Mercurial > repos > galaxyp > openms_idposteriorerrorprobability

annotate ctd/FeatureFinderIdentification.ctd @ 18:6daaa75ccb99 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
author galaxyp
date Sun, 13 Dec 2020 15:03:50 +0000
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18
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool ctdVersion="1.7" version="2.6.0-pre-exported-20201001" name="FeatureFinderIdentification" docurl="http://www.openms.de/documentation/TOPP_FeatureFinderIdentification.html" category="Quantitation" >
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3 <description><![CDATA[Detects features in MS1 data based on peptide identifications.]]></description>
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4 <manual><![CDATA[Detects features in MS1 data based on peptide identifications.]]></manual>
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5 <citations>
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6 <citation doi="10.1038/nmeth.3959" url="" />
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7 <citation doi="10.1021/acs.jproteome.7b00248" url="" />
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8 </citations>
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9 <PARAMETERS version="1.7.0" xsi:noNamespaceSchemaLocation="https://raw.githubusercontent.com/OpenMS/OpenMS/develop/share/OpenMS/SCHEMAS/Param_1_7_0.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
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10 <NODE name="FeatureFinderIdentification" description="Detects features in MS1 data based on peptide identifications.">
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11 <ITEM name="version" value="2.6.0-pre-exported-20201001" type="string" description="Version of the tool that generated this parameters file." required="false" advanced="true" />
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12 <NODE name="1" description="Instance &apos;1&apos; section for &apos;FeatureFinderIdentification&apos;">
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13 <ITEM name="in" value="" type="input-file" description="Input file: LC-MS raw data" required="true" advanced="false" supported_formats="*.mzML" />
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14 <ITEM name="id" value="" type="input-file" description="Input file: Peptide identifications derived directly from &apos;in&apos;" required="true" advanced="false" supported_formats="*.idXML" />
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15 <ITEM name="id_ext" value="" type="input-file" description="Input file: &apos;External&apos; peptide identifications (e.g. from aligned runs)" required="false" advanced="false" supported_formats="*.idXML" />
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16 <ITEM name="out" value="" type="output-file" description="Output file: Features" required="true" advanced="false" supported_formats="*.featureXML" />
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17 <ITEM name="lib_out" value="" type="output-file" description="Output file: Assay library" required="false" advanced="false" supported_formats="*.traML" />
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18 <ITEM name="chrom_out" value="" type="output-file" description="Output file: Chromatograms" required="false" advanced="false" supported_formats="*.mzML" />
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19 <ITEM name="candidates_out" value="" type="output-file" description="Output file: Feature candidates (before filtering and model fitting)" required="false" advanced="false" supported_formats="*.featureXML" />
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20 <ITEM name="candidates_in" value="" type="input-file" description="Input file: Feature candidates from a previous run. If set, only feature classification and elution model fitting are carried out, if enabled. Many parameters are ignored." required="false" advanced="true" supported_formats="*.featureXML" />
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21 <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" restrictions="0:" />
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22 <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
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23 <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
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24 <ITEM name="no_progress" value="false" type="bool" description="Disables progress logging to command line" required="false" advanced="true" />
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25 <ITEM name="force" value="false" type="bool" description="Overrides tool-specific checks" required="false" advanced="true" />
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26 <ITEM name="test" value="false" type="bool" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" />
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27 <NODE name="extract" description="Parameters for ion chromatogram extraction">
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28 <ITEM name="batch_size" value="1000" type="int" description="Nr of peptides used in each batch of chromatogram extraction. Smaller values decrease memory usage but increase runtime." required="false" advanced="false" restrictions="1:" />
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29 <ITEM name="mz_window" value="10.0" type="double" description="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" required="false" advanced="false" restrictions="0.0:" />
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30 <ITEM name="n_isotopes" value="2" type="int" description="Number of isotopes to include in each peptide assay." required="false" advanced="false" restrictions="2:" />
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31 <ITEM name="isotope_pmin" value="0.0" type="double" description="Minimum probability for an isotope to be included in the assay for a peptide. If set, this parameter takes precedence over &apos;extract:n_isotopes&apos;." required="false" advanced="true" restrictions="0.0:1.0" />
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32 <ITEM name="rt_quantile" value="0.95" type="double" description="Quantile of the RT deviations between aligned internal and external IDs to use for scaling the RT extraction window" required="false" advanced="true" restrictions="0.0:1.0" />
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33 <ITEM name="rt_window" value="0.0" type="double" description="RT window size (in sec.) for chromatogram extraction. If set, this parameter takes precedence over &apos;extract:rt_quantile&apos;." required="false" advanced="true" restrictions="0.0:" />
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34 </NODE>
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35 <NODE name="detect" description="Parameters for detecting features in extracted ion chromatograms">
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36 <ITEM name="peak_width" value="60.0" type="double" description="Expected elution peak width in seconds, for smoothing (Gauss filter). Also determines the RT extration window, unless set explicitly via &apos;extract:rt_window&apos;." required="false" advanced="false" restrictions="0.0:" />
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37 <ITEM name="min_peak_width" value="0.2" type="double" description="Minimum elution peak width. Absolute value in seconds if 1 or greater, else relative to &apos;peak_width&apos;." required="false" advanced="true" restrictions="0.0:" />
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38 <ITEM name="signal_to_noise" value="0.8" type="double" description="Signal-to-noise threshold for OpenSWATH feature detection" required="false" advanced="true" restrictions="0.1:" />
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39 <ITEM name="mapping_tolerance" value="0.0" type="double" description="RT tolerance (plus/minus) for mapping peptide IDs to features. Absolute value in seconds if 1 or greater, else relative to the RT span of the feature." required="false" advanced="false" restrictions="0.0:" />
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40 </NODE>
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41 <NODE name="svm" description="Parameters for scoring features using a support vector machine (SVM)">
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42 <ITEM name="samples" value="0" type="int" description="Number of observations to use for training (&apos;0&apos; for all)" required="false" advanced="false" restrictions="0:" />
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43 <ITEM name="no_selection" value="false" type="bool" description="By default, roughly the same number of positive and negative observations, with the same intensity distribution, are selected for training. 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 &apos;svm:samples&apos;)." required="false" advanced="false" />
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44 <ITEM name="xval_out" value="" type="output-file" description="Output file: SVM cross-validation (parameter optimization) results" required="false" advanced="false" supported_formats="*.csv" />
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45 <ITEM name="kernel" value="RBF" type="string" description="SVM kernel" required="false" advanced="false" restrictions="RBF,linear" />
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46 <ITEM name="xval" value="5" type="int" description="Number of partitions for cross-validation (parameter optimization)" required="false" advanced="false" restrictions="1:" />
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47 <ITEMLIST name="log2_C" type="double" description="Values to try for the SVM parameter &apos;C&apos; during parameter optimization. A value &apos;x&apos; is used as &apos;C = 2^x&apos;." required="false" advanced="false">
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48 <LISTITEM value="-5"/>
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49 <LISTITEM value="-3"/>
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50 <LISTITEM value="-1"/>
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51 <LISTITEM value="1"/>
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52 <LISTITEM value="3"/>
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53 <LISTITEM value="5"/>
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54 <LISTITEM value="7"/>
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55 <LISTITEM value="9"/>
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56 <LISTITEM value="11"/>
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57 <LISTITEM value="13"/>
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58 <LISTITEM value="15"/>
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59 </ITEMLIST>
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60 <ITEMLIST name="log2_gamma" type="double" description="Values to try for the SVM parameter &apos;gamma&apos; during parameter optimization (RBF kernel only). A value &apos;x&apos; is used as &apos;gamma = 2^x&apos;." required="false" advanced="false">
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61 <LISTITEM value="-15"/>
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62 <LISTITEM value="-13"/>
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63 <LISTITEM value="-11"/>
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64 <LISTITEM value="-9"/>
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65 <LISTITEM value="-7"/>
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66 <LISTITEM value="-5"/>
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67 <LISTITEM value="-3"/>
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68 <LISTITEM value="-1"/>
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69 <LISTITEM value="1"/>
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70 <LISTITEM value="3"/>
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71 </ITEMLIST>
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72 <ITEM name="epsilon" value="1.0e-03" type="double" description="Stopping criterion" required="false" advanced="true" restrictions="0.0:" />
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73 <ITEM name="cache_size" value="100.0" type="double" description="Size of the kernel cache (in MB)" required="false" advanced="true" restrictions="1.0:" />
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74 <ITEM name="no_shrinking" value="false" type="bool" description="Disable the shrinking heuristics" required="false" advanced="true" />
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75 <ITEM 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_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score" type="string" description="Names of OpenSWATH scores to use as predictors for the SVM (comma-separated list)" required="false" advanced="true" />
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76 <ITEM name="min_prob" value="0.0" type="double" description="Minimum probability of correctness, as predicted by the SVM, required to retain a feature candidate" required="false" advanced="true" restrictions="0.0:1.0" />
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77 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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78 <NODE name="model" description="Parameters for fitting elution models to features">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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79 <ITEM name="type" value="symmetric" type="string" description="Type of elution model to fit to features" required="false" advanced="false" restrictions="symmetric,asymmetric,none" />
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80 <ITEM name="add_zeros" value="0.2" type="double" description="Add zero-intensity points outside the feature range to constrain the model fit. This parameter sets the weight given to these points during model fitting; &apos;0&apos; to disable." required="false" advanced="true" restrictions="0.0:" />
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81 <ITEM name="unweighted_fit" value="false" type="bool" description="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" required="false" advanced="true" />
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82 <ITEM name="no_imputation" value="false" type="bool" description="If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate" required="false" advanced="true" />
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83 <ITEM name="each_trace" value="false" type="bool" description="Fit elution model to each individual mass trace" required="false" advanced="true" />
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84 <NODE name="check" description="Parameters for checking the validity of elution models (and rejecting them if necessary)">
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85 <ITEM name="min_area" value="1.0" type="double" description="Lower bound for the area under the curve of a valid elution model" required="false" advanced="true" restrictions="0.0:" />
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86 <ITEM name="boundaries" value="0.5" type="double" description="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" required="false" advanced="true" restrictions="0.0:1.0" />
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87 <ITEM name="width" value="10.0" type="double" description="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores. &apos;0&apos; to disable. Not applied to individual mass traces (parameter &apos;each_trace&apos;)." required="false" advanced="true" restrictions="0.0:" />
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88 <ITEM name="asymmetry" value="10.0" type="double" description="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores. &apos;0&apos; to disable. Not applied to individual mass traces (parameter &apos;each_trace&apos;)." required="false" advanced="true" restrictions="0.0:" />
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89 </NODE>
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90 </NODE>
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91 </NODE>
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92 </NODE>
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93 </PARAMETERS>
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94 </tool>