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comparison OpenSwathAnalyzer.xml @ 13:08488066d588 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:05:45 +0000
parents 7ca917175b23
children 9cdf469a3241
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12:0ced5bc9f4dd 13:08488066d588
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Targeted Experiments]--> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="OpenSwathAnalyzer" name="OpenSwathAnalyzer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="OpenSwathAnalyzer" name="OpenSwathAnalyzer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Picks peaks and finds features in an SWATH-MS or SRM experiment.</description> 5 <description>Picks peaks and finds features in an SWATH-MS or SRM experiment.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathAnalyzer</token> 7 <token name="@EXECUTABLE@">OpenSwathAnalyzer</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
23 #if $rt_norm: 21 #if $rt_norm:
24 mkdir rt_norm && 22 mkdir rt_norm &&
25 ln -s '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' && 23 ln -s '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' &&
26 #end if 24 #end if
27 mkdir out && 25 mkdir out &&
28 #if $swath_files: 26 #if $swath_files_cond.swath_files:
29 mkdir swath_files && 27 mkdir swath_files_cond.swath_files &&
30 ${ ' '.join(["ln -s '%s' 'swath_files/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $swath_files if _]) } 28 #if $swath_files_cond.swath_files_select == "no"
29 mkdir ${' '.join(["'swath_files_cond.swath_files/%s'" % (i) for i, f in enumerate($swath_files_cond.swath_files) if f])} &&
30 ${' '.join(["ln -s '%s' 'swath_files_cond.swath_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($swath_files_cond.swath_files) if f])}
31 #else
32 ln -s '$swath_files_cond.swath_files' 'swath_files_cond.swath_files/${re.sub("[^\w\-_]", "_", $swath_files_cond.swath_files.element_identifier)}.$gxy2omsext($swath_files_cond.swath_files.ext)' &&
33 #end if
31 #end if 34 #end if
32 35
33 ## Main program call 36 ## Main program call
34 37
35 set -o pipefail && 38 set -o pipefail &&
44 -rt_norm 47 -rt_norm
45 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' 48 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)'
46 #end if 49 #end if
47 -out 50 -out
48 'out/output.${gxy2omsext("featurexml")}' 51 'out/output.${gxy2omsext("featurexml")}'
49 #if $swath_files: 52 #if $swath_files_cond.swath_files:
50 -swath_files 53 -swath_files
51 ${' '.join(["'swath_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $swath_files if _])} 54 #if $swath_files_cond.swath_files_select == "no"
55 ${' '.join(["'swath_files_cond.swath_files/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($swath_files_cond.swath_files) if f])}
56 #else
57 'swath_files_cond.swath_files/${re.sub("[^\w\-_]", "_", $swath_files_cond.swath_files.element_identifier)}.$gxy2omsext($swath_files_cond.swath_files.ext)'
58 #end if
52 #end if 59 #end if
53 60
54 ## Postprocessing 61 ## Postprocessing
55 && mv 'out/output.${gxy2omsext("featurexml")}' '$out' 62 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
56 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 63 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
59 <configfiles> 66 <configfiles>
60 <inputs name="args_json" data_style="paths"/> 67 <inputs name="args_json" data_style="paths"/>
61 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 68 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
62 </configfiles> 69 </configfiles>
63 <inputs> 70 <inputs>
64 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file containing the chromatograms" help=" select mzml data sets(s)"/> 71 <param argument="-in" type="data" format="mzml" optional="false" label="input file containing the chromatograms" help=" select mzml data sets(s)"/>
65 <param name="tr" argument="-tr" type="data" format="traml" optional="false" label="transition file" help=" select traml data sets(s)"/> 72 <param argument="-tr" type="data" format="traml" optional="false" label="transition file" help=" select traml data sets(s)"/>
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)"/> 73 <param 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)"/>
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=""/> 74 <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=""/>
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)"/> 75 <conditional name="swath_files_cond">
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=""/> 76 <param name="swath_files_select" type="select" label="Run tool in batch mode for -swath_files">
77 <option value="no">No: process all datasets jointly</option>
78 <option value="yes">Yes: process each dataset in an independent job</option>
79 </param>
80 <when value="no">
81 <param 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)"/>
82 </when>
83 <when value="yes">
84 <param argument="-swath_files" type="data" format="mzml" multiple="false" 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)"/>
85 </when>
86 </conditional>
87 <param 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=""/>
70 <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false"> 88 <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
71 <param name="type" argument="-model:type" display="radio" type="select" optional="false" label="Type of model" help=""> 89 <param name="type" argument="-model:type" type="select" optional="true" label="Type of model" help="">
72 <option value="linear" selected="true">linear</option> 90 <option value="linear" selected="true">linear</option>
73 <option value="b_spline">b_spline</option> 91 <option value="b_spline">b_spline</option>
74 <option value="interpolated">interpolated</option> 92 <option value="interpolated">interpolated</option>
75 <option value="lowess">lowess</option> 93 <option value="lowess">lowess</option>
76 <expand macro="list_string_san"/> 94 <expand macro="list_string_san" name="type"/>
77 </param> 95 </param>
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'"/> 96 <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'"/>
79 </section> 97 </section>
80 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> 98 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
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=""/> 99 <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=""/>
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"/> 100 <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"/>
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)"/> 101 <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)"/>
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=""/> 102 <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=""/>
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=""/> 103 <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=""/>
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=""> 104 <param name="spectrum_addition_method" argument="-algorithm:spectrum_addition_method" type="select" optional="true" label="For spectrum addition, either use simple concatenation or use peak resampling" help="">
87 <option value="simple" selected="true">simple</option> 105 <option value="simple" selected="true">simple</option>
88 <option value="resample">resample</option> 106 <option value="resample">resample</option>
89 <expand macro="list_string_san"/> 107 <expand macro="list_string_san" name="spectrum_addition_method"/>
90 </param> 108 </param>
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=""/> 109 <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=""/>
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=""/> 110 <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=""/>
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=""/> 111 <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=""/>
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=""/> 112 <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=""/>
95 <param name="scoring_model" argument="-algorithm:scoring_model" display="radio" type="select" optional="false" label="Scoring model to use" help=""> 113 <param name="scoring_model" argument="-algorithm:scoring_model" type="select" optional="true" label="Scoring model to use" help="">
96 <option value="default" selected="true">default</option> 114 <option value="default" selected="true">default</option>
97 <option value="single_transition">single_transition</option> 115 <option value="single_transition">single_transition</option>
98 <expand macro="list_string_san"/> 116 <expand macro="list_string_san" name="scoring_model"/>
99 </param> 117 </param>
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)"/> 118 <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)"/>
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=""> 119 <param name="strict" argument="-algorithm:strict" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to error (true) or skip (false) if a transition in a transition group does not have a corresponding chromatogram" help=""/>
102 <expand macro="list_string_san"/>
103 </param>
104 <section name="TransitionGroupPicker" title="" help="" expanded="false"> 120 <section name="TransitionGroupPicker" title="" help="" expanded="false">
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=""/> 121 <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=""/>
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=""/> 122 <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=""/>
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=""/> 123 <param name="min_peak_width" argument="-algorithm:TransitionGroupPicker:min_peak_width" type="float" optional="true" value="0.001" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
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=""> 124 <param name="peak_integration" argument="-algorithm:TransitionGroupPicker:peak_integration" type="select" optional="true" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
109 <option value="original" selected="true">original</option> 125 <option value="original" selected="true">original</option>
110 <option value="smoothed">smoothed</option> 126 <option value="smoothed">smoothed</option>
111 <expand macro="list_string_san"/> 127 <expand macro="list_string_san" name="peak_integration"/>
112 </param> 128 </param>
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"> 129 <param name="background_subtraction" argument="-algorithm:TransitionGroupPicker:background_subtraction" type="select" optional="true" 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">
114 <option value="none" selected="true">none</option> 130 <option value="none" selected="true">none</option>
115 <option value="original">original</option> 131 <option value="original">original</option>
116 <option value="exact">exact</option> 132 <option value="exact">exact</option>
117 <expand macro="list_string_san"/> 133 <expand macro="list_string_san" name="background_subtraction"/>
118 </param> 134 </param>
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"/> 135 <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"/>
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=""/> 136 <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=""/>
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=""/> 137 <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=""/>
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)"/> 138 <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)"/>
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=""/> 139 <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=""/>
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=""/> 140 <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=""/>
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"/> 141 <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"/>
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"/> 142 <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"/>
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=""/> 143 <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=""/>
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=""> 144 <param name="boundary_selection_method" argument="-algorithm:TransitionGroupPicker:boundary_selection_method" type="select" optional="true" label="Method to use when selecting the best boundaries for peaks" help="">
129 <option value="largest" selected="true">largest</option> 145 <option value="largest" selected="true">largest</option>
130 <option value="widest">widest</option> 146 <option value="widest">widest</option>
131 <expand macro="list_string_san"/> 147 <expand macro="list_string_san" name="boundary_selection_method"/>
132 </param> 148 </param>
133 <section name="PeakPickerMRM" title="" help="" expanded="false"> 149 <section name="PeakPickerMRM" title="" help="" expanded="false">
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"/> 150 <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"/>
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=""/> 151 <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=""/>
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=""/> 152 <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=""/>
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"/> 155 <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"/>
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=""/> 156 <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=""/>
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=""/> 157 <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=""/>
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=""/> 158 <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=""/>
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=""/> 159 <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=""/>
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=""> 160 <param name="method" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:method" type="select" optional="true" 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="">
145 <option value="legacy">legacy</option> 161 <option value="legacy">legacy</option>
146 <option value="corrected" selected="true">corrected</option> 162 <option value="corrected" selected="true">corrected</option>
147 <option value="crawdad">crawdad</option> 163 <option value="crawdad">crawdad</option>
148 <expand macro="list_string_san"/> 164 <expand macro="list_string_san" name="method"/>
149 </param> 165 </param>
150 </section> 166 </section>
151 <section name="PeakIntegrator" title="" help="" expanded="false"> 167 <section name="PeakIntegrator" title="" help="" expanded="false">
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=""> 168 <param name="integration_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:integration_type" type="select" optional="true" 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="">
153 <option value="intensity_sum" selected="true">intensity_sum</option> 169 <option value="intensity_sum" selected="true">intensity_sum</option>
154 <option value="simpson">simpson</option> 170 <option value="simpson">simpson</option>
155 <option value="trapezoid">trapezoid</option> 171 <option value="trapezoid">trapezoid</option>
156 <expand macro="list_string_san"/> 172 <expand macro="list_string_san" name="integration_type"/>
157 </param> 173 </param>
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)"> 174 <param name="baseline_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:baseline_type" type="select" optional="true" 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)">
159 <option value="base_to_base" selected="true">base_to_base</option> 175 <option value="base_to_base" selected="true">base_to_base</option>
160 <option value="vertical_division">vertical_division</option> 176 <option value="vertical_division">vertical_division</option>
161 <option value="vertical_division_min">vertical_division_min</option> 177 <option value="vertical_division_min">vertical_division_min</option>
162 <option value="vertical_division_max">vertical_division_max</option> 178 <option value="vertical_division_max">vertical_division_max</option>
163 <expand macro="list_string_san"/> 179 <expand macro="list_string_san" name="baseline_type"/>
164 </param> 180 </param>
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=""/> 181 <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=""/>
166 </section> 182 </section>
167 </section> 183 </section>
168 <section name="DIAScoring" title="" help="" expanded="false"> 184 <section name="DIAScoring" title="" help="" expanded="false">
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=""/> 185 <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=""/>
170 <param name="dia_extraction_unit" argument="-algorithm:DIAScoring:dia_extraction_unit" display="radio" type="select" optional="false" label="DIA extraction window unit" help=""> 186 <param name="dia_extraction_unit" argument="-algorithm:DIAScoring:dia_extraction_unit" type="select" optional="true" label="DIA extraction window unit" help="">
171 <option value="Th" selected="true">Th</option> 187 <option value="Th" selected="true">Th</option>
172 <option value="ppm">ppm</option> 188 <option value="ppm">ppm</option>
173 <expand macro="list_string_san"/> 189 <expand macro="list_string_san" name="dia_extraction_unit"/>
174 </param> 190 </param>
175 <param name="dia_centroided" argument="-algorithm:DIAScoring:dia_centroided" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use centroided DIA data" help=""/> 191 <param name="dia_centroided" argument="-algorithm:DIAScoring:dia_centroided" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use centroided DIA data" help=""/>
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=""/> 192 <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=""/>
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=""/> 193 <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=""/>
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=""/> 194 <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=""/>
181 </section> 197 </section>
182 <section name="EMGScoring" title="" help="" expanded="false"> 198 <section name="EMGScoring" title="" help="" expanded="false">
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=""/> 199 <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=""/>
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=""/> 200 <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=""/>
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=""/> 201 <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=""/>
202 <param name="init_mom" argument="-algorithm:EMGScoring:init_mom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Initialize parameters using method of moments estimators" help=""/>
186 <section name="statistics" title="" help="" expanded="false"> 203 <section name="statistics" title="" help="" expanded="false">
187 <param name="mean" argument="-algorithm:EMGScoring:statistics:mean" type="float" optional="true" value="1.0" label="Centroid position of the model" help=""/> 204 <param name="mean" argument="-algorithm:EMGScoring:statistics:mean" type="float" optional="true" value="1.0" label="Centroid position of the model" help=""/>
188 <param name="variance" argument="-algorithm:EMGScoring:statistics:variance" type="float" optional="true" value="1.0" label="Variance of the model" help=""/> 205 <param name="variance" argument="-algorithm:EMGScoring:statistics:variance" type="float" optional="true" value="1.0" label="Variance of the model" help=""/>
189 </section> 206 </section>
190 </section> 207 </section>
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=""/> 222 <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=""/>
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=""/> 223 <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=""/>
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=""/> 224 <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=""/>
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=""/> 225 <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=""/>
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=""/> 226 <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=""/>
227 <param name="use_ionseries_scores" argument="-algorithm:Scores:use_ionseries_scores" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use MS2-level b/y ion-series scores for peptidoform identification" help=""/>
228 <param name="use_ms2_isotope_scores" argument="-algorithm:Scores:use_ms2_isotope_scores" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use MS2-level isotope scores (pearson &amp; manhattan) across product transitions (based on ID if annotated or averagine)" help=""/>
210 </section> 229 </section>
211 </section> 230 </section>
212 <expand macro="adv_opts_macro"> 231 <expand macro="adv_opts_macro">
213 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 232 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
214 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 233 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
215 <expand macro="list_string_san"/> 234 <expand macro="list_string_san" name="test"/>
216 </param> 235 </param>
217 </expand> 236 </expand>
218 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 237 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
219 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 238 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
220 </param> 239 </param>
223 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/> 242 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
224 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 243 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
225 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 244 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
226 </data> 245 </data>
227 </outputs> 246 </outputs>
228 <tests> 247 <tests><!-- TOPP_OpenSwathAnalyzer_test_1 -->
229 <expand macro="autotest_OpenSwathAnalyzer"/> 248 <test expect_num_outputs="2">
230 <expand macro="manutest_OpenSwathAnalyzer"/> 249 <section name="adv_opts">
250 <param name="force" value="false"/>
251 <param name="test" value="true"/>
252 </section>
253 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
254 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
255 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
256 <output name="out" file="OpenSwathAnalyzer_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
257 <param name="no_strict" value="false"/>
258 <param name="min_upper_edge_dist" value="0.0"/>
259 <section name="model">
260 <param name="type" value="linear"/>
261 <param name="symmetric_regression" value="false"/>
262 </section>
263 <section name="algorithm">
264 <param name="stop_report_after_feature" value="-1"/>
265 <param name="rt_extraction_window" value="-1.0"/>
266 <param name="rt_normalization_factor" value="1.0"/>
267 <param name="quantification_cutoff" value="0.0"/>
268 <param name="write_convex_hull" value="false"/>
269 <param name="spectrum_addition_method" value="simple"/>
270 <param name="add_up_spectra" value="1"/>
271 <param name="spacing_for_spectra_resampling" value="0.005"/>
272 <param name="uis_threshold_sn" value="-1"/>
273 <param name="uis_threshold_peak_area" value="0"/>
274 <param name="scoring_model" value="default"/>
275 <param name="im_extra_drift" value="0.0"/>
276 <param name="strict" value="true"/>
277 <section name="TransitionGroupPicker">
278 <param name="stop_after_feature" value="-1"/>
279 <param name="stop_after_intensity_ratio" value="0.0001"/>
280 <param name="min_peak_width" value="0.001"/>
281 <param name="peak_integration" value="original"/>
282 <param name="background_subtraction" value="none"/>
283 <param name="recalculate_peaks" value="false"/>
284 <param name="use_precursors" value="false"/>
285 <param name="use_consensus" value="true"/>
286 <param name="recalculate_peaks_max_z" value="1.0"/>
287 <param name="minimal_quality" value="-10000.0"/>
288 <param name="resample_boundary" value="15.0"/>
289 <param name="compute_peak_quality" value="false"/>
290 <param name="compute_peak_shape_metrics" value="false"/>
291 <param name="compute_total_mi" value="false"/>
292 <param name="boundary_selection_method" value="largest"/>
293 <section name="PeakPickerMRM">
294 <param name="sgolay_frame_length" value="15"/>
295 <param name="sgolay_polynomial_order" value="3"/>
296 <param name="gauss_width" value="50.0"/>
297 <param name="use_gauss" value="true"/>
298 <param name="peak_width" value="40.0"/>
299 <param name="signal_to_noise" value="1.0"/>
300 <param name="sn_win_len" value="1000.0"/>
301 <param name="sn_bin_count" value="30"/>
302 <param name="write_sn_log_messages" value="false"/>
303 <param name="remove_overlapping_peaks" value="false"/>
304 <param name="method" value="legacy"/>
305 </section>
306 <section name="PeakIntegrator">
307 <param name="integration_type" value="intensity_sum"/>
308 <param name="baseline_type" value="base_to_base"/>
309 <param name="fit_EMG" value="false"/>
310 </section>
311 </section>
312 <section name="DIAScoring">
313 <param name="dia_extraction_window" value="0.05"/>
314 <param name="dia_extraction_unit" value="Th"/>
315 <param name="dia_centroided" value="false"/>
316 <param name="dia_byseries_intensity_min" value="300.0"/>
317 <param name="dia_byseries_ppm_diff" value="10.0"/>
318 <param name="dia_nr_isotopes" value="4"/>
319 <param name="dia_nr_charges" value="4"/>
320 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
321 </section>
322 <section name="EMGScoring">
323 <param name="interpolation_step" value="0.2"/>
324 <param name="tolerance_stdev_bounding_box" value="3.0"/>
325 <param name="max_iteration" value="500"/>
326 <param name="init_mom" value="false"/>
327 <section name="statistics">
328 <param name="mean" value="1.0"/>
329 <param name="variance" value="1.0"/>
330 </section>
331 </section>
332 <section name="Scores">
333 <param name="use_shape_score" value="true"/>
334 <param name="use_coelution_score" value="true"/>
335 <param name="use_rt_score" value="true"/>
336 <param name="use_library_score" value="true"/>
337 <param name="use_elution_model_score" value="true"/>
338 <param name="use_intensity_score" value="true"/>
339 <param name="use_nr_peaks_score" value="true"/>
340 <param name="use_total_xic_score" value="true"/>
341 <param name="use_total_mi_score" value="false"/>
342 <param name="use_sn_score" value="true"/>
343 <param name="use_mi_score" value="false"/>
344 <param name="use_dia_scores" value="true"/>
345 <param name="use_ms1_correlation" value="false"/>
346 <param name="use_sonar_scores" value="false"/>
347 <param name="use_ion_mobility_scores" value="false"/>
348 <param name="use_ms1_fullscan" value="false"/>
349 <param name="use_ms1_mi" value="false"/>
350 <param name="use_uis_scores" value="false"/>
351 <param name="use_ionseries_scores" value="true"/>
352 <param name="use_ms2_isotope_scores" value="true"/>
353 </section>
354 </section>
355 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
356 <output name="ctd_out" ftype="xml">
357 <assert_contents>
358 <is_valid_xml/>
359 </assert_contents>
360 </output>
361 </test>
362 <!-- TOPP_OpenSwathAnalyzer_test_2 -->
363 <test expect_num_outputs="2">
364 <section name="adv_opts">
365 <param name="force" value="false"/>
366 <param name="test" value="true"/>
367 </section>
368 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
369 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
370 <output name="out" file="OpenSwathAnalyzer_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
371 <param name="no_strict" value="false"/>
372 <conditional name="swath_files_cond">
373 <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
374 </conditional>
375 <param name="min_upper_edge_dist" value="0.0"/>
376 <section name="model">
377 <param name="type" value="linear"/>
378 <param name="symmetric_regression" value="false"/>
379 </section>
380 <section name="algorithm">
381 <param name="stop_report_after_feature" value="-1"/>
382 <param name="rt_extraction_window" value="-1.0"/>
383 <param name="rt_normalization_factor" value="1.0"/>
384 <param name="quantification_cutoff" value="0.0"/>
385 <param name="write_convex_hull" value="false"/>
386 <param name="spectrum_addition_method" value="simple"/>
387 <param name="add_up_spectra" value="1"/>
388 <param name="spacing_for_spectra_resampling" value="0.005"/>
389 <param name="uis_threshold_sn" value="-1"/>
390 <param name="uis_threshold_peak_area" value="0"/>
391 <param name="scoring_model" value="default"/>
392 <param name="im_extra_drift" value="0.0"/>
393 <param name="strict" value="true"/>
394 <section name="TransitionGroupPicker">
395 <param name="stop_after_feature" value="-1"/>
396 <param name="stop_after_intensity_ratio" value="0.0001"/>
397 <param name="min_peak_width" value="0.001"/>
398 <param name="peak_integration" value="original"/>
399 <param name="background_subtraction" value="none"/>
400 <param name="recalculate_peaks" value="false"/>
401 <param name="use_precursors" value="false"/>
402 <param name="use_consensus" value="true"/>
403 <param name="recalculate_peaks_max_z" value="1.0"/>
404 <param name="minimal_quality" value="-10000.0"/>
405 <param name="resample_boundary" value="15.0"/>
406 <param name="compute_peak_quality" value="false"/>
407 <param name="compute_peak_shape_metrics" value="false"/>
408 <param name="compute_total_mi" value="false"/>
409 <param name="boundary_selection_method" value="largest"/>
410 <section name="PeakPickerMRM">
411 <param name="sgolay_frame_length" value="15"/>
412 <param name="sgolay_polynomial_order" value="3"/>
413 <param name="gauss_width" value="50.0"/>
414 <param name="use_gauss" value="true"/>
415 <param name="peak_width" value="40.0"/>
416 <param name="signal_to_noise" value="1.0"/>
417 <param name="sn_win_len" value="1000.0"/>
418 <param name="sn_bin_count" value="30"/>
419 <param name="write_sn_log_messages" value="false"/>
420 <param name="remove_overlapping_peaks" value="false"/>
421 <param name="method" value="legacy"/>
422 </section>
423 <section name="PeakIntegrator">
424 <param name="integration_type" value="intensity_sum"/>
425 <param name="baseline_type" value="base_to_base"/>
426 <param name="fit_EMG" value="false"/>
427 </section>
428 </section>
429 <section name="DIAScoring">
430 <param name="dia_extraction_window" value="0.05"/>
431 <param name="dia_extraction_unit" value="Th"/>
432 <param name="dia_centroided" value="false"/>
433 <param name="dia_byseries_intensity_min" value="300.0"/>
434 <param name="dia_byseries_ppm_diff" value="10.0"/>
435 <param name="dia_nr_isotopes" value="4"/>
436 <param name="dia_nr_charges" value="4"/>
437 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
438 </section>
439 <section name="EMGScoring">
440 <param name="interpolation_step" value="0.2"/>
441 <param name="tolerance_stdev_bounding_box" value="3.0"/>
442 <param name="max_iteration" value="500"/>
443 <param name="init_mom" value="false"/>
444 <section name="statistics">
445 <param name="mean" value="1.0"/>
446 <param name="variance" value="1.0"/>
447 </section>
448 </section>
449 <section name="Scores">
450 <param name="use_shape_score" value="true"/>
451 <param name="use_coelution_score" value="true"/>
452 <param name="use_rt_score" value="true"/>
453 <param name="use_library_score" value="true"/>
454 <param name="use_elution_model_score" value="true"/>
455 <param name="use_intensity_score" value="true"/>
456 <param name="use_nr_peaks_score" value="true"/>
457 <param name="use_total_xic_score" value="true"/>
458 <param name="use_total_mi_score" value="false"/>
459 <param name="use_sn_score" value="true"/>
460 <param name="use_mi_score" value="false"/>
461 <param name="use_dia_scores" value="true"/>
462 <param name="use_ms1_correlation" value="false"/>
463 <param name="use_sonar_scores" value="false"/>
464 <param name="use_ion_mobility_scores" value="false"/>
465 <param name="use_ms1_fullscan" value="false"/>
466 <param name="use_ms1_mi" value="false"/>
467 <param name="use_uis_scores" value="false"/>
468 <param name="use_ionseries_scores" value="true"/>
469 <param name="use_ms2_isotope_scores" value="true"/>
470 </section>
471 </section>
472 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
473 <output name="ctd_out" ftype="xml">
474 <assert_contents>
475 <is_valid_xml/>
476 </assert_contents>
477 </output>
478 </test>
479 <!-- TOPP_OpenSwathAnalyzer_test_5_mod -->
480 <test expect_num_outputs="2">
481 <section name="adv_opts">
482 <param name="force" value="false"/>
483 <param name="test" value="true"/>
484 </section>
485 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
486 <param name="tr" value="OpenSwathAnalyzer_mod_input.TraML"/>
487 <output name="out" file="OpenSwathAnalyzer_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
488 <param name="no_strict" value="false"/>
489 <conditional name="swath_files_cond">
490 <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
491 </conditional>
492 <param name="min_upper_edge_dist" value="0.0"/>
493 <section name="model">
494 <param name="type" value="linear"/>
495 <param name="symmetric_regression" value="false"/>
496 </section>
497 <section name="algorithm">
498 <param name="stop_report_after_feature" value="-1"/>
499 <param name="rt_extraction_window" value="-1.0"/>
500 <param name="rt_normalization_factor" value="1.0"/>
501 <param name="quantification_cutoff" value="0.0"/>
502 <param name="write_convex_hull" value="false"/>
503 <param name="spectrum_addition_method" value="simple"/>
504 <param name="add_up_spectra" value="1"/>
505 <param name="spacing_for_spectra_resampling" value="0.005"/>
506 <param name="uis_threshold_sn" value="-1"/>
507 <param name="uis_threshold_peak_area" value="0"/>
508 <param name="scoring_model" value="default"/>
509 <param name="im_extra_drift" value="0.0"/>
510 <param name="strict" value="true"/>
511 <section name="TransitionGroupPicker">
512 <param name="stop_after_feature" value="-1"/>
513 <param name="stop_after_intensity_ratio" value="0.0001"/>
514 <param name="min_peak_width" value="-1.0"/>
515 <param name="peak_integration" value="original"/>
516 <param name="background_subtraction" value="none"/>
517 <param name="recalculate_peaks" value="false"/>
518 <param name="use_precursors" value="false"/>
519 <param name="use_consensus" value="true"/>
520 <param name="recalculate_peaks_max_z" value="1.0"/>
521 <param name="minimal_quality" value="-10000.0"/>
522 <param name="resample_boundary" value="15.0"/>
523 <param name="compute_peak_quality" value="false"/>
524 <param name="compute_peak_shape_metrics" value="false"/>
525 <param name="compute_total_mi" value="false"/>
526 <param name="boundary_selection_method" value="largest"/>
527 <section name="PeakPickerMRM">
528 <param name="sgolay_frame_length" value="15"/>
529 <param name="sgolay_polynomial_order" value="3"/>
530 <param name="gauss_width" value="50.0"/>
531 <param name="use_gauss" value="true"/>
532 <param name="peak_width" value="40.0"/>
533 <param name="signal_to_noise" value="1.0"/>
534 <param name="sn_win_len" value="1000.0"/>
535 <param name="sn_bin_count" value="30"/>
536 <param name="write_sn_log_messages" value="true"/>
537 <param name="remove_overlapping_peaks" value="false"/>
538 <param name="method" value="legacy"/>
539 </section>
540 <section name="PeakIntegrator">
541 <param name="integration_type" value="intensity_sum"/>
542 <param name="baseline_type" value="base_to_base"/>
543 <param name="fit_EMG" value="false"/>
544 </section>
545 </section>
546 <section name="DIAScoring">
547 <param name="dia_extraction_window" value="0.05"/>
548 <param name="dia_extraction_unit" value="Th"/>
549 <param name="dia_centroided" value="false"/>
550 <param name="dia_byseries_intensity_min" value="8.0"/>
551 <param name="dia_byseries_ppm_diff" value="15.0"/>
552 <param name="dia_nr_isotopes" value="4"/>
553 <param name="dia_nr_charges" value="4"/>
554 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
555 </section>
556 <section name="EMGScoring">
557 <param name="interpolation_step" value="0.2"/>
558 <param name="tolerance_stdev_bounding_box" value="3.0"/>
559 <param name="max_iteration" value="500"/>
560 <param name="init_mom" value="false"/>
561 <section name="statistics">
562 <param name="mean" value="1.0"/>
563 <param name="variance" value="1.0"/>
564 </section>
565 </section>
566 <section name="Scores">
567 <param name="use_shape_score" value="true"/>
568 <param name="use_coelution_score" value="true"/>
569 <param name="use_rt_score" value="true"/>
570 <param name="use_library_score" value="true"/>
571 <param name="use_elution_model_score" value="true"/>
572 <param name="use_intensity_score" value="true"/>
573 <param name="use_nr_peaks_score" value="true"/>
574 <param name="use_total_xic_score" value="true"/>
575 <param name="use_total_mi_score" value="false"/>
576 <param name="use_sn_score" value="true"/>
577 <param name="use_mi_score" value="false"/>
578 <param name="use_dia_scores" value="true"/>
579 <param name="use_ms1_correlation" value="false"/>
580 <param name="use_sonar_scores" value="false"/>
581 <param name="use_ion_mobility_scores" value="false"/>
582 <param name="use_ms1_fullscan" value="false"/>
583 <param name="use_ms1_mi" value="false"/>
584 <param name="use_uis_scores" value="false"/>
585 <param name="use_ionseries_scores" value="true"/>
586 <param name="use_ms2_isotope_scores" value="true"/>
587 </section>
588 </section>
589 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
590 <output name="ctd_out" ftype="xml">
591 <assert_contents>
592 <is_valid_xml/>
593 </assert_contents>
594 </output>
595 </test>
596 <!-- TOPP_OpenSwathAnalyzer_test_6_nomod -->
597 <test expect_num_outputs="2">
598 <section name="adv_opts">
599 <param name="force" value="false"/>
600 <param name="test" value="true"/>
601 </section>
602 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
603 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
604 <output name="out" file="OpenSwathAnalyzer_6_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
605 <param name="no_strict" value="false"/>
606 <conditional name="swath_files_cond">
607 <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
608 </conditional>
609 <param name="min_upper_edge_dist" value="0.0"/>
610 <section name="model">
611 <param name="type" value="linear"/>
612 <param name="symmetric_regression" value="false"/>
613 </section>
614 <section name="algorithm">
615 <param name="stop_report_after_feature" value="-1"/>
616 <param name="rt_extraction_window" value="-1.0"/>
617 <param name="rt_normalization_factor" value="1.0"/>
618 <param name="quantification_cutoff" value="0.0"/>
619 <param name="write_convex_hull" value="false"/>
620 <param name="spectrum_addition_method" value="simple"/>
621 <param name="add_up_spectra" value="1"/>
622 <param name="spacing_for_spectra_resampling" value="0.005"/>
623 <param name="uis_threshold_sn" value="-1"/>
624 <param name="uis_threshold_peak_area" value="0"/>
625 <param name="scoring_model" value="default"/>
626 <param name="im_extra_drift" value="0.0"/>
627 <param name="strict" value="true"/>
628 <section name="TransitionGroupPicker">
629 <param name="stop_after_feature" value="-1"/>
630 <param name="stop_after_intensity_ratio" value="0.0001"/>
631 <param name="min_peak_width" value="-1.0"/>
632 <param name="peak_integration" value="original"/>
633 <param name="background_subtraction" value="none"/>
634 <param name="recalculate_peaks" value="false"/>
635 <param name="use_precursors" value="false"/>
636 <param name="use_consensus" value="true"/>
637 <param name="recalculate_peaks_max_z" value="1.0"/>
638 <param name="minimal_quality" value="-10000.0"/>
639 <param name="resample_boundary" value="15.0"/>
640 <param name="compute_peak_quality" value="false"/>
641 <param name="compute_peak_shape_metrics" value="false"/>
642 <param name="compute_total_mi" value="false"/>
643 <param name="boundary_selection_method" value="largest"/>
644 <section name="PeakPickerMRM">
645 <param name="sgolay_frame_length" value="15"/>
646 <param name="sgolay_polynomial_order" value="3"/>
647 <param name="gauss_width" value="50.0"/>
648 <param name="use_gauss" value="true"/>
649 <param name="peak_width" value="40.0"/>
650 <param name="signal_to_noise" value="1.0"/>
651 <param name="sn_win_len" value="1000.0"/>
652 <param name="sn_bin_count" value="30"/>
653 <param name="write_sn_log_messages" value="true"/>
654 <param name="remove_overlapping_peaks" value="false"/>
655 <param name="method" value="legacy"/>
656 </section>
657 <section name="PeakIntegrator">
658 <param name="integration_type" value="intensity_sum"/>
659 <param name="baseline_type" value="base_to_base"/>
660 <param name="fit_EMG" value="false"/>
661 </section>
662 </section>
663 <section name="DIAScoring">
664 <param name="dia_extraction_window" value="0.05"/>
665 <param name="dia_extraction_unit" value="Th"/>
666 <param name="dia_centroided" value="false"/>
667 <param name="dia_byseries_intensity_min" value="8.0"/>
668 <param name="dia_byseries_ppm_diff" value="15.0"/>
669 <param name="dia_nr_isotopes" value="4"/>
670 <param name="dia_nr_charges" value="4"/>
671 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
672 </section>
673 <section name="EMGScoring">
674 <param name="interpolation_step" value="0.2"/>
675 <param name="tolerance_stdev_bounding_box" value="3.0"/>
676 <param name="max_iteration" value="500"/>
677 <param name="init_mom" value="false"/>
678 <section name="statistics">
679 <param name="mean" value="1.0"/>
680 <param name="variance" value="1.0"/>
681 </section>
682 </section>
683 <section name="Scores">
684 <param name="use_shape_score" value="true"/>
685 <param name="use_coelution_score" value="true"/>
686 <param name="use_rt_score" value="true"/>
687 <param name="use_library_score" value="true"/>
688 <param name="use_elution_model_score" value="true"/>
689 <param name="use_intensity_score" value="true"/>
690 <param name="use_nr_peaks_score" value="true"/>
691 <param name="use_total_xic_score" value="true"/>
692 <param name="use_total_mi_score" value="false"/>
693 <param name="use_sn_score" value="true"/>
694 <param name="use_mi_score" value="false"/>
695 <param name="use_dia_scores" value="true"/>
696 <param name="use_ms1_correlation" value="false"/>
697 <param name="use_sonar_scores" value="false"/>
698 <param name="use_ion_mobility_scores" value="false"/>
699 <param name="use_ms1_fullscan" value="false"/>
700 <param name="use_ms1_mi" value="false"/>
701 <param name="use_uis_scores" value="false"/>
702 <param name="use_ionseries_scores" value="true"/>
703 <param name="use_ms2_isotope_scores" value="true"/>
704 </section>
705 </section>
706 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
707 <output name="ctd_out" ftype="xml">
708 <assert_contents>
709 <is_valid_xml/>
710 </assert_contents>
711 </output>
712 </test>
713 <!-- TOPP_OpenSwathAnalyzer_test_7_backgroundSubtraction -->
714 <test expect_num_outputs="2">
715 <section name="adv_opts">
716 <param name="force" value="false"/>
717 <param name="test" value="true"/>
718 </section>
719 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
720 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
721 <output name="out" file="OpenSwathAnalyzer_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
722 <param name="no_strict" value="false"/>
723 <param name="min_upper_edge_dist" value="0.0"/>
724 <section name="model">
725 <param name="type" value="linear"/>
726 <param name="symmetric_regression" value="false"/>
727 </section>
728 <section name="algorithm">
729 <param name="stop_report_after_feature" value="-1"/>
730 <param name="rt_extraction_window" value="-1.0"/>
731 <param name="rt_normalization_factor" value="1.0"/>
732 <param name="quantification_cutoff" value="0.0"/>
733 <param name="write_convex_hull" value="false"/>
734 <param name="spectrum_addition_method" value="simple"/>
735 <param name="add_up_spectra" value="1"/>
736 <param name="spacing_for_spectra_resampling" value="0.005"/>
737 <param name="uis_threshold_sn" value="-1"/>
738 <param name="uis_threshold_peak_area" value="0"/>
739 <param name="scoring_model" value="default"/>
740 <param name="im_extra_drift" value="0.0"/>
741 <param name="strict" value="true"/>
742 <section name="TransitionGroupPicker">
743 <param name="stop_after_feature" value="-1"/>
744 <param name="stop_after_intensity_ratio" value="0.0001"/>
745 <param name="min_peak_width" value="-1.0"/>
746 <param name="peak_integration" value="original"/>
747 <param name="background_subtraction" value="original"/>
748 <param name="recalculate_peaks" value="false"/>
749 <param name="use_precursors" value="false"/>
750 <param name="use_consensus" value="true"/>
751 <param name="recalculate_peaks_max_z" value="1.0"/>
752 <param name="minimal_quality" value="-10000.0"/>
753 <param name="resample_boundary" value="15.0"/>
754 <param name="compute_peak_quality" value="false"/>
755 <param name="compute_peak_shape_metrics" value="false"/>
756 <param name="compute_total_mi" value="false"/>
757 <param name="boundary_selection_method" value="largest"/>
758 <section name="PeakPickerMRM">
759 <param name="sgolay_frame_length" value="15"/>
760 <param name="sgolay_polynomial_order" value="3"/>
761 <param name="gauss_width" value="50.0"/>
762 <param name="use_gauss" value="true"/>
763 <param name="peak_width" value="40.0"/>
764 <param name="signal_to_noise" value="1.0"/>
765 <param name="sn_win_len" value="1000.0"/>
766 <param name="sn_bin_count" value="30"/>
767 <param name="write_sn_log_messages" value="true"/>
768 <param name="remove_overlapping_peaks" value="false"/>
769 <param name="method" value="legacy"/>
770 </section>
771 <section name="PeakIntegrator">
772 <param name="integration_type" value="intensity_sum"/>
773 <param name="baseline_type" value="base_to_base"/>
774 <param name="fit_EMG" value="false"/>
775 </section>
776 </section>
777 <section name="DIAScoring">
778 <param name="dia_extraction_window" value="0.05"/>
779 <param name="dia_extraction_unit" value="Th"/>
780 <param name="dia_centroided" value="false"/>
781 <param name="dia_byseries_intensity_min" value="300.0"/>
782 <param name="dia_byseries_ppm_diff" value="10.0"/>
783 <param name="dia_nr_isotopes" value="4"/>
784 <param name="dia_nr_charges" value="4"/>
785 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
786 </section>
787 <section name="EMGScoring">
788 <param name="interpolation_step" value="0.2"/>
789 <param name="tolerance_stdev_bounding_box" value="3.0"/>
790 <param name="max_iteration" value="500"/>
791 <param name="init_mom" value="false"/>
792 <section name="statistics">
793 <param name="mean" value="1.0"/>
794 <param name="variance" value="1.0"/>
795 </section>
796 </section>
797 <section name="Scores">
798 <param name="use_shape_score" value="true"/>
799 <param name="use_coelution_score" value="true"/>
800 <param name="use_rt_score" value="true"/>
801 <param name="use_library_score" value="true"/>
802 <param name="use_elution_model_score" value="true"/>
803 <param name="use_intensity_score" value="true"/>
804 <param name="use_nr_peaks_score" value="true"/>
805 <param name="use_total_xic_score" value="true"/>
806 <param name="use_total_mi_score" value="false"/>
807 <param name="use_sn_score" value="true"/>
808 <param name="use_mi_score" value="false"/>
809 <param name="use_dia_scores" value="true"/>
810 <param name="use_ms1_correlation" value="false"/>
811 <param name="use_sonar_scores" value="false"/>
812 <param name="use_ion_mobility_scores" value="false"/>
813 <param name="use_ms1_fullscan" value="false"/>
814 <param name="use_ms1_mi" value="false"/>
815 <param name="use_uis_scores" value="false"/>
816 <param name="use_ionseries_scores" value="true"/>
817 <param name="use_ms2_isotope_scores" value="true"/>
818 </section>
819 </section>
820 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
821 <output name="ctd_out" ftype="xml">
822 <assert_contents>
823 <is_valid_xml/>
824 </assert_contents>
825 </output>
826 </test>
827 <!-- TOPP_OpenSwathAnalyzer_test_8 -->
828 <test expect_num_outputs="2">
829 <section name="adv_opts">
830 <param name="force" value="false"/>
831 <param name="test" value="true"/>
832 </section>
833 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
834 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
835 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
836 <output name="out" file="OpenSwathAnalyzer_8_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
837 <param name="no_strict" value="false"/>
838 <param name="min_upper_edge_dist" value="0.0"/>
839 <section name="model">
840 <param name="type" value="linear"/>
841 <param name="symmetric_regression" value="false"/>
842 </section>
843 <section name="algorithm">
844 <param name="stop_report_after_feature" value="-1"/>
845 <param name="rt_extraction_window" value="-1.0"/>
846 <param name="rt_normalization_factor" value="1.0"/>
847 <param name="quantification_cutoff" value="0.0"/>
848 <param name="write_convex_hull" value="false"/>
849 <param name="spectrum_addition_method" value="simple"/>
850 <param name="add_up_spectra" value="1"/>
851 <param name="spacing_for_spectra_resampling" value="0.005"/>
852 <param name="uis_threshold_sn" value="-1"/>
853 <param name="uis_threshold_peak_area" value="0"/>
854 <param name="scoring_model" value="default"/>
855 <param name="im_extra_drift" value="0.0"/>
856 <param name="strict" value="true"/>
857 <section name="TransitionGroupPicker">
858 <param name="stop_after_feature" value="-1"/>
859 <param name="stop_after_intensity_ratio" value="0.0001"/>
860 <param name="min_peak_width" value="0.001"/>
861 <param name="peak_integration" value="original"/>
862 <param name="background_subtraction" value="none"/>
863 <param name="recalculate_peaks" value="false"/>
864 <param name="use_precursors" value="false"/>
865 <param name="use_consensus" value="true"/>
866 <param name="recalculate_peaks_max_z" value="1.0"/>
867 <param name="minimal_quality" value="-10000.0"/>
868 <param name="resample_boundary" value="15.0"/>
869 <param name="compute_peak_quality" value="false"/>
870 <param name="compute_peak_shape_metrics" value="false"/>
871 <param name="compute_total_mi" value="false"/>
872 <param name="boundary_selection_method" value="largest"/>
873 <section name="PeakPickerMRM">
874 <param name="sgolay_frame_length" value="15"/>
875 <param name="sgolay_polynomial_order" value="3"/>
876 <param name="gauss_width" value="50.0"/>
877 <param name="use_gauss" value="true"/>
878 <param name="peak_width" value="40.0"/>
879 <param name="signal_to_noise" value="1.0"/>
880 <param name="sn_win_len" value="1000.0"/>
881 <param name="sn_bin_count" value="30"/>
882 <param name="write_sn_log_messages" value="false"/>
883 <param name="remove_overlapping_peaks" value="false"/>
884 <param name="method" value="legacy"/>
885 </section>
886 <section name="PeakIntegrator">
887 <param name="integration_type" value="intensity_sum"/>
888 <param name="baseline_type" value="base_to_base"/>
889 <param name="fit_EMG" value="false"/>
890 </section>
891 </section>
892 <section name="DIAScoring">
893 <param name="dia_extraction_window" value="0.05"/>
894 <param name="dia_extraction_unit" value="Th"/>
895 <param name="dia_centroided" value="false"/>
896 <param name="dia_byseries_intensity_min" value="300.0"/>
897 <param name="dia_byseries_ppm_diff" value="10.0"/>
898 <param name="dia_nr_isotopes" value="4"/>
899 <param name="dia_nr_charges" value="4"/>
900 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
901 </section>
902 <section name="EMGScoring">
903 <param name="interpolation_step" value="0.2"/>
904 <param name="tolerance_stdev_bounding_box" value="3.0"/>
905 <param name="max_iteration" value="500"/>
906 <param name="init_mom" value="false"/>
907 <section name="statistics">
908 <param name="mean" value="1.0"/>
909 <param name="variance" value="1.0"/>
910 </section>
911 </section>
912 <section name="Scores">
913 <param name="use_shape_score" value="true"/>
914 <param name="use_coelution_score" value="true"/>
915 <param name="use_rt_score" value="true"/>
916 <param name="use_library_score" value="true"/>
917 <param name="use_elution_model_score" value="true"/>
918 <param name="use_intensity_score" value="true"/>
919 <param name="use_nr_peaks_score" value="true"/>
920 <param name="use_total_xic_score" value="true"/>
921 <param name="use_total_mi_score" value="true"/>
922 <param name="use_sn_score" value="true"/>
923 <param name="use_mi_score" value="true"/>
924 <param name="use_dia_scores" value="true"/>
925 <param name="use_ms1_correlation" value="false"/>
926 <param name="use_sonar_scores" value="false"/>
927 <param name="use_ion_mobility_scores" value="false"/>
928 <param name="use_ms1_fullscan" value="false"/>
929 <param name="use_ms1_mi" value="true"/>
930 <param name="use_uis_scores" value="false"/>
931 <param name="use_ionseries_scores" value="true"/>
932 <param name="use_ms2_isotope_scores" value="true"/>
933 </section>
934 </section>
935 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
936 <output name="ctd_out" ftype="xml">
937 <assert_contents>
938 <is_valid_xml/>
939 </assert_contents>
940 </output>
941 </test>
942 <!-- TOPP_OpenSwathAnalyzer_test_9 -->
943 <test expect_num_outputs="2">
944 <section name="adv_opts">
945 <param name="force" value="false"/>
946 <param name="test" value="true"/>
947 </section>
948 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
949 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
950 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
951 <output name="out" file="OpenSwathAnalyzer_9_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
952 <param name="no_strict" value="false"/>
953 <param name="min_upper_edge_dist" value="0.0"/>
954 <section name="model">
955 <param name="type" value="linear"/>
956 <param name="symmetric_regression" value="false"/>
957 </section>
958 <section name="algorithm">
959 <param name="stop_report_after_feature" value="-1"/>
960 <param name="rt_extraction_window" value="-1.0"/>
961 <param name="rt_normalization_factor" value="1.0"/>
962 <param name="quantification_cutoff" value="0.0"/>
963 <param name="write_convex_hull" value="false"/>
964 <param name="spectrum_addition_method" value="simple"/>
965 <param name="add_up_spectra" value="1"/>
966 <param name="spacing_for_spectra_resampling" value="0.005"/>
967 <param name="uis_threshold_sn" value="-1"/>
968 <param name="uis_threshold_peak_area" value="0"/>
969 <param name="scoring_model" value="default"/>
970 <param name="im_extra_drift" value="0.0"/>
971 <param name="strict" value="true"/>
972 <section name="TransitionGroupPicker">
973 <param name="stop_after_feature" value="-1"/>
974 <param name="stop_after_intensity_ratio" value="0.0001"/>
975 <param name="min_peak_width" value="0.001"/>
976 <param name="peak_integration" value="original"/>
977 <param name="background_subtraction" value="none"/>
978 <param name="recalculate_peaks" value="false"/>
979 <param name="use_precursors" value="false"/>
980 <param name="use_consensus" value="true"/>
981 <param name="recalculate_peaks_max_z" value="1.0"/>
982 <param name="minimal_quality" value="-10000.0"/>
983 <param name="resample_boundary" value="15.0"/>
984 <param name="compute_peak_quality" value="false"/>
985 <param name="compute_peak_shape_metrics" value="false"/>
986 <param name="compute_total_mi" value="false"/>
987 <param name="boundary_selection_method" value="largest"/>
988 <section name="PeakPickerMRM">
989 <param name="sgolay_frame_length" value="15"/>
990 <param name="sgolay_polynomial_order" value="3"/>
991 <param name="gauss_width" value="50.0"/>
992 <param name="use_gauss" value="true"/>
993 <param name="peak_width" value="40.0"/>
994 <param name="signal_to_noise" value="1.0"/>
995 <param name="sn_win_len" value="1000.0"/>
996 <param name="sn_bin_count" value="30"/>
997 <param name="write_sn_log_messages" value="false"/>
998 <param name="remove_overlapping_peaks" value="false"/>
999 <param name="method" value="legacy"/>
1000 </section>
1001 <section name="PeakIntegrator">
1002 <param name="integration_type" value="intensity_sum"/>
1003 <param name="baseline_type" value="base_to_base"/>
1004 <param name="fit_EMG" value="false"/>
1005 </section>
1006 </section>
1007 <section name="DIAScoring">
1008 <param name="dia_extraction_window" value="0.05"/>
1009 <param name="dia_extraction_unit" value="Th"/>
1010 <param name="dia_centroided" value="false"/>
1011 <param name="dia_byseries_intensity_min" value="300.0"/>
1012 <param name="dia_byseries_ppm_diff" value="10.0"/>
1013 <param name="dia_nr_isotopes" value="4"/>
1014 <param name="dia_nr_charges" value="4"/>
1015 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
1016 </section>
1017 <section name="EMGScoring">
1018 <param name="interpolation_step" value="0.2"/>
1019 <param name="tolerance_stdev_bounding_box" value="3.0"/>
1020 <param name="max_iteration" value="500"/>
1021 <param name="init_mom" value="false"/>
1022 <section name="statistics">
1023 <param name="mean" value="1.0"/>
1024 <param name="variance" value="1.0"/>
1025 </section>
1026 </section>
1027 <section name="Scores">
1028 <param name="use_shape_score" value="true"/>
1029 <param name="use_coelution_score" value="true"/>
1030 <param name="use_rt_score" value="true"/>
1031 <param name="use_library_score" value="true"/>
1032 <param name="use_elution_model_score" value="true"/>
1033 <param name="use_intensity_score" value="true"/>
1034 <param name="use_nr_peaks_score" value="true"/>
1035 <param name="use_total_xic_score" value="true"/>
1036 <param name="use_total_mi_score" value="false"/>
1037 <param name="use_sn_score" value="true"/>
1038 <param name="use_mi_score" value="true"/>
1039 <param name="use_dia_scores" value="true"/>
1040 <param name="use_ms1_correlation" value="false"/>
1041 <param name="use_sonar_scores" value="false"/>
1042 <param name="use_ion_mobility_scores" value="false"/>
1043 <param name="use_ms1_fullscan" value="false"/>
1044 <param name="use_ms1_mi" value="false"/>
1045 <param name="use_uis_scores" value="false"/>
1046 <param name="use_ionseries_scores" value="true"/>
1047 <param name="use_ms2_isotope_scores" value="true"/>
1048 </section>
1049 </section>
1050 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1051 <output name="ctd_out" ftype="xml">
1052 <assert_contents>
1053 <is_valid_xml/>
1054 </assert_contents>
1055 </output>
1056 </test>
1057 <!-- TOPP_OpenSwathAnalyzer_test_10 -->
1058 <test expect_num_outputs="2">
1059 <section name="adv_opts">
1060 <param name="force" value="false"/>
1061 <param name="test" value="true"/>
1062 </section>
1063 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
1064 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
1065 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
1066 <output name="out" file="OpenSwathAnalyzer_10_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
1067 <param name="no_strict" value="false"/>
1068 <param name="min_upper_edge_dist" value="0.0"/>
1069 <section name="model">
1070 <param name="type" value="linear"/>
1071 <param name="symmetric_regression" value="false"/>
1072 </section>
1073 <section name="algorithm">
1074 <param name="stop_report_after_feature" value="-1"/>
1075 <param name="rt_extraction_window" value="-1.0"/>
1076 <param name="rt_normalization_factor" value="1.0"/>
1077 <param name="quantification_cutoff" value="0.0"/>
1078 <param name="write_convex_hull" value="false"/>
1079 <param name="spectrum_addition_method" value="simple"/>
1080 <param name="add_up_spectra" value="1"/>
1081 <param name="spacing_for_spectra_resampling" value="0.005"/>
1082 <param name="uis_threshold_sn" value="-1"/>
1083 <param name="uis_threshold_peak_area" value="0"/>
1084 <param name="scoring_model" value="default"/>
1085 <param name="im_extra_drift" value="0.0"/>
1086 <param name="strict" value="true"/>
1087 <section name="TransitionGroupPicker">
1088 <param name="stop_after_feature" value="-1"/>
1089 <param name="stop_after_intensity_ratio" value="0.0001"/>
1090 <param name="min_peak_width" value="0.001"/>
1091 <param name="peak_integration" value="original"/>
1092 <param name="background_subtraction" value="none"/>
1093 <param name="recalculate_peaks" value="false"/>
1094 <param name="use_precursors" value="false"/>
1095 <param name="use_consensus" value="true"/>
1096 <param name="recalculate_peaks_max_z" value="1.0"/>
1097 <param name="minimal_quality" value="-10000.0"/>
1098 <param name="resample_boundary" value="15.0"/>
1099 <param name="compute_peak_quality" value="false"/>
1100 <param name="compute_peak_shape_metrics" value="false"/>
1101 <param name="compute_total_mi" value="false"/>
1102 <param name="boundary_selection_method" value="largest"/>
1103 <section name="PeakPickerMRM">
1104 <param name="sgolay_frame_length" value="15"/>
1105 <param name="sgolay_polynomial_order" value="3"/>
1106 <param name="gauss_width" value="50.0"/>
1107 <param name="use_gauss" value="true"/>
1108 <param name="peak_width" value="40.0"/>
1109 <param name="signal_to_noise" value="1.0"/>
1110 <param name="sn_win_len" value="1000.0"/>
1111 <param name="sn_bin_count" value="30"/>
1112 <param name="write_sn_log_messages" value="false"/>
1113 <param name="remove_overlapping_peaks" value="false"/>
1114 <param name="method" value="legacy"/>
1115 </section>
1116 <section name="PeakIntegrator">
1117 <param name="integration_type" value="intensity_sum"/>
1118 <param name="baseline_type" value="base_to_base"/>
1119 <param name="fit_EMG" value="false"/>
1120 </section>
1121 </section>
1122 <section name="DIAScoring">
1123 <param name="dia_extraction_window" value="0.05"/>
1124 <param name="dia_extraction_unit" value="Th"/>
1125 <param name="dia_centroided" value="false"/>
1126 <param name="dia_byseries_intensity_min" value="300.0"/>
1127 <param name="dia_byseries_ppm_diff" value="10.0"/>
1128 <param name="dia_nr_isotopes" value="4"/>
1129 <param name="dia_nr_charges" value="4"/>
1130 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
1131 </section>
1132 <section name="EMGScoring">
1133 <param name="interpolation_step" value="0.2"/>
1134 <param name="tolerance_stdev_bounding_box" value="3.0"/>
1135 <param name="max_iteration" value="500"/>
1136 <param name="init_mom" value="false"/>
1137 <section name="statistics">
1138 <param name="mean" value="1.0"/>
1139 <param name="variance" value="1.0"/>
1140 </section>
1141 </section>
1142 <section name="Scores">
1143 <param name="use_shape_score" value="true"/>
1144 <param name="use_coelution_score" value="true"/>
1145 <param name="use_rt_score" value="true"/>
1146 <param name="use_library_score" value="true"/>
1147 <param name="use_elution_model_score" value="true"/>
1148 <param name="use_intensity_score" value="true"/>
1149 <param name="use_nr_peaks_score" value="true"/>
1150 <param name="use_total_xic_score" value="true"/>
1151 <param name="use_total_mi_score" value="true"/>
1152 <param name="use_sn_score" value="true"/>
1153 <param name="use_mi_score" value="true"/>
1154 <param name="use_dia_scores" value="true"/>
1155 <param name="use_ms1_correlation" value="false"/>
1156 <param name="use_sonar_scores" value="false"/>
1157 <param name="use_ion_mobility_scores" value="false"/>
1158 <param name="use_ms1_fullscan" value="false"/>
1159 <param name="use_ms1_mi" value="false"/>
1160 <param name="use_uis_scores" value="false"/>
1161 <param name="use_ionseries_scores" value="true"/>
1162 <param name="use_ms2_isotope_scores" value="true"/>
1163 </section>
1164 </section>
1165 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1166 <output name="ctd_out" ftype="xml">
1167 <assert_contents>
1168 <is_valid_xml/>
1169 </assert_contents>
1170 </output>
1171 </test>
1172 <!-- TOPP_OpenSwathAnalyzer_test_11 -->
1173 <test expect_num_outputs="2">
1174 <section name="adv_opts">
1175 <param name="force" value="false"/>
1176 <param name="test" value="true"/>
1177 </section>
1178 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
1179 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
1180 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
1181 <output name="out" file="OpenSwathAnalyzer_11_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
1182 <param name="no_strict" value="false"/>
1183 <param name="min_upper_edge_dist" value="0.0"/>
1184 <section name="model">
1185 <param name="type" value="linear"/>
1186 <param name="symmetric_regression" value="false"/>
1187 </section>
1188 <section name="algorithm">
1189 <param name="stop_report_after_feature" value="-1"/>
1190 <param name="rt_extraction_window" value="-1.0"/>
1191 <param name="rt_normalization_factor" value="1.0"/>
1192 <param name="quantification_cutoff" value="0.0"/>
1193 <param name="write_convex_hull" value="false"/>
1194 <param name="spectrum_addition_method" value="simple"/>
1195 <param name="add_up_spectra" value="1"/>
1196 <param name="spacing_for_spectra_resampling" value="0.005"/>
1197 <param name="uis_threshold_sn" value="-1"/>
1198 <param name="uis_threshold_peak_area" value="0"/>
1199 <param name="scoring_model" value="default"/>
1200 <param name="im_extra_drift" value="0.0"/>
1201 <param name="strict" value="true"/>
1202 <section name="TransitionGroupPicker">
1203 <param name="stop_after_feature" value="-1"/>
1204 <param name="stop_after_intensity_ratio" value="0.0001"/>
1205 <param name="min_peak_width" value="0.001"/>
1206 <param name="peak_integration" value="original"/>
1207 <param name="background_subtraction" value="none"/>
1208 <param name="recalculate_peaks" value="false"/>
1209 <param name="use_precursors" value="false"/>
1210 <param name="use_consensus" value="true"/>
1211 <param name="recalculate_peaks_max_z" value="1.0"/>
1212 <param name="minimal_quality" value="-10000.0"/>
1213 <param name="resample_boundary" value="15.0"/>
1214 <param name="compute_peak_quality" value="false"/>
1215 <param name="compute_peak_shape_metrics" value="false"/>
1216 <param name="compute_total_mi" value="false"/>
1217 <param name="boundary_selection_method" value="largest"/>
1218 <section name="PeakPickerMRM">
1219 <param name="sgolay_frame_length" value="15"/>
1220 <param name="sgolay_polynomial_order" value="3"/>
1221 <param name="gauss_width" value="50.0"/>
1222 <param name="use_gauss" value="true"/>
1223 <param name="peak_width" value="40.0"/>
1224 <param name="signal_to_noise" value="1.0"/>
1225 <param name="sn_win_len" value="1000.0"/>
1226 <param name="sn_bin_count" value="30"/>
1227 <param name="write_sn_log_messages" value="false"/>
1228 <param name="remove_overlapping_peaks" value="false"/>
1229 <param name="method" value="legacy"/>
1230 </section>
1231 <section name="PeakIntegrator">
1232 <param name="integration_type" value="intensity_sum"/>
1233 <param name="baseline_type" value="base_to_base"/>
1234 <param name="fit_EMG" value="false"/>
1235 </section>
1236 </section>
1237 <section name="DIAScoring">
1238 <param name="dia_extraction_window" value="0.05"/>
1239 <param name="dia_extraction_unit" value="Th"/>
1240 <param name="dia_centroided" value="false"/>
1241 <param name="dia_byseries_intensity_min" value="300.0"/>
1242 <param name="dia_byseries_ppm_diff" value="10.0"/>
1243 <param name="dia_nr_isotopes" value="4"/>
1244 <param name="dia_nr_charges" value="4"/>
1245 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
1246 </section>
1247 <section name="EMGScoring">
1248 <param name="interpolation_step" value="0.2"/>
1249 <param name="tolerance_stdev_bounding_box" value="3.0"/>
1250 <param name="max_iteration" value="500"/>
1251 <param name="init_mom" value="false"/>
1252 <section name="statistics">
1253 <param name="mean" value="1.0"/>
1254 <param name="variance" value="1.0"/>
1255 </section>
1256 </section>
1257 <section name="Scores">
1258 <param name="use_shape_score" value="true"/>
1259 <param name="use_coelution_score" value="true"/>
1260 <param name="use_rt_score" value="true"/>
1261 <param name="use_library_score" value="true"/>
1262 <param name="use_elution_model_score" value="true"/>
1263 <param name="use_intensity_score" value="true"/>
1264 <param name="use_nr_peaks_score" value="true"/>
1265 <param name="use_total_xic_score" value="true"/>
1266 <param name="use_total_mi_score" value="true"/>
1267 <param name="use_sn_score" value="true"/>
1268 <param name="use_mi_score" value="false"/>
1269 <param name="use_dia_scores" value="true"/>
1270 <param name="use_ms1_correlation" value="false"/>
1271 <param name="use_sonar_scores" value="false"/>
1272 <param name="use_ion_mobility_scores" value="false"/>
1273 <param name="use_ms1_fullscan" value="false"/>
1274 <param name="use_ms1_mi" value="false"/>
1275 <param name="use_uis_scores" value="false"/>
1276 <param name="use_ionseries_scores" value="true"/>
1277 <param name="use_ms2_isotope_scores" value="true"/>
1278 </section>
1279 </section>
1280 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1281 <output name="ctd_out" ftype="xml">
1282 <assert_contents>
1283 <is_valid_xml/>
1284 </assert_contents>
1285 </output>
1286 </test>
231 </tests> 1287 </tests>
232 <help><![CDATA[Picks peaks and finds features in an SWATH-MS or SRM experiment. 1288 <help><![CDATA[Picks peaks and finds features in an SWATH-MS or SRM experiment.
233 1289
234 1290
235 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_OpenSwathAnalyzer.html]]></help> 1291 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathAnalyzer.html]]></help>
236 <expand macro="references"/> 1292 <expand macro="references"/>
237 </tool> 1293 </tool>