Mercurial > repos > galaxyp > openms_featurefinderidentification

comparison FeatureFinderIdentification.xml @ 3:c040ffc3ac9b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:54:55 -0400
parents 6a3bbd5b8cb6
children 39ccf2ebfe49
comparison
equal deleted inserted replaced
2:d12500c4d67e 3:c040ffc3ac9b
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 CTD2Galaxy.--> 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: [Quantitation]--> 3 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="FeatureFinderIdentification" name="FeatureFinderIdentification" version="2.1.0"> 4 <tool id="FeatureFinderIdentification" name="FeatureFinderIdentification" version="2.2.0">
5 <description>Detects features in MS1 data based on peptide identifications.</description> 5 <description>Detects features in MS1 data based on peptide identifications.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FeatureFinderIdentification</token> 7 <token name="@EXECUTABLE@">FeatureFinderIdentification</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
16 -in $param_in 16 -in $param_in
17 #end if 17 #end if
18 #if $param_id: 18 #if $param_id:
19 -id $param_id 19 -id $param_id
20 #end if 20 #end if
21 #if $param_id_ext:
22 -id_ext $param_id_ext
23 #end if
21 #if $param_out: 24 #if $param_out:
22 -out $param_out 25 -out $param_out
23 #end if 26 #end if
24 #if $param_lib_out: 27 #if $param_lib_out:
25 -lib_out $param_lib_out 28 -lib_out $param_lib_out
26 #end if 29 #end if
27 #if $param_chrom_out: 30 #if $param_chrom_out:
28 -chrom_out $param_chrom_out 31 -chrom_out $param_chrom_out
29 #end if 32 #end if
30 #if $param_trafo_out: 33 #if $param_candidates_out:
31 -trafo_out $param_trafo_out 34 -candidates_out $param_candidates_out
32 #end if
33 #if $param_extract_reference_rt:
34 -extract:reference_rt
35 #if " " in str($param_extract_reference_rt):
36 "$param_extract_reference_rt"
37 #else
38 $param_extract_reference_rt
39 #end if
40 #end if
41 #if $param_extract_rt_window:
42 -extract:rt_window $param_extract_rt_window
43 #end if 35 #end if
44 #if $param_extract_mz_window: 36 #if $param_extract_mz_window:
45 -extract:mz_window $param_extract_mz_window 37 -extract:mz_window $param_extract_mz_window
46 #end if 38 #end if
47 #if $param_extract_isotope_pmin: 39 #if $param_extract_n_isotopes:
48 -extract:isotope_pmin $param_extract_isotope_pmin 40 -extract:n_isotopes $param_extract_n_isotopes
49 #end if 41 #end if
50 #if $param_detect_peak_width: 42 #if $param_detect_peak_width:
51 -detect:peak_width $param_detect_peak_width 43 -detect:peak_width $param_detect_peak_width
44 #end if
45 #if $param_detect_mapping_tolerance:
46 -detect:mapping_tolerance $param_detect_mapping_tolerance
47 #end if
48 #if $param_svm_samples:
49 -svm:samples $param_svm_samples
50 #end if
51 #if $param_svm_no_selection:
52 -svm:no_selection
53 #end if
54 #if $param_svm_xval_out:
55 -svm:xval_out $param_svm_xval_out
56 #end if
57 #if $param_svm_kernel:
58 -svm:kernel
59 #if " " in str($param_svm_kernel):
60 "$param_svm_kernel"
61 #else
62 $param_svm_kernel
63 #end if
64 #end if
65 #if $param_svm_xval:
66 -svm:xval $param_svm_xval
67 #end if
68
69 #if $rep_param_svm_log2_C:
70 -svm:log2_C
71 #for token in $rep_param_svm_log2_C:
72 #if " " in str(token):
73 "$token.param_svm_log2_C"
74 #else
75 $token.param_svm_log2_C
76 #end if
77 #end for
78 #end if
79
80 #if $rep_param_svm_log2_gamma:
81 -svm:log2_gamma
82 #for token in $rep_param_svm_log2_gamma:
83 #if " " in str(token):
84 "$token.param_svm_log2_gamma"
85 #else
86 $token.param_svm_log2_gamma
87 #end if
88 #end for
52 #end if 89 #end if
53 #if $param_model_type: 90 #if $param_model_type:
54 -model:type 91 -model:type
55 #if " " in str($param_model_type): 92 #if " " in str($param_model_type):
56 "$param_model_type" 93 "$param_model_type"
57 #else 94 #else
58 $param_model_type 95 $param_model_type
59 #end if 96 #end if
60 #end if 97 #end if
61 #if $adv_opts.adv_opts_selector=='advanced': 98 #if $adv_opts.adv_opts_selector=='advanced':
99 #if $adv_opts.param_candidates_in:
100 -candidates_in $adv_opts.param_candidates_in
101 #end if
62 #if $adv_opts.param_force: 102 #if $adv_opts.param_force:
63 -force 103 -force
64 #end if 104 #end if
65 #if $adv_opts.param_detect_all_features: 105 #if $adv_opts.param_extract_isotope_pmin:
66 -detect:all_features 106 -extract:isotope_pmin $adv_opts.param_extract_isotope_pmin
107 #end if
108 #if $adv_opts.param_extract_rt_quantile:
109 -extract:rt_quantile $adv_opts.param_extract_rt_quantile
110 #end if
111 #if $adv_opts.param_extract_rt_window:
112 -extract:rt_window $adv_opts.param_extract_rt_window
113 #end if
114 #if $adv_opts.param_detect_min_peak_width:
115 -detect:min_peak_width $adv_opts.param_detect_min_peak_width
116 #end if
117 #if $adv_opts.param_detect_signal_to_noise:
118 -detect:signal_to_noise $adv_opts.param_detect_signal_to_noise
119 #end if
120 #if $adv_opts.param_svm_epsilon:
121 -svm:epsilon $adv_opts.param_svm_epsilon
122 #end if
123 #if $adv_opts.param_svm_cache_size:
124 -svm:cache_size $adv_opts.param_svm_cache_size
125 #end if
126 #if $adv_opts.param_svm_no_shrinking:
127 -svm:no_shrinking
128 #end if
129 #if $adv_opts.param_svm_predictors:
130 -svm:predictors "$adv_opts.param_svm_predictors"
131 #end if
132 #if $adv_opts.param_svm_min_prob:
133 -svm:min_prob $adv_opts.param_svm_min_prob
67 #end if 134 #end if
68 #if $adv_opts.param_model_add_zeros: 135 #if $adv_opts.param_model_add_zeros:
69 -model:add_zeros $adv_opts.param_model_add_zeros 136 -model:add_zeros $adv_opts.param_model_add_zeros
70 #end if 137 #end if
71 #if $adv_opts.param_model_unweighted_fit: 138 #if $adv_opts.param_model_unweighted_fit:
72 -model:unweighted_fit 139 -model:unweighted_fit
73 #end if 140 #end if
74 #if $adv_opts.param_model_no_imputation: 141 #if $adv_opts.param_model_no_imputation:
75 -model:no_imputation 142 -model:no_imputation
76 #end if 143 #end if
144 #if $adv_opts.param_model_check_min_area:
145 -model:check:min_area $adv_opts.param_model_check_min_area
146 #end if
77 #if $adv_opts.param_model_check_boundaries: 147 #if $adv_opts.param_model_check_boundaries:
78 -model:check:boundaries $adv_opts.param_model_check_boundaries 148 -model:check:boundaries $adv_opts.param_model_check_boundaries
79 #end if 149 #end if
80 #if $adv_opts.param_model_check_width: 150 #if $adv_opts.param_model_check_width:
81 -model:check:width $adv_opts.param_model_check_width 151 -model:check:width $adv_opts.param_model_check_width
84 -model:check:asymmetry $adv_opts.param_model_check_asymmetry 154 -model:check:asymmetry $adv_opts.param_model_check_asymmetry
85 #end if 155 #end if
86 #end if 156 #end if
87 </command> 157 </command>
88 <inputs> 158 <inputs>
89 <param name="param_in" type="data" format="mzml" optional="False" label="Input file (LC-MS raw data)" help="(-in) "/> 159 <param name="param_in" type="data" format="mzml" optional="False" label="Input file: LC-MS raw data" help="(-in) "/>
90 <param name="param_id" type="data" format="idxml" optional="False" label="Input file (peptide identifications)" help="(-id) "/> 160 <param name="param_id" type="data" format="idxml" optional="False" label="Input file: Peptide identifications derived directly from 'in'" help="(-id) "/>
91 <param name="param_extract_reference_rt" type="select" optional="False" value="adapt" label="Method for selecting the reference RT, if there are multiple IDs for a peptide and charge" help="(-reference_rt) 'adapt': adapt (extend) RT windows based on IDs; 'score': RT of the best-scoring ID; 'intensity': RT of the ID with the most intense precursor; 'median': median RT of all IDs; 'all': no single reference, use RTs of all IDs (requires further processing of results)"> 161 <param name="param_id_ext" type="data" format="idxml" optional="True" label="Input file: 'External' peptide identifications (" help="(-id_ext) e.g. from aligned runs)"/>
92 <option value="adapt" selected="true">adapt</option> 162 <param name="param_extract_mz_window" type="float" min="0.0" optional="True" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help="(-mz_window) "/>
93 <option value="score">score</option> 163 <param name="param_extract_n_isotopes" type="integer" min="2" optional="True" value="2" label="Number of isotopes to include in each peptide assay" help="(-n_isotopes) "/>
94 <option value="intensity">intensity</option> 164 <param name="param_detect_peak_width" type="float" min="0.0" optional="True" value="60.0" label="Expected elution peak width in seconds, for smoothing (Gauss filter)" help="(-peak_width) Also determines the RT extration window, unless set explicitly via 'extract:rt_window'"/>
95 <option value="median">median</option> 165 <param name="param_detect_mapping_tolerance" type="float" min="0.0" optional="True" value="0.0" label="RT tolerance (plus/minus) for mapping peptide IDs to features" help="(-mapping_tolerance) Absolute value in seconds if 1 or greater, else relative to the RT span of the feature"/>
96 <option value="all">all</option> 166 <param name="param_svm_samples" type="integer" min="0" optional="True" value="0" label="Number of observations to use for training ('0' for all)" help="(-samples) "/>
167 <param name="param_svm_no_selection" display="radio" type="boolean" truevalue="-svm:no_selection" falsevalue="" checked="false" optional="True" label="By default, roughly the same number of positive and negative observations, with the same intensity distribution, are selected for training" help="(-no_selection) This aims to reduce biases, but also reduces the amount of training data. Set this flag to skip this procedure and consider all available observations (subject to 'svm:samples')"/>
168 <param name="param_svm_kernel" display="radio" type="select" optional="False" value="RBF" label="SVM kernel" help="(-kernel) ">
169 <option value="RBF" selected="true">RBF</option>
170 <option value="linear">linear</option>
97 </param> 171 </param>
98 <param name="param_extract_rt_window" type="float" min="0.0" optional="True" value="60.0" label="RT window size (in sec.) for chromatogram extraction" help="(-rt_window) "/> 172 <param name="param_svm_xval" type="integer" min="1" optional="True" value="5" label="Number of partitions for cross-validation (parameter optimization)" help="(-xval) "/>
99 <param name="param_extract_mz_window" type="float" min="0.0" optional="True" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help="(-mz_window) "/> 173 <repeat name="rep_param_svm_log2_C" min="0" max="1" title="param_svm_log2_C">
100 <param name="param_extract_isotope_pmin" type="float" min="0.0" max="1.0" optional="True" value="0.03" label="Minimum probability for an isotope to be included in the assay for a peptide" help="(-isotope_pmin) "/> 174 <param name="param_svm_log2_C" type="text" size="30" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0" label="Values to try for the SVM parameter 'C' during parameter optimization" help="(-log2_C) A value 'x' is used as 'C = 2^x'">
101 <param name="param_detect_peak_width" type="float" min="0.0" optional="True" value="30.0" label="Elution peak width in seconds for smoothing (Gauss filter)" help="(-peak_width) "/> 175 <sanitizer>
176 <valid initial="string.printable">
177 <remove value="'"/>
178 <remove value="&quot;"/>
179 </valid>
180 </sanitizer>
181 </param>
182 </repeat>
183 <repeat name="rep_param_svm_log2_gamma" min="0" max="1" title="param_svm_log2_gamma">
184 <param name="param_svm_log2_gamma" type="text" size="30" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0" label="Values to try for the SVM parameter 'gamma' during parameter optimization (RBF kernel only)" help="(-log2_gamma) A value 'x' is used as 'gamma = 2^x'">
185 <sanitizer>
186 <valid initial="string.printable">
187 <remove value="'"/>
188 <remove value="&quot;"/>
189 </valid>
190 </sanitizer>
191 </param>
192 </repeat>
102 <param name="param_model_type" display="radio" type="select" optional="False" value="symmetric" label="Type of elution model to fit to features" help="(-type) "> 193 <param name="param_model_type" display="radio" type="select" optional="False" value="symmetric" label="Type of elution model to fit to features" help="(-type) ">
103 <option value="symmetric" selected="true">symmetric</option> 194 <option value="symmetric" selected="true">symmetric</option>
104 <option value="asymmetric">asymmetric</option> 195 <option value="asymmetric">asymmetric</option>
105 <option value="none">none</option> 196 <option value="none">none</option>
106 </param> 197 </param>
107 <expand macro="advanced_options"> 198 <expand macro="advanced_options">
199 <param name="param_candidates_in" type="data" format="featurexml" optional="True" label="Input file: Feature candidates from a previous run" help="(-candidates_in) If set, only feature classification and elution model fitting are carried out, if enabled. Many parameters are ignored"/>
108 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 200 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
109 <param name="param_detect_all_features" display="radio" type="boolean" truevalue="-detect:all_features" falsevalue="" checked="false" optional="True" label="Return all features detected by OpenSWATH for an assay, instead of only the best one" help="(-all_features) (This requires further processing of the results.)"/> 201 <param name="param_extract_isotope_pmin" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Minimum probability for an isotope to be included in the assay for a peptide" help="(-isotope_pmin) If set, this parameter takes precedence over 'extract:n_isotopes'"/>
202 <param name="param_extract_rt_quantile" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="Quantile of the RT deviations between aligned internal and external IDs to use for scaling the RT extraction window" help="(-rt_quantile) "/>
203 <param name="param_extract_rt_window" type="float" min="0.0" optional="True" value="0.0" label="RT window size (in sec.) for chromatogram extraction" help="(-rt_window) If set, this parameter takes precedence over 'extract:rt_quantile'"/>
204 <param name="param_detect_min_peak_width" type="float" min="0.0" optional="True" value="0.2" label="Minimum elution peak width" help="(-min_peak_width) Absolute value in seconds if 1 or greater, else relative to 'peak_width'"/>
205 <param name="param_detect_signal_to_noise" type="float" min="0.1" optional="True" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help="(-signal_to_noise) "/>
206 <param name="param_svm_epsilon" type="float" min="0.0" optional="True" value="0.001" label="Stopping criterion" help="(-epsilon) "/>
207 <param name="param_svm_cache_size" type="float" min="1.0" optional="True" value="100.0" label="Size of the kernel cache (in MB)" help="(-cache_size) "/>
208 <param name="param_svm_no_shrinking" display="radio" type="boolean" truevalue="-svm:no_shrinking" falsevalue="" checked="false" optional="True" label="Disable the shrinking heuristics" help="(-no_shrinking) "/>
209 <param name="param_svm_predictors" type="text" size="30" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score" label="Names of OpenSWATH scores to use as predictors for the SVM (comma-separated list)" help="(-predictors) ">
210 <sanitizer>
211 <valid initial="string.printable">
212 <remove value="'"/>
213 <remove value="&quot;"/>
214 </valid>
215 </sanitizer>
216 </param>
217 <param name="param_svm_min_prob" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Minimum probability of correctness, as predicted by the SVM, required to retain a feature candidate" help="(-min_prob) "/>
110 <param name="param_model_add_zeros" type="float" min="0.0" optional="True" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="(-add_zeros) This parameter sets the weight given to these points during model fitting; '0' to disable"/> 218 <param name="param_model_add_zeros" type="float" min="0.0" optional="True" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="(-add_zeros) This parameter sets the weight given to these points during model fitting; '0' to disable"/>
111 <param name="param_model_unweighted_fit" display="radio" type="boolean" truevalue="-model:unweighted_fit" falsevalue="" checked="false" optional="True" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help="(-unweighted_fit) "/> 219 <param name="param_model_unweighted_fit" display="radio" type="boolean" truevalue="-model:unweighted_fit" falsevalue="" checked="false" optional="True" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help="(-unweighted_fit) "/>
112 <param name="param_model_no_imputation" display="radio" type="boolean" truevalue="-model:no_imputation" falsevalue="" checked="false" optional="True" label="If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate" help="(-no_imputation) "/> 220 <param name="param_model_no_imputation" display="radio" type="boolean" truevalue="-model:no_imputation" falsevalue="" checked="false" optional="True" label="If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate" help="(-no_imputation) "/>
221 <param name="param_model_check_min_area" type="float" min="0.0" optional="True" value="1.0" label="Lower bound for the area under the curve of a valid elution model" help="(-min_area) "/>
113 <param name="param_model_check_boundaries" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help="(-boundaries) "/> 222 <param name="param_model_check_boundaries" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help="(-boundaries) "/>
114 <param name="param_model_check_width" type="float" min="0.0" optional="True" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores; '0' to disable" help="(-width) "/> 223 <param name="param_model_check_width" type="float" min="0.0" optional="True" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores; '0' to disable" help="(-width) "/>
115 <param name="param_model_check_asymmetry" type="float" min="0.0" optional="True" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable" help="(-asymmetry) "/> 224 <param name="param_model_check_asymmetry" type="float" min="0.0" optional="True" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable" help="(-asymmetry) "/>
116 </expand> 225 </expand>
117 </inputs> 226 </inputs>
118 <outputs> 227 <outputs>
119 <data name="param_out" format="featurexml"/> 228 <data name="param_out" format="featurexml"/>
120 <data name="param_lib_out" format="traml"/> 229 <data name="param_lib_out" format="traml"/>
121 <data name="param_chrom_out" format="mzml"/> 230 <data name="param_chrom_out" format="mzml"/>
122 <data name="param_trafo_out" format="trafoxml"/> 231 <data name="param_candidates_out" format="featurexml"/>
232 <data name="param_svm_xval_out" format="tabular"/>
123 </outputs> 233 </outputs>
124 <help>Detects features in MS1 data based on peptide identifications. 234 <help>Detects features in MS1 data based on peptide identifications.
125 235
126 236
127 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderIdentification.html</help> 237 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderIdentification.html</help>