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comparison PrecursorIonSelector.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="PrecursorIonSelector" name="PrecursorIonSelector" version="2.0.0">
3 <description>PrecursorIonSelector</description>
4 <macros>
5 <token name="@EXECUTABLE@">PrecursorIonSelector</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>PrecursorIonSelector
11
12 #if $param_in:
13 -in $param_in
14 #end if
15 #if $param_out:
16 -out $param_out
17 #end if
18 #if $param_next_feat:
19 -next_feat $param_next_feat
20 #end if
21 #if $param_ids:
22 -ids $param_ids
23 #end if
24 #if $param_num_precursors:
25 -num_precursors $param_num_precursors
26 #end if
27 #if $param_raw_data:
28 -raw_data $param_raw_data
29 #end if
30 #if $param_load_preprocessing:
31 -load_preprocessing
32 #end if
33 #if $param_store_preprocessing:
34 -store_preprocessing
35 #end if
36 #if $param_simulation:
37 -simulation
38 #end if
39 #if $param_sim_results:
40 -sim_results "$param_sim_results"
41 #end if
42 #if $param_db_path:
43 -db_path $param_db_path
44 #end if
45 #if $param_rt_model:
46 -rt_model "$param_rt_model"
47 #end if
48 #if $param_dt_model:
49 -dt_model "$param_dt_model"
50 #end if
51
52 #if $rep_param_fixed_modifications:
53 -fixed_modifications
54 #for token in $rep_param_fixed_modifications:
55 #if " " in str(token):
56 "$token.param_fixed_modifications"
57 #else
58 $token.param_fixed_modifications
59 #end if
60 #end for
61 #end if
62 -threads \${GALAXY_SLOTS:-24}
63 #if $param_algorithm_type:
64 -algorithm:type
65 #if " " in str($param_algorithm_type):
66 "$param_algorithm_type"
67 #else
68 $param_algorithm_type
69 #end if
70 #end if
71 #if $param_algorithm_max_iteration:
72 -algorithm:max_iteration $param_algorithm_max_iteration
73 #end if
74 #if $param_algorithm_rt_bin_capacity:
75 -algorithm:rt_bin_capacity $param_algorithm_rt_bin_capacity
76 #end if
77 #if $param_algorithm_step_size:
78 -algorithm:step_size $param_algorithm_step_size
79 #end if
80 #if $param_algorithm_peptide_min_prob:
81 -algorithm:peptide_min_prob $param_algorithm_peptide_min_prob
82 #end if
83 #if $param_algorithm_sequential_spectrum_order:
84 -algorithm:sequential_spectrum_order
85 #end if
86 #if $param_algorithm_MIPFormulation_thresholds_min_protein_probability:
87 -algorithm:MIPFormulation:thresholds:min_protein_probability $param_algorithm_MIPFormulation_thresholds_min_protein_probability
88 #end if
89 #if $param_algorithm_MIPFormulation_thresholds_min_protein_id_probability:
90 -algorithm:MIPFormulation:thresholds:min_protein_id_probability $param_algorithm_MIPFormulation_thresholds_min_protein_id_probability
91 #end if
92 #if $param_algorithm_MIPFormulation_thresholds_min_pt_weight:
93 -algorithm:MIPFormulation:thresholds:min_pt_weight $param_algorithm_MIPFormulation_thresholds_min_pt_weight
94 #end if
95 #if $param_algorithm_MIPFormulation_thresholds_min_mz:
96 -algorithm:MIPFormulation:thresholds:min_mz $param_algorithm_MIPFormulation_thresholds_min_mz
97 #end if
98 #if $param_algorithm_MIPFormulation_thresholds_max_mz:
99 -algorithm:MIPFormulation:thresholds:max_mz $param_algorithm_MIPFormulation_thresholds_max_mz
100 #end if
101 #if $param_algorithm_MIPFormulation_thresholds_min_pred_pep_prob:
102 -algorithm:MIPFormulation:thresholds:min_pred_pep_prob $param_algorithm_MIPFormulation_thresholds_min_pred_pep_prob
103 #end if
104 #if $param_algorithm_MIPFormulation_thresholds_min_rt_weight:
105 -algorithm:MIPFormulation:thresholds:min_rt_weight $param_algorithm_MIPFormulation_thresholds_min_rt_weight
106 #end if
107 #if $param_algorithm_MIPFormulation_thresholds_use_peptide_rule:
108 -algorithm:MIPFormulation:thresholds:use_peptide_rule
109 #end if
110 #if $param_algorithm_MIPFormulation_thresholds_min_peptide_ids:
111 -algorithm:MIPFormulation:thresholds:min_peptide_ids $param_algorithm_MIPFormulation_thresholds_min_peptide_ids
112 #end if
113 #if $param_algorithm_MIPFormulation_thresholds_min_peptide_probability:
114 -algorithm:MIPFormulation:thresholds:min_peptide_probability $param_algorithm_MIPFormulation_thresholds_min_peptide_probability
115 #end if
116 #if $param_algorithm_MIPFormulation_combined_ilp_k1:
117 -algorithm:MIPFormulation:combined_ilp:k1 $param_algorithm_MIPFormulation_combined_ilp_k1
118 #end if
119 #if $param_algorithm_MIPFormulation_combined_ilp_k2:
120 -algorithm:MIPFormulation:combined_ilp:k2 $param_algorithm_MIPFormulation_combined_ilp_k2
121 #end if
122 #if $param_algorithm_MIPFormulation_combined_ilp_k3:
123 -algorithm:MIPFormulation:combined_ilp:k3 $param_algorithm_MIPFormulation_combined_ilp_k3
124 #end if
125 #if $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs:
126 -algorithm:MIPFormulation:combined_ilp:scale_matching_probs
127 #end if
128 #if $param_algorithm_MIPFormulation_feature_based_no_intensity_normalization:
129 -algorithm:MIPFormulation:feature_based:no_intensity_normalization
130 #end if
131 #if $param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature:
132 -algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature $param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature
133 #end if
134 #if $param_algorithm_Preprocessing_precursor_mass_tolerance:
135 -algorithm:Preprocessing:precursor_mass_tolerance $param_algorithm_Preprocessing_precursor_mass_tolerance
136 #end if
137 #if $param_algorithm_Preprocessing_precursor_mass_tolerance_unit:
138 -algorithm:Preprocessing:precursor_mass_tolerance_unit
139 #if " " in str($param_algorithm_Preprocessing_precursor_mass_tolerance_unit):
140 "$param_algorithm_Preprocessing_precursor_mass_tolerance_unit"
141 #else
142 $param_algorithm_Preprocessing_precursor_mass_tolerance_unit
143 #end if
144 #end if
145 #if $param_algorithm_Preprocessing_preprocessed_db_path:
146 -algorithm:Preprocessing:preprocessed_db_path "$param_algorithm_Preprocessing_preprocessed_db_path"
147 #end if
148 #if $param_algorithm_Preprocessing_preprocessed_db_pred_rt_path:
149 -algorithm:Preprocessing:preprocessed_db_pred_rt_path "$param_algorithm_Preprocessing_preprocessed_db_pred_rt_path"
150 #end if
151 #if $param_algorithm_Preprocessing_preprocessed_db_pred_dt_path:
152 -algorithm:Preprocessing:preprocessed_db_pred_dt_path "$param_algorithm_Preprocessing_preprocessed_db_pred_dt_path"
153 #end if
154 #if $param_algorithm_Preprocessing_max_peptides_per_run:
155 -algorithm:Preprocessing:max_peptides_per_run $param_algorithm_Preprocessing_max_peptides_per_run
156 #end if
157 #if $param_algorithm_Preprocessing_missed_cleavages:
158 -algorithm:Preprocessing:missed_cleavages $param_algorithm_Preprocessing_missed_cleavages
159 #end if
160 #if $param_algorithm_Preprocessing_taxonomy:
161 -algorithm:Preprocessing:taxonomy "$param_algorithm_Preprocessing_taxonomy"
162 #end if
163 #if $param_algorithm_Preprocessing_tmp_dir:
164 -algorithm:Preprocessing:tmp_dir "$param_algorithm_Preprocessing_tmp_dir"
165 #end if
166 #if $param_algorithm_Preprocessing_store_peptide_sequences:
167 -algorithm:Preprocessing:store_peptide_sequences "$param_algorithm_Preprocessing_store_peptide_sequences"
168 #end if
169 #if $param_algorithm_Preprocessing_rt_settings_min_rt:
170 -algorithm:Preprocessing:rt_settings:min_rt $param_algorithm_Preprocessing_rt_settings_min_rt
171 #end if
172 #if $param_algorithm_Preprocessing_rt_settings_max_rt:
173 -algorithm:Preprocessing:rt_settings:max_rt $param_algorithm_Preprocessing_rt_settings_max_rt
174 #end if
175 #if $param_algorithm_Preprocessing_rt_settings_rt_step_size:
176 -algorithm:Preprocessing:rt_settings:rt_step_size $param_algorithm_Preprocessing_rt_settings_rt_step_size
177 #end if
178 #if $param_algorithm_Preprocessing_rt_settings_gauss_mean:
179 -algorithm:Preprocessing:rt_settings:gauss_mean $param_algorithm_Preprocessing_rt_settings_gauss_mean
180 #end if
181 #if $param_algorithm_Preprocessing_rt_settings_gauss_sigma:
182 -algorithm:Preprocessing:rt_settings:gauss_sigma $param_algorithm_Preprocessing_rt_settings_gauss_sigma
183 #end if
184 #if $adv_opts.adv_opts_selector=='advanced':
185 #if $adv_opts.param_solver:
186 -solver
187 #if " " in str($adv_opts.param_solver):
188 "$adv_opts.param_solver"
189 #else
190 $adv_opts.param_solver
191 #end if
192 #end if
193 #if $adv_opts.param_force:
194 -force
195 #end if
196 #end if
197 </command>
198 <inputs>
199 <param name="param_in" type="data" format="featurexml" optional="False" label="Input feature map file (featureXML)" help="(-in) "/>
200 <param name="param_ids" type="data" format="idxml" optional="False" label="file containing results of identification" help="(-ids) "/>
201 <param name="param_num_precursors" type="integer" value="1" label="number of precursors to be selected" help="(-num_precursors) "/>
202 <param name="param_raw_data" type="data" format="mzml" optional="True" label="Input profile data" help="(-raw_data) "/>
203 <param name="param_load_preprocessing" type="boolean" truevalue="-load_preprocessing" falsevalue="" checked="false" optional="True" label="The preprocessed db is loaded from file, not calculated" help="(-load_preprocessing) "/>
204 <param name="param_store_preprocessing" type="boolean" truevalue="-store_preprocessing" falsevalue="" checked="false" optional="True" label="The preprocessed db is stored" help="(-store_preprocessing) "/>
205 <param name="param_simulation" type="boolean" truevalue="-simulation" falsevalue="" checked="false" optional="True" label="Simulate the whole LC-MS/MS run" help="(-simulation) "/>
206 <param name="param_sim_results" type="text" size="30" label="File containing the results of the simulation run" help="(-sim_results) ">
207 <sanitizer>
208 <valid initial="string.printable">
209 <remove value="'"/>
210 <remove value="&quot;"/>
211 </valid>
212 </sanitizer>
213 </param>
214 <param name="param_db_path" type="data" format="fasta" optional="True" label="db file" help="(-db_path) "/>
215 <param name="param_rt_model" type="text" size="30" label="SVM Model for RTPredict" help="(-rt_model) ">
216 <sanitizer>
217 <valid initial="string.printable">
218 <remove value="'"/>
219 <remove value="&quot;"/>
220 </valid>
221 </sanitizer>
222 </param>
223 <param name="param_dt_model" type="text" size="30" label="SVM Model for PTPredict" help="(-dt_model) ">
224 <sanitizer>
225 <valid initial="string.printable">
226 <remove value="'"/>
227 <remove value="&quot;"/>
228 </valid>
229 </sanitizer>
230 </param>
231 <repeat name="rep_param_fixed_modifications" min="0" title="param_fixed_modifications">
232 <param name="param_fixed_modifications" type="text" size="30" label="the modifications i.e. Carboxymethyl (C)" help="(-fixed_modifications) ">
233 <sanitizer>
234 <valid initial="string.printable">
235 <remove value="'"/>
236 <remove value="&quot;"/>
237 </valid>
238 </sanitizer>
239 </param>
240 </repeat>
241 <param name="param_algorithm_type" type="select" optional="True" value="IPS" label="Strategy for precursor ion selection" help="(-type) ">
242 <option value="ILP_IPS">ILP_IPS</option>
243 <option value="IPS">IPS</option>
244 <option value="SPS">SPS</option>
245 <option value="Upshift">Upshift</option>
246 <option value="Downshift">Downshift</option>
247 <option value="DEX">DEX</option>
248 </param>
249 <param name="param_algorithm_max_iteration" type="integer" min="1" optional="True" value="100" label="Maximal number of iterations" help="(-max_iteration) "/>
250 <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) "/>
251 <param name="param_algorithm_step_size" type="integer" min="1" optional="True" value="1" label="Maximal number of precursors per iteration" help="(-step_size) "/>
252 <param name="param_algorithm_peptide_min_prob" type="float" value="0.2" label="Minimal peptide probability" help="(-peptide_min_prob) "/>
253 <param name="param_algorithm_sequential_spectrum_order" 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) "/>
254 <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) "/>
255 <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) "/>
256 <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) "/>
257 <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) "/>
258 <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) "/>
259 <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) "/>
260 <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) "/>
261 <param name="param_algorithm_MIPFormulation_thresholds_use_peptide_rule" 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) "/>
262 <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) "/>
263 <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) "/>
264 <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) "/>
265 <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) "/>
266 <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) "/>
267 <param name="param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs" type="boolean" truevalue="-algorithm:MIPFormulation:combined_ilp:scale_matching_probs" falsevalue="" checked="true" optional="True" label="flag if detectability * rt_weight shall be scaled to cover all [0,1]" help="(-scale_matching_probs) "/>
268 <param name="param_algorithm_MIPFormulation_feature_based_no_intensity_normalization" 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"/>
269 <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) "/>
270 <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) "/>
271 <param name="param_algorithm_Preprocessing_precursor_mass_tolerance_unit" type="select" optional="True" value="ppm" label="Precursor mass tolerance unit" help="(-precursor_mass_tolerance_unit) ">
272 <option value="ppm">ppm</option>
273 <option value="Da">Da</option>
274 </param>
275 <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) ">
276 <sanitizer>
277 <valid initial="string.printable">
278 <remove value="'"/>
279 <remove value="&quot;"/>
280 </valid>
281 </sanitizer>
282 </param>
283 <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) ">
284 <sanitizer>
285 <valid initial="string.printable">
286 <remove value="'"/>
287 <remove value="&quot;"/>
288 </valid>
289 </sanitizer>
290 </param>
291 <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) ">
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_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) "/>
300 <param name="param_algorithm_Preprocessing_missed_cleavages" type="integer" min="0" optional="True" value="1" label="Number of allowed missed cleavages" help="(-missed_cleavages) "/>
301 <param name="param_algorithm_Preprocessing_taxonomy" type="text" size="30" label="Taxonomy" help="(-taxonomy) ">
302 <sanitizer>
303 <valid initial="string.printable">
304 <remove value="'"/>
305 <remove value="&quot;"/>
306 </valid>
307 </sanitizer>
308 </param>
309 <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) ">
310 <sanitizer>
311 <valid initial="string.printable">
312 <remove value="'"/>
313 <remove value="&quot;"/>
314 </valid>
315 </sanitizer>
316 </param>
317 <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) ">
318 <sanitizer>
319 <valid initial="string.printable">
320 <remove value="'"/>
321 <remove value="&quot;"/>
322 </valid>
323 </sanitizer>
324 </param>
325 <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) "/>
326 <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) "/>
327 <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) "/>
328 <param name="param_algorithm_Preprocessing_rt_settings_gauss_mean" type="float" value="-1.0" label="mean of the gauss curve" help="(-gauss_mean) "/>
329 <param name="param_algorithm_Preprocessing_rt_settings_gauss_sigma" type="float" value="3.0" label="std of the gauss curve" help="(-gauss_sigma) "/>
330 <expand macro="advanced_options">
331 <param name="param_solver" type="select" optional="True" value="GLPK" label="LP solver type" help="(-solver) ">
332 <option value="GLPK">GLPK</option>
333 <option value="COINOR">COINOR</option>
334 </param>
335 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
336 </expand>
337 </inputs>
338 <outputs>
339 <data name="param_out" format="featurexml"/>
340 <data name="param_next_feat" format="featurexml"/>
341 </outputs>
342 <help>**What it does**
343
344 PrecursorIonSelector
345
346
347 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PrecursorIonSelector.html</help>
348 <expand macro="references"/>
349 </tool>