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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:44:29 +0000
parents 5dc928c83939
children
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15:5dc928c83939 16:65bdfab68571
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.--> 1 <!--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]--> 2 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="FeatureFinderIdentification" name="FeatureFinderIdentification" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="FeatureFinderIdentification" name="FeatureFinderIdentification" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Detects features in MS1 data based on peptide identifications.</description> 4 <description>Detects features in MS1 data based on peptide identifications</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">FeatureFinderIdentification</token> 6 <token name="@EXECUTABLE@">FeatureFinderIdentification</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir id && 18 mkdir id &&
20 ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && 19 cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
21 #if $id_ext: 20 #if $id_ext:
22 mkdir id_ext && 21 mkdir id_ext &&
23 ln -s '$id_ext' 'id_ext/${re.sub("[^\w\-_]", "_", $id_ext.element_identifier)}.$gxy2omsext($id_ext.ext)' && 22 cp '$id_ext' 'id_ext/${re.sub("[^\w\-_]", "_", $id_ext.element_identifier)}.$gxy2omsext($id_ext.ext)' &&
24 #end if 23 #end if
25 mkdir out && 24 mkdir out &&
26 #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 25 #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
27 mkdir lib_out && 26 mkdir lib_out &&
28 #end if 27 #end if
33 mkdir candidates_out && 32 mkdir candidates_out &&
34 #end if 33 #end if
35 #if "xval_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 34 #if "xval_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
36 mkdir svm_xval_out && 35 mkdir svm_xval_out &&
37 #end if 36 #end if
37 ## advanced options
38 #if $adv_opts.candidates_in: 38 #if $adv_opts.candidates_in:
39 mkdir adv_opts.candidates_in && 39 mkdir adv_opts.candidates_in &&
40 ln -s '$adv_opts.candidates_in' 'adv_opts.candidates_in/${re.sub("[^\w\-_]", "_", $adv_opts.candidates_in.element_identifier)}.$gxy2omsext($adv_opts.candidates_in.ext)' && 40 cp '$adv_opts.candidates_in' 'adv_opts.candidates_in/${re.sub("[^\w\-_]", "_", $adv_opts.candidates_in.element_identifier)}.$gxy2omsext($adv_opts.candidates_in.ext)' &&
41 #end if 41 #end if
42
42 43
43 ## Main program call 44 ## Main program call
44 45
45 set -o pipefail && 46 set -o pipefail &&
46 @EXECUTABLE@ -write_ctd ./ && 47 @EXECUTABLE@ -write_ctd ./ &&
70 #end if 71 #end if
71 #if "xval_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 72 #if "xval_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
72 -svm:xval_out 73 -svm:xval_out
73 'svm_xval_out/output.${gxy2omsext("csv")}' 74 'svm_xval_out/output.${gxy2omsext("csv")}'
74 #end if 75 #end if
76 ## advanced options
75 #if $adv_opts.candidates_in: 77 #if $adv_opts.candidates_in:
76 -candidates_in 78 -candidates_in
77 'adv_opts.candidates_in/${re.sub("[^\w\-_]", "_", $adv_opts.candidates_in.element_identifier)}.$gxy2omsext($adv_opts.candidates_in.ext)' 79 'adv_opts.candidates_in/${re.sub("[^\w\-_]", "_", $adv_opts.candidates_in.element_identifier)}.$gxy2omsext($adv_opts.candidates_in.ext)'
78 #end if 80 #end if
81
79 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 82 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
80 | tee '$stdout' 83 | tee '$stdout'
81 #end if 84 #end if
82 85
83 ## Postprocessing 86 ## Postprocessing
100 <configfiles> 103 <configfiles>
101 <inputs name="args_json" data_style="paths"/> 104 <inputs name="args_json" data_style="paths"/>
102 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 105 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
103 </configfiles> 106 </configfiles>
104 <inputs> 107 <inputs>
105 <param argument="-in" type="data" format="mzml" optional="false" label="Input file: LC-MS raw data" help=" select mzml data sets(s)"/> 108 <param argument="-in" type="data" format="mzml" label="Input file: LC-MS raw data" help=" select mzml data sets(s)"/>
106 <param argument="-id" type="data" format="idxml" optional="false" label="Input file: Peptide identifications derived directly from 'in'" help=" select idxml data sets(s)"/> 109 <param argument="-id" type="data" format="idxml" label="Input file: Peptide identifications derived directly from 'in'" help=" select idxml data sets(s)"/>
107 <param 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)"/> 110 <param 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)"/>
108 <param argument="-quantify_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether decoy peptides should be quantified (true) or skipped (false)" help=""/> 111 <param argument="-quantify_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether decoy peptides should be quantified (true) or skipped (false)" help=""/>
112 <param argument="-min_psm_cutoff" type="text" value="none" label="Minimum score for the best PSM of a spectrum to be used as seed" help="Use 'none' for no cutoff">
113 <expand macro="list_string_san" name="min_psm_cutoff"/>
114 </param>
115 <param argument="-add_mass_offset_peptides" type="float" min="0.0" value="0.0" label="If for every peptide (or seed) also an offset peptide is extracted (true)" help="Can be used to downstream to determine MBR false transfer rates. (0.0 = disabled)"/>
109 <section name="extract" title="Parameters for ion chromatogram extraction" help="" expanded="false"> 116 <section name="extract" title="Parameters for ion chromatogram extraction" help="" expanded="false">
110 <param name="batch_size" argument="-extract:batch_size" type="integer" optional="true" min="1" value="5000" label="Nr of peptides used in each batch of chromatogram extraction" help="Smaller values decrease memory usage but increase runtime"/> 117 <param name="batch_size" argument="-extract:batch_size" type="integer" min="1" value="5000" label="Nr of peptides used in each batch of chromatogram extraction" help="Smaller values decrease memory usage but increase runtime"/>
111 <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=""/> 118 <param name="mz_window" argument="-extract:mz_window" type="float" min="0.0" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help=""/>
112 <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=""/> 119 <param name="n_isotopes" argument="-extract:n_isotopes" type="integer" min="2" value="2" label="Number of isotopes to include in each peptide assay" help=""/>
113 <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'"/> 120 <param name="isotope_pmin" argument="-extract:isotope_pmin" type="float" 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'"/>
114 <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=""/> 121 <param name="rt_quantile" argument="-extract:rt_quantile" type="float" 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=""/>
115 <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'"/> 122 <param name="rt_window" argument="-extract:rt_window" type="float" 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'"/>
116 </section> 123 </section>
117 <section name="detect" title="Parameters for detecting features in extracted ion chromatograms" help="" expanded="false"> 124 <section name="detect" title="Parameters for detecting features in extracted ion chromatograms" help="" expanded="false">
118 <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'"/> 125 <param name="peak_width" argument="-detect:peak_width" type="float" 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'"/>
119 <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'"/> 126 <param name="min_peak_width" argument="-detect:min_peak_width" type="float" 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'"/>
120 <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=""/> 127 <param name="signal_to_noise" argument="-detect:signal_to_noise" type="float" min="0.1" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help=""/>
121 <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"/> 128 <param name="mapping_tolerance" argument="-detect:mapping_tolerance" type="float" 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"/>
122 </section> 129 </section>
123 <section name="svm" title="Parameters for scoring features using a support vector machine (SVM)" help="" expanded="false"> 130 <section name="svm" title="Parameters for scoring features using a support vector machine (SVM)" help="" expanded="false">
124 <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=""/> 131 <param name="samples" argument="-svm:samples" type="integer" min="0" value="0" label="Number of observations to use for training ('0' for all)" help=""/>
125 <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')"/> 132 <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')"/>
126 <param name="kernel" argument="-svm:kernel" type="select" optional="true" label="SVM kernel" help=""> 133 <param name="kernel" argument="-svm:kernel" type="select" label="SVM kernel" help="">
127 <option value="RBF" selected="true">RBF</option> 134 <option value="RBF" selected="true">RBF</option>
128 <option value="linear">linear</option> 135 <option value="linear">linear</option>
129 <expand macro="list_string_san" name="kernel"/> 136 <expand macro="list_string_san" name="kernel"/>
130 </param> 137 </param>
131 <param name="xval" argument="-svm:xval" type="integer" optional="true" min="1" value="5" label="Number of partitions for cross-validation (parameter optimization)" help=""/> 138 <param name="xval" argument="-svm:xval" type="integer" min="1" value="5" label="Number of partitions for cross-validation (parameter optimization)" help=""/>
132 <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)"> 139 <param name="log2_C" argument="-svm:log2_C" type="text" 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)">
133 <expand macro="list_float_valsan" name="log2_C"/> 140 <expand macro="list_float_valsan" name="log2_C"/>
134 </param> 141 </param>
135 <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)"> 142 <param name="log2_gamma" argument="-svm:log2_gamma" type="text" 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)">
136 <expand macro="list_float_valsan" name="log2_gamma"/> 143 <expand macro="list_float_valsan" name="log2_gamma"/>
137 </param> 144 </param>
138 <param name="epsilon" argument="-svm:epsilon" type="float" optional="true" min="0.0" value="0.001" label="Stopping criterion" help=""/> 145 <param name="log2_p" argument="-svm:log2_p" type="text" value="-15.0 -12.0 -9.0 -6.0 -3.32192809489 0.0 3.32192809489 6.0 9.0 12.0 15.0" label="Values to try for the SVM parameter 'epsilon' during parameter optimization (epsilon-SVR only)" help="A value 'x' is used as 'epsilon = 2^x' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
139 <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=""/> 146 <expand macro="list_float_valsan" name="log2_p"/>
147 </param>
148 <param name="epsilon" argument="-svm:epsilon" type="float" min="0.0" value="0.001" label="Stopping criterion" help=""/>
149 <param name="cache_size" argument="-svm:cache_size" type="float" min="1.0" value="100.0" label="Size of the kernel cache (in MB)" help=""/>
140 <param name="no_shrinking" argument="-svm:no_shrinking" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable the shrinking heuristics" help=""/> 150 <param name="no_shrinking" argument="-svm:no_shrinking" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable the shrinking heuristics" help=""/>
141 <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_ms1_isotope_correlation_score,var_ms1_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=""> 151 <param name="predictors" argument="-svm:predictors" type="text" 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_ms1_isotope_correlation_score,var_ms1_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="">
142 <expand macro="list_string_san" name="predictors"/> 152 <expand macro="list_string_san" name="predictors"/>
143 </param> 153 </param>
144 <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=""/> 154 <param name="min_prob" argument="-svm:min_prob" type="float" 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=""/>
145 </section> 155 </section>
146 <section name="model" title="Parameters for fitting elution models to features" help="" expanded="false"> 156 <section name="model" title="Parameters for fitting elution models to features" help="" expanded="false">
147 <param name="type" argument="-model:type" type="select" optional="true" label="Type of elution model to fit to features" help=""> 157 <param name="type" argument="-model:type" type="select" label="Type of elution model to fit to features" help="">
148 <option value="symmetric" selected="true">symmetric</option> 158 <option value="symmetric" selected="true">symmetric</option>
149 <option value="asymmetric">asymmetric</option> 159 <option value="asymmetric">asymmetric</option>
150 <option value="none">none</option> 160 <option value="none">none</option>
151 <expand macro="list_string_san" name="type"/> 161 <expand macro="list_string_san" name="type"/>
152 </param> 162 </param>
153 <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"/> 163 <param name="add_zeros" argument="-model:add_zeros" type="float" 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"/>
154 <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=""/> 164 <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=""/>
155 <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=""/> 165 <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=""/>
156 <param name="each_trace" argument="-model:each_trace" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Fit elution model to each individual mass trace" help=""/> 166 <param name="each_trace" argument="-model:each_trace" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Fit elution model to each individual mass trace" help=""/>
157 <section name="check" title="Parameters for checking the validity of elution models (and rejecting them if necessary)" help="" expanded="false"> 167 <section name="check" title="Parameters for checking the validity of elution models (and rejecting them if necessary)" help="" expanded="false">
158 <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=""/> 168 <param name="min_area" argument="-model:check:min_area" type="float" min="0.0" value="1.0" label="Lower bound for the area under the curve of a valid elution model" help=""/>
159 <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=""/> 169 <param name="boundaries" argument="-model:check:boundaries" type="float" 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=""/>
160 <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" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/> 170 <param name="width" argument="-model:check:width" type="float" 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" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/>
161 <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" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/> 171 <param name="asymmetry" argument="-model:check:asymmetry" type="float" 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" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/>
162 </section> 172 </section>
163 </section> 173 </section>
164 <section name="EMGScoring" title="Parameters for fitting exp" help="mod. Gaussians to mass traces" expanded="false"> 174 <section name="EMGScoring" title="Parameters for fitting exp" help="mod. Gaussians to mass traces" expanded="false">
165 <param name="max_iteration" argument="-EMGScoring:max_iteration" type="integer" optional="true" min="1" value="100" label="Maximum number of iterations for EMG fitting" help=""/> 175 <param name="max_iteration" argument="-EMGScoring:max_iteration" type="integer" min="1" value="100" label="Maximum number of iterations for EMG fitting" help=""/>
166 <param name="init_mom" argument="-EMGScoring:init_mom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Alternative initial parameters for fitting through method of moments" help=""/> 176 <param name="init_mom" argument="-EMGScoring:init_mom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Alternative initial parameters for fitting through method of moments" help=""/>
167 </section> 177 </section>
168 <expand macro="adv_opts_macro"> 178 <expand macro="adv_opts_macro">
169 <param 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)"/> 179 <param 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 argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 180 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
171 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 181 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
172 <expand macro="list_string_san" name="test"/> 182 <expand macro="list_string_san" name="test"/>
173 </param> 183 </param>
174 </expand> 184 </expand>
175 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 185 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
176 <option value="lib_out_FLAG">lib_out (Output file: Assay library)</option> 186 <option value="lib_out_FLAG">lib_out (Output file: Assay library)</option>
196 </data> 206 </data>
197 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 207 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
198 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 208 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
199 </data> 209 </data>
200 </outputs> 210 </outputs>
201 <tests><!-- TOPP_FeatureFinderIdentification_1 --> 211 <tests>
212 <!-- TOPP_FeatureFinderIdentification_1 -->
202 <test expect_num_outputs="2"> 213 <test expect_num_outputs="2">
203 <section name="adv_opts"> 214 <section name="adv_opts">
204 <param name="force" value="false"/> 215 <param name="force" value="false"/>
205 <param name="test" value="true"/> 216 <param name="test" value="true"/>
206 </section> 217 </section>
207 <param name="in" value="FeatureFinderIdentification_1_input.mzML"/> 218 <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
208 <param name="id" value="FeatureFinderIdentification_1_input.idXML"/> 219 <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
209 <output name="out" file="FeatureFinderIdentification_1.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 220 <output name="out" value="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
210 <param name="quantify_decoys" value="false"/> 221 <param name="quantify_decoys" value="false"/>
222 <param name="min_psm_cutoff" value="none"/>
223 <param name="add_mass_offset_peptides" value="0.0"/>
211 <section name="extract"> 224 <section name="extract">
212 <param name="batch_size" value="5000"/> 225 <param name="batch_size" value="5000"/>
213 <param name="mz_window" value="0.1"/> 226 <param name="mz_window" value="0.1"/>
214 <param name="n_isotopes" value="2"/> 227 <param name="n_isotopes" value="2"/>
215 <param name="isotope_pmin" value="0.0"/> 228 <param name="isotope_pmin" value="0.0"/>
227 <param name="no_selection" value="false"/> 240 <param name="no_selection" value="false"/>
228 <param name="kernel" value="RBF"/> 241 <param name="kernel" value="RBF"/>
229 <param name="xval" value="5"/> 242 <param name="xval" value="5"/>
230 <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/> 243 <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/>
231 <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/> 244 <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/>
245 <param name="log2_p" value="-15.0 -12.0 -9.0 -6.0 -3.32192809489 0.0 3.32192809489 6.0 9.0 12.0 15.0"/>
232 <param name="epsilon" value="0.001"/> 246 <param name="epsilon" value="0.001"/>
233 <param name="cache_size" value="100.0"/> 247 <param name="cache_size" value="100.0"/>
234 <param name="no_shrinking" value="false"/> 248 <param name="no_shrinking" value="false"/>
235 <param name="predictors" 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_ms1_isotope_correlation_score,var_ms1_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/> 249 <param name="predictors" 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_ms1_isotope_correlation_score,var_ms1_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/>
236 <param name="min_prob" value="0.0"/> 250 <param name="min_prob" value="0.0"/>
256 <output name="ctd_out" ftype="xml"> 270 <output name="ctd_out" ftype="xml">
257 <assert_contents> 271 <assert_contents>
258 <is_valid_xml/> 272 <is_valid_xml/>
259 </assert_contents> 273 </assert_contents>
260 </output> 274 </output>
275 <assert_stdout>
276 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
277 </assert_stdout>
261 </test> 278 </test>
262 <!-- TOPP_FeatureFinderIdentification_3 --> 279 <!-- TOPP_FeatureFinderIdentification_3 -->
263 <test expect_num_outputs="2"> 280 <test expect_num_outputs="2">
264 <section name="adv_opts"> 281 <section name="adv_opts">
265 <param name="force" value="false"/> 282 <param name="force" value="false"/>
266 <param name="test" value="true"/> 283 <param name="test" value="true"/>
267 </section> 284 </section>
268 <param name="in" value="FeatureFinderIdentification_1_input.mzML"/> 285 <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
269 <param name="id" value="FeatureFinderIdentification_1_input.idXML"/> 286 <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
270 <output name="out" file="FeatureFinderIdentification_3.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 287 <output name="out" value="FeatureFinderIdentification_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
271 <param name="quantify_decoys" value="false"/> 288 <param name="quantify_decoys" value="false"/>
289 <param name="min_psm_cutoff" value="none"/>
290 <param name="add_mass_offset_peptides" value="0.0"/>
272 <section name="extract"> 291 <section name="extract">
273 <param name="batch_size" value="5000"/> 292 <param name="batch_size" value="5000"/>
274 <param name="mz_window" value="0.1"/> 293 <param name="mz_window" value="0.1"/>
275 <param name="n_isotopes" value="2"/> 294 <param name="n_isotopes" value="2"/>
276 <param name="isotope_pmin" value="0.0"/> 295 <param name="isotope_pmin" value="0.0"/>
288 <param name="no_selection" value="false"/> 307 <param name="no_selection" value="false"/>
289 <param name="kernel" value="RBF"/> 308 <param name="kernel" value="RBF"/>
290 <param name="xval" value="5"/> 309 <param name="xval" value="5"/>
291 <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/> 310 <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/>
292 <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/> 311 <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/>
312 <param name="log2_p" value="-15.0 -12.0 -9.0 -6.0 -3.32192809489 0.0 3.32192809489 6.0 9.0 12.0 15.0"/>
293 <param name="epsilon" value="0.001"/> 313 <param name="epsilon" value="0.001"/>
294 <param name="cache_size" value="100.0"/> 314 <param name="cache_size" value="100.0"/>
295 <param name="no_shrinking" value="false"/> 315 <param name="no_shrinking" value="false"/>
296 <param name="predictors" 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_ms1_isotope_correlation_score,var_ms1_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/> 316 <param name="predictors" 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_ms1_isotope_correlation_score,var_ms1_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/>
297 <param name="min_prob" value="0.0"/> 317 <param name="min_prob" value="0.0"/>
317 <output name="ctd_out" ftype="xml"> 337 <output name="ctd_out" ftype="xml">
318 <assert_contents> 338 <assert_contents>
319 <is_valid_xml/> 339 <is_valid_xml/>
320 </assert_contents> 340 </assert_contents>
321 </output> 341 </output>
342 <assert_stdout>
343 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
344 </assert_stdout>
322 </test> 345 </test>
323 <!-- TOPP_FeatureFinderIdentification_5 --> 346 <!-- TOPP_FeatureFinderIdentification_5 -->
324 <test expect_num_outputs="3"> 347 <test expect_num_outputs="3">
325 <section name="adv_opts"> 348 <section name="adv_opts">
326 <param name="force" value="false"/> 349 <param name="force" value="false"/>
327 <param name="test" value="true"/> 350 <param name="test" value="true"/>
328 </section> 351 </section>
329 <param name="in" value="FeatureFinderIdentification_1_input.mzML"/> 352 <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
330 <param name="id" value="FeatureFinderIdentification_1_input.idXML"/> 353 <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
331 <output name="out" file="FeatureFinderIdentification_5.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 354 <output name="out" value="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
332 <output name="candidates_out" file="FeatureFinderIdentification_5_candidates.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 355 <output name="candidates_out" value="FeatureFinderIdentification_5_candidates.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
333 <param name="quantify_decoys" value="false"/> 356 <param name="quantify_decoys" value="false"/>
357 <param name="min_psm_cutoff" value="none"/>
358 <param name="add_mass_offset_peptides" value="0.0"/>
334 <section name="extract"> 359 <section name="extract">
335 <param name="batch_size" value="10"/> 360 <param name="batch_size" value="10"/>
336 <param name="mz_window" value="0.1"/> 361 <param name="mz_window" value="0.1"/>
337 <param name="n_isotopes" value="2"/> 362 <param name="n_isotopes" value="2"/>
338 <param name="isotope_pmin" value="0.0"/> 363 <param name="isotope_pmin" value="0.0"/>
350 <param name="no_selection" value="false"/> 375 <param name="no_selection" value="false"/>
351 <param name="kernel" value="RBF"/> 376 <param name="kernel" value="RBF"/>
352 <param name="xval" value="5"/> 377 <param name="xval" value="5"/>
353 <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/> 378 <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/>
354 <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/> 379 <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/>
380 <param name="log2_p" value="-15.0 -12.0 -9.0 -6.0 -3.32192809489 0.0 3.32192809489 6.0 9.0 12.0 15.0"/>
355 <param name="epsilon" value="0.001"/> 381 <param name="epsilon" value="0.001"/>
356 <param name="cache_size" value="100.0"/> 382 <param name="cache_size" value="100.0"/>
357 <param name="no_shrinking" value="false"/> 383 <param name="no_shrinking" value="false"/>
358 <param name="predictors" 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_ms1_isotope_correlation_score,var_ms1_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/> 384 <param name="predictors" 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_ms1_isotope_correlation_score,var_ms1_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/>
359 <param name="min_prob" value="0.0"/> 385 <param name="min_prob" value="0.0"/>
379 <output name="ctd_out" ftype="xml"> 405 <output name="ctd_out" ftype="xml">
380 <assert_contents> 406 <assert_contents>
381 <is_valid_xml/> 407 <is_valid_xml/>
382 </assert_contents> 408 </assert_contents>
383 </output> 409 </output>
410 <assert_stdout>
411 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
412 </assert_stdout>
384 </test> 413 </test>
385 </tests> 414 </tests>
386 <help><![CDATA[Detects features in MS1 data based on peptide identifications. 415 <help><![CDATA[Detects features in MS1 data based on peptide identifications.
387 416
388 417
389 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureFinderIdentification.html]]></help> 418 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureFinderIdentification.html]]></help>
390 <expand macro="references"/> 419 <expand macro="references"/>
391 </tool> 420 </tool>