if $param_db_path:
46 -db_path $param_db_path
47 #end if
48 #if $param_rt_model:
49 -rt_model "$param_rt_model"
50 #end if
51 #if $param_dt_model:
52 -dt_model "$param_dt_model"
53 #end if
54
55 #if $rep_param_fixed_modifications:
56 -fixed_modifications
57 #for token in $rep_param_fixed_modifications:
58 #if " " in str(token):
59 "$token.param_fixed_modifications"
60 #else
61 $token.param_fixed_modifications
62 #end if
63 #end for
64 #end if
65 #if $param_algorithm_type:
66 -algorithm:type $param_algorithm_type
67 #end if
68 #if $param_algorithm_max_iteration:
69 -algorithm:max_iteration $param_algorithm_max_iteration
70 #end if
71 #if $param_algorithm_rt_bin_capacity:
72 -algorithm:rt_bin_capacity $param_algorithm_rt_bin_capacity
73 #end if
74 #if $param_algorithm_step_size:
75 -algorithm:step_size $param_algorithm_step_size
76 #end if
77 #if $param_algorithm_peptide_min_prob:
78 -algorithm:peptide_min_prob $param_algorithm_peptide_min_prob
79 #end if
80 #if $param_algorithm_sequential_spectrum_order:
81 -algorithm:sequential_spectrum_order
82 #end if
83 #if $param_algorithm_MIPFormulation_thresholds_min_protein_probability:
84 -algorithm:MIPFormulation:thresholds:min_protein_probability $param_algorithm_MIPFormulation_thresholds_min_protein_probability
85 #end if
86 #if $param_algorithm_MIPFormulation_thresholds_min_protein_id_probability:
87 -algorithm:MIPFormulation:thresholds:min_protein_id_probability $param_algorithm_MIPFormulation_thresholds_min_protein_id_probability
88 #end if
89 #if $param_algorithm_MIPFormulation_thresholds_min_pt_weight:
90 -algorithm:MIPFormulation:thresholds:min_pt_weight $param_algorithm_MIPFormulation_thresholds_min_pt_weight
91 #end if
92 #if $param_algorithm_MIPFormulation_thresholds_min_mz:
93 -algorithm:MIPFormulation:thresholds:min_mz $param_algorithm_MIPFormulation_thresholds_min_mz
94 #end if
95 #if $param_algorithm_MIPFormulation_thresholds_max_mz:
96 -algorithm:MIPFormulation:thresholds:max_mz $param_algorithm_MIPFormulation_thresholds_max_mz
97 #end if
98 #if $param_algorithm_MIPFormulation_thresholds_min_pred_pep_prob:
99 -algorithm:MIPFormulation:thresholds:min_pred_pep_prob $param_algorithm_MIPFormulation_thresholds_min_pred_pep_prob
100 #end if
101 #if $param_algorithm_MIPFormulation_thresholds_min_rt_weight:
102 -algorithm:MIPFormulation:thresholds:min_rt_weight $param_algorithm_MIPFormulation_thresholds_min_rt_weight
103 #end if
104 #if $param_algorithm_MIPFormulation_thresholds_use_peptide_rule:
105 -algorithm:MIPFormulation:thresholds:use_peptide_rule
106 #end if
107 #if $param_algorithm_MIPFormulation_thresholds_min_peptide_ids:
108 -algorithm:MIPFormulation:thresholds:min_peptide_ids $param_algorithm_MIPFormulation_thresholds_min_peptide_ids
109 #end if
110 #if $param_algorithm_MIPFormulation_thresholds_min_peptide_probability:
111 -algorithm:MIPFormulation:thresholds:min_peptide_probability $param_algorithm_MIPFormulation_thresholds_min_peptide_probability
112 #end if
113 #if $param_algorithm_MIPFormulation_combined_ilp_k1:
114 -algorithm:MIPFormulation:combined_ilp:k1 $param_algorithm_MIPFormulation_combined_ilp_k1
115 #end if
116 #if $param_algorithm_MIPFormulation_combined_ilp_k2:
117 -algorithm:MIPFormulation:combined_ilp:k2 $param_algorithm_MIPFormulation_combined_ilp_k2
118 #end if
119 #if $param_algorithm_MIPFormulation_combined_ilp_k3:
120 -algorithm:MIPFormulation:combined_ilp:k3 $param_algorithm_MIPFormulation_combined_ilp_k3
121 #end if
122 #if $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs:
123 -algorithm:MIPFormulation:combined_ilp:scale_matching_probs $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs
124 #end if
125 #if $param_algorithm_MIPFormulation_feature_based_no_intensity_normalization:
126 -algorithm:MIPFormulation:feature_based:no_intensity_normalization
127 #end if
128 #if $param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature:
129 -algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature $param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature
130 #end if
131 #if $param_algorithm_Preprocessing_precursor_mass_tolerance:
132 -algorithm:Preprocessing:precursor_mass_tolerance $param_algorithm_Preprocessing_precursor_mass_tolerance
133 #end if
134 #if $param_algorithm_Preprocessing_precursor_mass_tolerance_unit:
135 -algorithm:Preprocessing:precursor_mass_tolerance_unit $param_algorithm_Preprocessing_precursor_mass_tolerance_unit
136 #end if
137 #if $param_algorithm_Preprocessing_preprocessed_db_path:
138 -algorithm:Preprocessing:preprocessed_db_path "$param_algorithm_Preprocessing_preprocessed_db_path"
139 #end if
140 #if $param_algorithm_Preprocessing_preprocessed_db_pred_rt_path:
141 -algorithm:Preprocessing:preprocessed_db_pred_rt_path "$param_algorithm_Preprocessing_preprocessed_db_pred_rt_path"
142 #end if
143 #if $param_algorithm_Preprocessing_preprocessed_db_pred_dt_path:
144 -algorithm:Preprocessing:preprocessed_db_pred_dt_path "$param_algorithm_Preprocessing_preprocessed_db_pred_dt_path"
145 #end if
146 #if $param_algorithm_Preprocessing_max_peptides_per_run:
147 -algorithm:Preprocessing:max_peptides_per_run $param_algorithm_Preprocessing_max_peptides_per_run
148 #end if
149 #if $param_algorithm_Preprocessing_missed_cleavages:
150 -algorithm:Preprocessing:missed_cleavages $param_algorithm_Preprocessing_missed_cleavages
151 #end if
152 #if $param_algorithm_Preprocessing_taxonomy:
153 -algorithm:Preprocessing:taxonomy "$param_algorithm_Preprocessing_taxonomy"
154 #end if
155 #if $param_algorithm_Preprocessing_tmp_dir:
156 -algorithm:Preprocessing:tmp_dir "$param_algorithm_Preprocessing_tmp_dir"
157 #end if
158 #if $param_algorithm_Preprocessing_store_peptide_sequences:
159 -algorithm:Preprocessing:store_peptide_sequences "$param_algorithm_Preprocessing_store_peptide_sequences"
160 #end if
161 #if $param_algorithm_Preprocessing_rt_settings_min_rt:
162 -algorithm:Preprocessing:rt_settings:min_rt $param_algorithm_Preprocessing_rt_settings_min_rt
163 #end if
164 #if $param_algorithm_Preprocessing_rt_settings_max_rt:
165 -algorithm:Preprocessing:rt_settings:max_rt $param_algorithm_Preprocessing_rt_settings_max_rt
166 #end if
167 #if $param_algorithm_Preprocessing_rt_settings_rt_step_size:
168 -algorithm:Preprocessing:rt_settings:rt_step_size $param_algorithm_Preprocessing_rt_settings_rt_step_size
169 #end if
170 #if $param_algorithm_Preprocessing_rt_settings_gauss_mean:
171 -algorithm:Preprocessing:rt_settings:gauss_mean $param_algorithm_Preprocessing_rt_settings_gauss_mean
172 #end if
173 #if $param_algorithm_Preprocessing_rt_settings_gauss_sigma:
174 -algorithm:Preprocessing:rt_settings:gauss_sigma $param_algorithm_Preprocessing_rt_settings_gauss_sigma
175 #end if
176 #if $adv_opts.adv_opts_selector=='advanced':
177 #if $adv_opts.param_solver:
178 -solver $adv_opts.param_solver
179 #end if
180 #if $adv_opts.param_force:
181 -force
182 #end if
183 #end if
184 </command>
185 <inputs>
186 <param name="param_in" type="data" format="featurexml" optional="False" label="Input feature map file (featureXML)" help="(-in) "/>
187 <param name="param_ids" type="data" format="idxml" optional="False" label="file containing results of identification" help="(-ids) "/>
188 <param name="param_num_precursors" type="integer" value="1" label="number of precursors to be selected" help="(-num_precursors) "/>
189 <param name="param_raw_data" type="data" format="mzml" optional="True" label="Input profile data" help="(-raw_data) "/>
190 <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) "/>
191 <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) "/>
192 <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) "/>
193 <param name="param_sim_results" type="text" size="30" label="File containing the results of the simulation run" help="(-sim_results) ">
194 <sanitizer>
195 <valid initial="string.printable">
196 <remove value="'"/>
197 <remove value="&quot;"/>
198 </valid>
199 </sanitizer>
200 </param>
201 <param name="param_db_path" type="data" format="fasta" optional="True" label="db file" help="(-db_path) "/>
202 <param name="param_rt_model" type="text" size="30" label="SVM Model for RTPredict" help="(-rt_model) ">
203 <sanitizer>
204 <valid initial="string.printable">
205 <remove value="'"/>
206 <remove value="&quot;"/>
207 </valid>
208 </sanitizer>
209 </param>
210 <param name="param_dt_model" type="text" size="30" label="SVM Model for PTPredict" help="(-dt_model) ">
211 <sanitizer>
212 <valid initial="string.printable">
213 <remove value="'"/>
214 <remove value="&quot;"/>
215 </valid>
216 </sanitizer>
217 </param>
218 <repeat name="rep_param_fixed_modifications" min="0" max="1" title="param_fixed_modifications">
219 <param name="param_fixed_modifications" type="text" size="30" label="the modifications i.e. Carboxymethyl (C)" help="(-fixed_modifications) ">
220 <sanitizer>
221 <valid initial="string.printable">
222 <remove value="'"/>
223 <remove value="&quot;"/>
224 </valid>
225 </sanitizer>
226 </param>
227 </repeat>
228 <param name="param_algorithm_type" type="select" optional="False" value="IPS" label="Strategy for precursor ion selection" help="(-type) ">
229 <option value="ILP_IPS">ILP_IPS</option>
230 <option value="IPS" selected="true">IPS</option>
231 <option value="SPS">SPS</option>
232 <option value="Upshift">Upshift</option>
233 <option value="Downshift">Downshift</option>
234 <option value="DEX">DEX</option>
235 </param>
236 <param name="param_algorithm_max_iteration" type="integer" min="1" optional="True" value="100" label="Maximal number of iterations" help="(-max_iteration) "/>
237 <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) "/>
238 <param name="param_algorithm_step_size" type="integer" min="1" optional="True" value="1" label="Maximal number of precursors per iteration" help="(-step_size) "/>
239 <param name="param_algorithm_peptide_min_prob" type="float" value="0.2" label="Minimal peptide probability" help="(-peptide_min_prob) "/>
240 <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) "/>
241 <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) "/>
242 <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) "/>
243 <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) "/>
244 <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) "/>
245 <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) "/>
246 <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) "/>
247 <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) "/>
248 <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) "/>
249 <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) "/>
250 <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) "/>
251 <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) "/>
252 <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) "/>
253 <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) "/>
254 <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) ">
255 <option value="true" selected="true">true</option>
256 <option value="false">false</option>
257 </param>
258 <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"/>
259 <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) "/>
260 <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) "/>
261 <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) ">
262 <option value="ppm" selected="true">ppm</option>
263 <option value="Da">Da</option>
264 </param>
265 <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) ">
266 <sanitizer>
267 <valid initial="string.printable">
268 <remove value="'"/>
269 <remove value="&quot;"/>
270 </valid>
271 </sanitizer>
272 </param>
273 <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) ">
274 <sanitizer>
275 <valid initial="string.printable">
276 <remove value="'"/>
277 <remove value="&quot;"/>
278 </valid>
279 </sanitizer>
280 </param>
281 <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) ">
282 <sanitizer>
283 <valid initial="string.printable">
284 <remove value="'"/>
285 <remove value="&quot;"/>
286 </valid>
287 </sanitizer>
288 </param>
289 <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) "/>
290 <param name="param_algorithm_Preprocessing_missed_cleavages" type="integer" min="0" optional="True" value="1" label="Number of allowed missed cleavages" help="(-missed_cleavages) "/>
291 <param name="param_algorithm_Preprocessing_taxonomy" type="text" size="30" label="Taxonomy" help="(-taxonomy) ">
292 <sanitizer>
293 <valid initial="string.printable">
294 <remove value="'"/>
295 <remove value="&quot;"/>
296 </valid>
297 </sanitizer>
298 </param>
299 <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) ">
300 <sanitizer>
301 <valid initial="string.printable">
302 <remove value="'"/>
303 <remove value="&quot;"/>
304 </valid>
305 </sanitizer>
306 </param>
307 <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) ">
308 <sanitizer>
309 <valid initial="string.printable">
310 <remove value="'"/>
311 <remove value="&quot;"/>
312 </valid>
313 </sanitizer>
314 </param>
315 <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) "/>
316 <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) "/>
317 <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) "/>
318 <param name="param_algorithm_Preprocessing_rt_settings_gauss_mean" type="float" value="-1.0" label="mean of the gauss curve" help="(-gauss_mean) "/>
319 <param name="param_algorithm_Preprocessing_rt_settings_gauss_sigma" type="float" value="3.0" label="std of the gauss curve" help="(-gauss_sigma) "/>
320 <expand macro="advanced_options">
321 <param name="param_solver" display="radio" type="select" optional="False" value="GLPK" label="LP solver type" help="(-solver) ">
322 <option value="GLPK" selected="true">GLPK</option>
323 <option value="COINOR">COINOR</option>
324 </param>
325 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
326 </expand>
327 </inputs>
328 <outputs>
329 <data name="param_out" format="featurexml"/>
330 <data name="param_next_feat" format="featurexml"/>
331 </outputs>
332 <help>PrecursorIonSelector
333
334
335 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PrecursorIonSelector.html</help>
336 </tool>