Mercurial > repos > galaxyp > openms_openswathanalyzer

annotate OpenSwathAnalyzer.xml @ 11:7ca917175b23 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 19:43:44 +0000
parents bc57c90ba60f
children 08488066d588
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [Targeted Experiments]-->
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4 <tool id="OpenSwathAnalyzer" name="OpenSwathAnalyzer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Picks peaks and finds features in an SWATH-MS or SRM experiment.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">OpenSwathAnalyzer</token>
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8 <import>macros.xml</import>
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9 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
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11 </macros>
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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15 @EXT_FOO@
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16 #import re
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17
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18 ## Preprocessing
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19 mkdir in &&
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20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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21 mkdir tr &&
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22 ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
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23 #if $rt_norm:
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24 mkdir rt_norm &&
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25 ln -s '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' &&
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26 #end if
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27 mkdir out &&
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28 #if $swath_files:
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29 mkdir swath_files &&
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30 ${ ' '.join(["ln -s '%s' 'swath_files/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $swath_files if _]) }
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31 #end if
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33 ## Main program call
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35 set -o pipefail &&
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36 @EXECUTABLE@ -write_ctd ./ &&
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37 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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38 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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39 -in
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40 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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41 -tr
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42 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
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43 #if $rt_norm:
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44 -rt_norm
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45 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)'
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46 #end if
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47 -out
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48 'out/output.${gxy2omsext("featurexml")}'
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49 #if $swath_files:
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50 -swath_files
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51 ${' '.join(["'swath_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $swath_files if _])}
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52 #end if
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53
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54 ## Postprocessing
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55 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
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56 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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57 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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58 #end if]]></command>
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59 <configfiles>
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60 <inputs name="args_json" data_style="paths"/>
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61 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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62 </configfiles>
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63 <inputs>
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64 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file containing the chromatograms" help=" select mzml data sets(s)"/>
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65 <param name="tr" argument="-tr" type="data" format="traml" optional="false" label="transition file" help=" select traml data sets(s)"/>
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66 <param name="rt_norm" argument="-rt_norm" type="data" format="trafoxml" optional="true" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help=" select trafoxml data sets(s)"/>
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67 <param name="no_strict" argument="-no-strict" type="boolean" truevalue="true" falsevalue="false" checked="false" label="run in non-strict mode and allow some chromatograms to not be mapped" help=""/>
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68 <param name="swath_files" argument="-swath_files" type="data" format="mzml" multiple="true" optional="true" label="[applies only if you have full MS2 spectra maps] Swath files that were used to extract the transitions" help="If present, SWATH specific scoring will be used select mzml data sets(s)"/>
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69 <param name="min_upper_edge_dist" argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="[applies only if you have full MS2 spectra maps] Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help=""/>
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70 <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
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71 <param name="type" argument="-model:type" display="radio" type="select" optional="false" label="Type of model" help="">
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72 <option value="linear" selected="true">linear</option>
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73 <option value="b_spline">b_spline</option>
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74 <option value="interpolated">interpolated</option>
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75 <option value="lowess">lowess</option>
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76 <expand macro="list_string_san"/>
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77 </param>
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78 <param name="symmetric_regression" argument="-model:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
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79 </section>
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80 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
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81 <param name="stop_report_after_feature" argument="-algorithm:stop_report_after_feature" type="integer" optional="true" value="-1" label="Stop reporting after feature (ordered by quality; -1 means do not stop)" help=""/>
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82 <param name="rt_extraction_window" argument="-algorithm:rt_extraction_window" type="float" optional="true" value="-1.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 500 means to extract around +/- 500 s of the expected elution)" help="For this to work, the TraML input file needs to contain normalized RT values"/>
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83 <param name="rt_normalization_factor" argument="-algorithm:rt_normalization_factor" type="float" optional="true" value="1.0" label="The normalized RT is expected to be between 0 and 1" help="If your normalized RT has a different range, pass this here (e.g. it goes from 0 to 100, set this value to 100)"/>
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84 <param name="quantification_cutoff" argument="-algorithm:quantification_cutoff" type="float" optional="true" min="0.0" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help=""/>
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85 <param name="write_convex_hull" argument="-algorithm:write_convex_hull" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to write out all points of all features into the featureXML" help=""/>
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86 <param name="spectrum_addition_method" argument="-algorithm:spectrum_addition_method" display="radio" type="select" optional="false" label="For spectrum addition, either use simple concatenation or use peak resampling" help="">
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87 <option value="simple" selected="true">simple</option>
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88 <option value="resample">resample</option>
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89 <expand macro="list_string_san"/>
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90 </param>
9
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91 <param name="add_up_spectra" argument="-algorithm:add_up_spectra" type="integer" optional="true" min="1" value="1" label="Add up spectra around the peak apex (needs to be a non-even integer)" help=""/>
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92 <param name="spacing_for_spectra_resampling" argument="-algorithm:spacing_for_spectra_resampling" type="float" optional="true" min="0.0" value="0.005" label="If spectra are to be added, use this spacing to add them up" help=""/>
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93 <param name="uis_threshold_sn" argument="-algorithm:uis_threshold_sn" type="integer" optional="true" value="-1" label="S/N threshold to consider identification transition (set to -1 to consider all)" help=""/>
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94 <param name="uis_threshold_peak_area" argument="-algorithm:uis_threshold_peak_area" type="integer" optional="true" value="0" label="Peak area threshold to consider identification transition (set to -1 to consider all)" help=""/>
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95 <param name="scoring_model" argument="-algorithm:scoring_model" display="radio" type="select" optional="false" label="Scoring model to use" help="">
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96 <option value="default" selected="true">default</option>
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97 <option value="single_transition">single_transition</option>
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98 <expand macro="list_string_san"/>
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99 </param>
9
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100 <param name="im_extra_drift" argument="-algorithm:im_extra_drift" type="float" optional="true" min="0.0" value="0.0" label="Extra drift time to extract for IM scoring (as a fraction" help="e.g. 0.25 means 25% extra on each side)"/>
11
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101 <param name="strict" argument="-algorithm:strict" type="text" optional="true" value="true" label="Whether to error (true) or skip (false) if a transition in a transition group does not have a corresponding chromatogram" help="">
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102 <expand macro="list_string_san"/>
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103 </param>
9
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104 <section name="TransitionGroupPicker" title="" help="" expanded="false">
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105 <param name="stop_after_feature" argument="-algorithm:TransitionGroupPicker:stop_after_feature" type="integer" optional="true" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
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106 <param name="stop_after_intensity_ratio" argument="-algorithm:TransitionGroupPicker:stop_after_intensity_ratio" type="float" optional="true" value="0.0001" label="Stop after reaching intensity ratio" help=""/>
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107 <param name="min_peak_width" argument="-algorithm:TransitionGroupPicker:min_peak_width" type="float" optional="true" value="-1.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
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108 <param name="peak_integration" argument="-algorithm:TransitionGroupPicker:peak_integration" display="radio" type="select" optional="false" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
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109 <option value="original" selected="true">original</option>
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110 <option value="smoothed">smoothed</option>
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111 <expand macro="list_string_san"/>
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112 </param>
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113 <param name="background_subtraction" argument="-algorithm:TransitionGroupPicker:background_subtraction" display="radio" type="select" optional="false" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation">
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114 <option value="none" selected="true">none</option>
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115 <option value="original">original</option>
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116 <option value="exact">exact</option>
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117 <expand macro="list_string_san"/>
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118 </param>
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119 <param name="recalculate_peaks" argument="-algorithm:TransitionGroupPicker:recalculate_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="Tries to use the consensus (median) peak border if the variation within the picked peaks is too large"/>
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120 <param name="use_precursors" argument="-algorithm:TransitionGroupPicker:use_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use precursor chromatogram for peak picking (note that this may lead to precursor signal driving the peak picking)" help=""/>
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121 <param name="use_consensus" argument="-algorithm:TransitionGroupPicker:use_consensus" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use consensus peak boundaries when computing transition group picking (if false, compute independent peak boundaries for each transition)" help=""/>
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122 <param name="recalculate_peaks_max_z" argument="-algorithm:TransitionGroupPicker:recalculate_peaks_max_z" type="float" optional="true" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
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123 <param name="minimal_quality" argument="-algorithm:TransitionGroupPicker:minimal_quality" type="float" optional="true" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help=""/>
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124 <param name="resample_boundary" argument="-algorithm:TransitionGroupPicker:resample_boundary" type="float" optional="true" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help=""/>
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125 <param name="compute_peak_quality" argument="-algorithm:TransitionGroupPicker:compute_peak_quality" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
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126 <param name="compute_peak_shape_metrics" argument="-algorithm:TransitionGroupPicker:compute_peak_shape_metrics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculates various peak shape metrics" help="(e.g., tailing) that can be used for downstream QC/QA"/>
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127 <param name="compute_total_mi" argument="-algorithm:TransitionGroupPicker:compute_total_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring" help=""/>
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128 <param name="boundary_selection_method" argument="-algorithm:TransitionGroupPicker:boundary_selection_method" display="radio" type="select" optional="false" label="Method to use when selecting the best boundaries for peaks" help="">
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129 <option value="largest" selected="true">largest</option>
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130 <option value="widest">widest</option>
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131 <expand macro="list_string_san"/>
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132 </param>
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133 <section name="PeakPickerMRM" title="" help="" expanded="false">
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134 <param name="sgolay_frame_length" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length" type="integer" optional="true" value="15" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/>
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135 <param name="sgolay_polynomial_order" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order" type="integer" optional="true" value="3" label="Order of the polynomial that is fitted" help=""/>
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136 <param name="gauss_width" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width" type="float" optional="true" value="50.0" label="Gaussian width in seconds, estimated peak size" help=""/>
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137 <param name="use_gauss" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help=""/>
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138 <param name="peak_width" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width" type="float" optional="true" value="-1.0" label="Force a certain minimal peak_width on the data" help="(e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
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139 <param name="signal_to_noise" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise" type="float" optional="true" min="0.0" value="1.0" label="Signal-to-noise threshold at which a peak will not be extended any more" help="Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured"/>
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140 <param name="sn_win_len" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len" type="float" optional="true" value="1000.0" label="Signal to noise window length" help=""/>
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141 <param name="sn_bin_count" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count" type="integer" optional="true" value="30" label="Signal to noise bin count" help=""/>
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142 <param name="write_sn_log_messages" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" help=""/>
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143 <param name="remove_overlapping_peaks" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to remove overlapping peaks during peak picking" help=""/>
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144 <param name="method" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:method" display="radio" type="select" optional="false" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="">
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145 <option value="legacy">legacy</option>
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146 <option value="corrected" selected="true">corrected</option>
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147 <option value="crawdad">crawdad</option>
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148 <expand macro="list_string_san"/>
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149 </param>
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150 </section>
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151 <section name="PeakIntegrator" title="" help="" expanded="false">
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152 <param name="integration_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:integration_type" display="radio" type="select" optional="false" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help="">
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153 <option value="intensity_sum" selected="true">intensity_sum</option>
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154 <option value="simpson">simpson</option>
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155 <option value="trapezoid">trapezoid</option>
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156 <expand macro="list_string_san"/>
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157 </param>
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158 <param name="baseline_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:baseline_type" display="radio" type="select" optional="false" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)">
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159 <option value="base_to_base" selected="true">base_to_base</option>
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160 <option value="vertical_division">vertical_division</option>
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161 <option value="vertical_division_min">vertical_division_min</option>
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162 <option value="vertical_division_max">vertical_division_max</option>
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163 <expand macro="list_string_san"/>
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164 </param>
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165 <param name="fit_EMG" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:fit_EMG" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Fit the chromatogram/spectrum to the EMG peak model" help=""/>
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166 </section>
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167 </section>
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168 <section name="DIAScoring" title="" help="" expanded="false">
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169 <param name="dia_extraction_window" argument="-algorithm:DIAScoring:dia_extraction_window" type="float" optional="true" min="0.0" value="0.05" label="DIA extraction window in Th or ppm" help=""/>
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170 <param name="dia_extraction_unit" argument="-algorithm:DIAScoring:dia_extraction_unit" display="radio" type="select" optional="false" label="DIA extraction window unit" help="">
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171 <option value="Th" selected="true">Th</option>
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172 <option value="ppm">ppm</option>
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173 <expand macro="list_string_san"/>
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174 </param>
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175 <param name="dia_centroided" argument="-algorithm:DIAScoring:dia_centroided" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use centroided DIA data" help=""/>
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176 <param name="dia_byseries_intensity_min" argument="-algorithm:DIAScoring:dia_byseries_intensity_min" type="float" optional="true" min="0.0" value="300.0" label="DIA b/y series minimum intensity to conside" help=""/>
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177 <param name="dia_byseries_ppm_diff" argument="-algorithm:DIAScoring:dia_byseries_ppm_diff" type="float" optional="true" min="0.0" value="10.0" label="DIA b/y series minimal difference in ppm to conside" help=""/>
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178 <param name="dia_nr_isotopes" argument="-algorithm:DIAScoring:dia_nr_isotopes" type="integer" optional="true" min="0" value="4" label="DIA number of isotopes to conside" help=""/>
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179 <param name="dia_nr_charges" argument="-algorithm:DIAScoring:dia_nr_charges" type="integer" optional="true" min="0" value="4" label="DIA number of charges to conside" help=""/>
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180 <param name="peak_before_mono_max_ppm_diff" argument="-algorithm:DIAScoring:peak_before_mono_max_ppm_diff" type="float" optional="true" min="0.0" value="20.0" label="DIA maximal difference in ppm to count a peak at lower m/z when searching for evidence that a peak might not be monoisotopic" help=""/>
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181 </section>
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182 <section name="EMGScoring" title="" help="" expanded="false">
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183 <param name="interpolation_step" argument="-algorithm:EMGScoring:interpolation_step" type="float" optional="true" value="0.2" label="Sampling rate for the interpolation of the model function" help=""/>
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184 <param name="tolerance_stdev_bounding_box" argument="-algorithm:EMGScoring:tolerance_stdev_bounding_box" type="float" optional="true" value="3.0" label="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data" help=""/>
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185 <param name="max_iteration" argument="-algorithm:EMGScoring:max_iteration" type="integer" optional="true" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help=""/>
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186 <section name="statistics" title="" help="" expanded="false">
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187 <param name="mean" argument="-algorithm:EMGScoring:statistics:mean" type="float" optional="true" value="1.0" label="Centroid position of the model" help=""/>
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188 <param name="variance" argument="-algorithm:EMGScoring:statistics:variance" type="float" optional="true" value="1.0" label="Variance of the model" help=""/>
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189 </section>
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190 </section>
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191 <section name="Scores" title="" help="" expanded="false">
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192 <param name="use_shape_score" argument="-algorithm:Scores:use_shape_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)" help=""/>
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193 <param name="use_coelution_score" argument="-algorithm:Scores:use_coelution_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation)" help=""/>
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194 <param name="use_rt_score" argument="-algorithm:Scores:use_rt_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the retention time score (this score measure the difference in retention time)" help=""/>
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195 <param name="use_library_score" argument="-algorithm:Scores:use_library_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the library score" help=""/>
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196 <param name="use_elution_model_score" argument="-algorithm:Scores:use_elution_model_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the elution model (EMG) score (this score fits a gaussian model to the peak and checks the fit)" help=""/>
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197 <param name="use_intensity_score" argument="-algorithm:Scores:use_intensity_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the intensity score" help=""/>
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198 <param name="use_nr_peaks_score" argument="-algorithm:Scores:use_nr_peaks_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the number of peaks score" help=""/>
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199 <param name="use_total_xic_score" argument="-algorithm:Scores:use_total_xic_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the total XIC score" help=""/>
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200 <param name="use_total_mi_score" argument="-algorithm:Scores:use_total_mi_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the total MI score" help=""/>
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201 <param name="use_sn_score" argument="-algorithm:Scores:use_sn_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the SN (signal to noise) score" help=""/>
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202 <param name="use_mi_score" argument="-algorithm:Scores:use_mi_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the MI (mutual information) score" help=""/>
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203 <param name="use_dia_scores" argument="-algorithm:Scores:use_dia_scores" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the DIA (SWATH) scores" help="If turned off, will not use fragment ion spectra for scoring"/>
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204 <param name="use_ms1_correlation" argument="-algorithm:Scores:use_ms1_correlation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the correlation scores with the MS1 elution profiles" help=""/>
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205 <param name="use_sonar_scores" argument="-algorithm:Scores:use_sonar_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the scores for SONAR scans (scanning swath)" help=""/>
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206 <param name="use_ion_mobility_scores" argument="-algorithm:Scores:use_ion_mobility_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the scores for Ion Mobility scans" help=""/>
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207 <param name="use_ms1_fullscan" argument="-algorithm:Scores:use_ms1_fullscan" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)" help=""/>
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208 <param name="use_ms1_mi" argument="-algorithm:Scores:use_ms1_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the MS1 MI score" help=""/>
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209 <param name="use_uis_scores" argument="-algorithm:Scores:use_uis_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use UIS scores for peptidoform identification" help=""/>
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210 </section>
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211 </section>
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212 <expand macro="adv_opts_macro">
11
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213 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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214 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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215 <expand macro="list_string_san"/>
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216 </param>
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217 </expand>
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218 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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219 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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220 </param>
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221 </inputs>
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222 <outputs>
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223 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
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224 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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225 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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226 </data>
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227 </outputs>
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228 <tests>
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229 <expand macro="autotest_OpenSwathAnalyzer"/>
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230 <expand macro="manutest_OpenSwathAnalyzer"/>
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231 </tests>
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232 <help><![CDATA[Picks peaks and finds features in an SWATH-MS or SRM experiment.
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233
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234
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235 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_OpenSwathAnalyzer.html]]></help>
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236 <expand macro="references"/>
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237 </tool>