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comparison FeatureFinderIdentification.xml @ 11:c1beeebc9db7 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 19:53:44 +0000
parents edfd559ead1c
children 5471eba33b70
comparison
equal deleted inserted replaced
10:2bb25fa86a8f 11:c1beeebc9db7
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: [Quantitation]--> 3 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="FeatureFinderIdentification" name="FeatureFinderIdentification" version="2.3.0"> 4 <tool id="FeatureFinderIdentification" name="FeatureFinderIdentification" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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 <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[FeatureFinderIdentification 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 $param_id: 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 -id $param_id 21 mkdir id &&
20 #end if 22 ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
21 #if $param_id_ext: 23 #if $id_ext:
22 -id_ext $param_id_ext 24 mkdir id_ext &&
23 #end if 25 ln -s '$id_ext' 'id_ext/${re.sub("[^\w\-_]", "_", $id_ext.element_identifier)}.$gxy2omsext($id_ext.ext)' &&
24 #if $param_out: 26 #end if
25 -out $param_out 27 mkdir out &&
26 #end if 28 #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
27 #if $param_lib_out: 29 mkdir lib_out &&
28 -lib_out $param_lib_out 30 #end if
29 #end if 31 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
30 #if $param_chrom_out: 32 mkdir chrom_out &&
31 -chrom_out $param_chrom_out 33 #end if
32 #end if 34 #if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
33 #if $param_candidates_out: 35 mkdir candidates_out &&
34 -candidates_out $param_candidates_out 36 #end if
35 #end if 37 #if "xval_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
36 #if $param_extract_mz_window: 38 mkdir svm_xval_out &&
37 -extract:mz_window $param_extract_mz_window 39 #end if
38 #end if 40 #if $adv_opts_cond.adv_opts_selector=='advanced':
39 #if $param_extract_n_isotopes: 41 #if $adv_opts_cond.candidates_in:
40 -extract:n_isotopes $param_extract_n_isotopes 42 mkdir adv_opts_cond.candidates_in &&
41 #end if 43 ln -s '$adv_opts_cond.candidates_in' 'adv_opts_cond.candidates_in/${re.sub("[^\w\-_]", "_", $adv_opts_cond.candidates_in.element_identifier)}.$gxy2omsext($adv_opts_cond.candidates_in.ext)' &&
42 #if $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 44 #end if
64 #end if 45 #end if
65 #if $param_svm_xval: 46
66 -svm:xval $param_svm_xval 47 ## Main program call
67 #end if 48
68 49 set -o pipefail &&
69 #if $rep_param_svm_log2_C: 50 @EXECUTABLE@ -write_ctd ./ &&
70 -svm:log2_C 51 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
71 #for token in $rep_param_svm_log2_C: 52 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
72 #if " " in str(token): 53 -in
73 "$token.param_svm_log2_C" 54 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
74 #else 55 -id
75 $token.param_svm_log2_C 56 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)'
76 #end if 57 #if $id_ext:
77 #end for 58 -id_ext
78 #end if 59 'id_ext/${re.sub("[^\w\-_]", "_", $id_ext.element_identifier)}.$gxy2omsext($id_ext.ext)'
79 60 #end if
80 #if $rep_param_svm_log2_gamma: 61 -out
81 -svm:log2_gamma 62 'out/output.${gxy2omsext("featurexml")}'
82 #for token in $rep_param_svm_log2_gamma: 63 #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
83 #if " " in str(token): 64 -lib_out
84 "$token.param_svm_log2_gamma" 65 'lib_out/output.${gxy2omsext("traml")}'
85 #else 66 #end if
86 $token.param_svm_log2_gamma 67 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
87 #end if 68 -chrom_out
88 #end for 69 'chrom_out/output.${gxy2omsext("mzml")}'
89 #end if 70 #end if
90 #if $param_model_type: 71 #if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
91 -model:type 72 -candidates_out
92 #if " " in str($param_model_type): 73 'candidates_out/output.${gxy2omsext("featurexml")}'
93 "$param_model_type" 74 #end if
94 #else 75 #if "xval_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
95 $param_model_type 76 -svm:xval_out
77 'svm_xval_out/output.${gxy2omsext("csv")}'
78 #end if
79 #if $adv_opts_cond.adv_opts_selector=='advanced':
80 #if $adv_opts_cond.candidates_in:
81 -candidates_in
82 'adv_opts_cond.candidates_in/${re.sub("[^\w\-_]", "_", $adv_opts_cond.candidates_in.element_identifier)}.$gxy2omsext($adv_opts_cond.candidates_in.ext)'
96 #end if 83 #end if
97 #end if 84 #end if
98 #if $adv_opts.adv_opts_selector=='advanced': 85 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
99 #if $adv_opts.param_candidates_in: 86 | tee '$stdout'
100 -candidates_in $adv_opts.param_candidates_in 87 #end if
101 #end if 88
102 #if $adv_opts.param_force: 89 ## Postprocessing
103 -force 90 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
104 #end if 91 #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
105 #if $adv_opts.param_extract_isotope_pmin: 92 && mv 'lib_out/output.${gxy2omsext("traml")}' '$lib_out'
106 -extract:isotope_pmin $adv_opts.param_extract_isotope_pmin 93 #end if
107 #end if 94 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
108 #if $adv_opts.param_extract_rt_quantile: 95 && mv 'chrom_out/output.${gxy2omsext("mzml")}' '$chrom_out'
109 -extract:rt_quantile $adv_opts.param_extract_rt_quantile 96 #end if
110 #end if 97 #if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
111 #if $adv_opts.param_extract_rt_window: 98 && mv 'candidates_out/output.${gxy2omsext("featurexml")}' '$candidates_out'
112 -extract:rt_window $adv_opts.param_extract_rt_window 99 #end if
113 #end if 100 #if "xval_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
114 #if $adv_opts.param_detect_min_peak_width: 101 && mv 'svm_xval_out/output.${gxy2omsext("csv")}' '$svm_xval_out'
115 -detect:min_peak_width $adv_opts.param_detect_min_peak_width 102 #end if
116 #end if 103 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
117 #if $adv_opts.param_detect_signal_to_noise: 104 && mv '@EXECUTABLE@.ctd' '$ctd_out'
118 -detect:signal_to_noise $adv_opts.param_detect_signal_to_noise 105 #end if]]></command>
119 #end if 106 <configfiles>
120 #if $adv_opts.param_svm_epsilon: 107 <inputs name="args_json" data_style="paths"/>
121 -svm:epsilon $adv_opts.param_svm_epsilon 108 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
122 #end if 109 </configfiles>
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
134 #end if
135 #if $adv_opts.param_model_add_zeros:
136 -model:add_zeros $adv_opts.param_model_add_zeros
137 #end if
138 #if $adv_opts.param_model_unweighted_fit:
139 -model:unweighted_fit
140 #end if
141 #if $adv_opts.param_model_no_imputation:
142 -model:no_imputation
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
147 #if $adv_opts.param_model_check_boundaries:
148 -model:check:boundaries $adv_opts.param_model_check_boundaries
149 #end if
150 #if $adv_opts.param_model_check_width:
151 -model:check:width $adv_opts.param_model_check_width
152 #end if
153 #if $adv_opts.param_model_check_asymmetry:
154 -model:check:asymmetry $adv_opts.param_model_check_asymmetry
155 #end if
156 #end if
157 ]]></command>
158 <inputs> 110 <inputs>
159 <param name="param_in" type="data" format="mzml" optional="False" label="Input file: LC-MS raw data" help="(-in) "/> 111 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file: LC-MS raw data" help=" select mzml data sets(s)"/>
160 <param name="param_id" type="data" format="idxml" optional="False" label="Input file: Peptide identifications derived directly from 'in'" help="(-id) "/> 112 <param name="id" argument="-id" type="data" format="idxml" optional="false" label="Input file: Peptide identifications derived directly from 'in'" help=" select idxml data sets(s)"/>
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)"/> 113 <param name="id_ext" argument="-id_ext" type="data" format="idxml" optional="true" label="Input file: 'External' peptide identifications" help="(e.g. from aligned runs) select idxml data sets(s)"/>
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) "/> 114 <section name="extract" title="Parameters for ion chromatogram extraction" help="" expanded="false">
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) "/> 115 <param name="batch_size" argument="-extract:batch_size" type="integer" optional="true" min="1" value="1000" label="Nr of peptides used in each batch of chromatogram extraction" help="Smaller values decrease memory usage but increase runtime"/>
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'"/> 116 <param name="mz_window" argument="-extract:mz_window" type="float" optional="true" min="0.0" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help=""/>
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"/> 117 <param name="n_isotopes" argument="-extract:n_isotopes" type="integer" optional="true" min="2" value="2" label="Number of isotopes to include in each peptide assay" help=""/>
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) "/> 118 <param name="isotope_pmin" argument="-extract:isotope_pmin" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Minimum probability for an isotope to be included in the assay for a peptide" help="If set, this parameter takes precedence over 'extract:n_isotopes'"/>
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')"/> 119 <param name="rt_quantile" argument="-extract:rt_quantile" type="float" optional="true" min="0.0" max="1.0" value="0.95" label="Quantile of the RT deviations between aligned internal and external IDs to use for scaling the RT extraction window" help=""/>
168 <param name="param_svm_kernel" display="radio" type="select" optional="False" value="RBF" label="SVM kernel" help="(-kernel) "> 120 <param name="rt_window" argument="-extract:rt_window" type="float" optional="true" min="0.0" value="0.0" label="RT window size (in sec.) for chromatogram extraction" help="If set, this parameter takes precedence over 'extract:rt_quantile'"/>
169 <option value="RBF" selected="true">RBF</option> 121 </section>
170 <option value="linear">linear</option> 122 <section name="detect" title="Parameters for detecting features in extracted ion chromatograms" help="" expanded="false">
123 <param name="peak_width" argument="-detect:peak_width" type="float" optional="true" min="0.0" value="60.0" label="Expected elution peak width in seconds, for smoothing (Gauss filter)" help="Also determines the RT extration window, unless set explicitly via 'extract:rt_window'"/>
124 <param name="min_peak_width" argument="-detect:min_peak_width" type="float" optional="true" min="0.0" value="0.2" label="Minimum elution peak width" help="Absolute value in seconds if 1 or greater, else relative to 'peak_width'"/>
125 <param name="signal_to_noise" argument="-detect:signal_to_noise" type="float" optional="true" min="0.1" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help=""/>
126 <param name="mapping_tolerance" argument="-detect:mapping_tolerance" type="float" optional="true" min="0.0" value="0.0" label="RT tolerance (plus/minus) for mapping peptide IDs to features" help="Absolute value in seconds if 1 or greater, else relative to the RT span of the feature"/>
127 </section>
128 <section name="svm" title="Parameters for scoring features using a support vector machine (SVM)" help="" expanded="false">
129 <param name="samples" argument="-svm:samples" type="integer" optional="true" min="0" value="0" label="Number of observations to use for training ('0' for all)" help=""/>
130 <param name="no_selection" argument="-svm:no_selection" type="boolean" truevalue="true" falsevalue="false" checked="false" label="By default, roughly the same number of positive and negative observations, with the same intensity distribution, are selected for training" help="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')"/>
131 <param name="kernel" argument="-svm:kernel" display="radio" type="select" optional="false" label="SVM kernel" help="">
132 <option value="RBF" selected="true">RBF</option>
133 <option value="linear">linear</option>
134 <expand macro="list_string_san"/>
135 </param>
136 <param name="xval" argument="-svm:xval" type="integer" optional="true" min="1" value="5" label="Number of partitions for cross-validation (parameter optimization)" help=""/>
137 <param name="log2_C" argument="-svm:log2_C" type="text" optional="true" 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="A value 'x' is used as 'C = 2^x' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
138 <expand macro="list_float_valsan"/>
139 </param>
140 <param name="log2_gamma" argument="-svm:log2_gamma" type="text" optional="true" 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="A value 'x' is used as 'gamma = 2^x' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
141 <expand macro="list_float_valsan"/>
142 </param>
143 <param name="epsilon" argument="-svm:epsilon" type="float" optional="true" min="0.0" value="0.001" label="Stopping criterion" help=""/>
144 <param name="cache_size" argument="-svm:cache_size" type="float" optional="true" min="1.0" value="100.0" label="Size of the kernel cache (in MB)" help=""/>
145 <param name="no_shrinking" argument="-svm:no_shrinking" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable the shrinking heuristics" help=""/>
146 <param name="predictors" argument="-svm:predictors" type="text" optional="true" 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="">
147 <expand macro="list_string_san"/>
148 </param>
149 <param name="min_prob" argument="-svm:min_prob" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Minimum probability of correctness, as predicted by the SVM, required to retain a feature candidate" help=""/>
150 </section>
151 <section name="model" title="Parameters for fitting elution models to features" help="" expanded="false">
152 <param name="type" argument="-model:type" display="radio" type="select" optional="false" label="Type of elution model to fit to features" help="">
153 <option value="symmetric" selected="true">symmetric</option>
154 <option value="asymmetric">asymmetric</option>
155 <option value="none">none</option>
156 <expand macro="list_string_san"/>
157 </param>
158 <param name="add_zeros" argument="-model:add_zeros" type="float" optional="true" min="0.0" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="This parameter sets the weight given to these points during model fitting; '0' to disable"/>
159 <param name="unweighted_fit" argument="-model:unweighted_fit" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help=""/>
160 <param name="no_imputation" argument="-model:no_imputation" type="boolean" truevalue="true" falsevalue="false" checked="false" 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=""/>
161 <section name="check" title="Parameters for checking the validity of elution models (and rejecting them if necessary)" help="" expanded="false">
162 <param name="min_area" argument="-model:check:min_area" type="float" optional="true" min="0.0" value="1.0" label="Lower bound for the area under the curve of a valid elution model" help=""/>
163 <param name="boundaries" argument="-model:check:boundaries" type="float" optional="true" min="0.0" max="1.0" 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=""/>
164 <param name="width" argument="-model:check:width" type="float" optional="true" min="0.0" 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=""/>
165 <param name="asymmetry" argument="-model:check:asymmetry" type="float" optional="true" min="0.0" 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=""/>
166 </section>
167 </section>
168 <expand macro="adv_opts_macro">
169 <param name="candidates_in" argument="-candidates_in" type="data" format="featurexml" optional="true" label="Input file: Feature candidates from a previous run" help="If set, only feature classification and elution model fitting are carried out, if enabled. Many parameters are ignored select featurexml data sets(s)"/>
170 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
171 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
172 <expand macro="list_string_san"/>
173 </param>
174 </expand>
175 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
176 <option value="lib_out_FLAG">lib_out (Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable)</option>
177 <option value="chrom_out_FLAG">chrom_out (Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable)</option>
178 <option value="candidates_out_FLAG">candidates_out (Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable)</option>
179 <option value="xval_out_FLAG">xval_out (Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable)</option>
180 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
171 </param> 181 </param>
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) "/>
173 <repeat name="rep_param_svm_log2_C" min="0" max="1" title="param_svm_log2_C">
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'">
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>
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) ">
194 <option value="symmetric" selected="true">symmetric</option>
195 <option value="asymmetric">asymmetric</option>
196 <option value="none">none</option>
197 </param>
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"/>
200 <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="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) "/>
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"/>
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) "/>
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) "/>
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) "/>
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) "/>
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) "/>
225 </expand>
226 </inputs> 182 </inputs>
227 <outputs> 183 <outputs>
228 <data name="param_out" format="featurexml"/> 184 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
229 <data name="param_lib_out" format="traml"/> 185 <data name="lib_out" label="${tool.name} on ${on_string}: lib_out" format="traml">
230 <data name="param_chrom_out" format="mzml"/> 186 <filter>OPTIONAL_OUTPUTS is not None and "lib_out_FLAG" in OPTIONAL_OUTPUTS</filter>
231 <data name="param_candidates_out" format="featurexml"/> 187 </data>
232 <data name="param_svm_xval_out" format="tabular"/> 188 <data name="chrom_out" label="${tool.name} on ${on_string}: chrom_out" format="mzml">
189 <filter>OPTIONAL_OUTPUTS is not None and "chrom_out_FLAG" in OPTIONAL_OUTPUTS</filter>
190 </data>
191 <data name="candidates_out" label="${tool.name} on ${on_string}: candidates_out" format="featurexml">
192 <filter>OPTIONAL_OUTPUTS is not None and "candidates_out_FLAG" in OPTIONAL_OUTPUTS</filter>
193 </data>
194 <data name="svm_xval_out" label="${tool.name} on ${on_string}: svm:xval_out" format="csv">
195 <filter>OPTIONAL_OUTPUTS is not None and "xval_out_FLAG" in OPTIONAL_OUTPUTS</filter>
196 </data>
197 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
198 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
199 </data>
233 </outputs> 200 </outputs>
234 <help>Detects features in MS1 data based on peptide identifications. 201 <tests>
235 202 <expand macro="autotest_FeatureFinderIdentification"/>
236 203 <expand macro="manutest_FeatureFinderIdentification"/>
237 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureFinderIdentification.html</help> 204 </tests>
205 <help><![CDATA[Detects features in MS1 data based on peptide identifications.
206
207
208 For more information, visit http://www.openms.de/documentation/TOPP_FeatureFinderIdentification.html]]></help>
209 <expand macro="references"/>
238 </tool> 210 </tool>