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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:37:00 +0000
parents d31426ef20f6
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13:d31426ef20f6 14:0eaf3d4219cf
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 1 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Targeted Experiments]--> 2 <!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
4 <tool id="OpenSwathRTNormalizer" name="OpenSwathRTNormalizer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="OpenSwathRTNormalizer" name="OpenSwathRTNormalizer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space.</description> 4 <description>This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">OpenSwathRTNormalizer</token> 6 <token name="@EXECUTABLE@">OpenSwathRTNormalizer</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in_cond.in && 16 mkdir in_cond.in &&
18 #if $in_cond.in_select == "no" 17 #if $in_cond.in_select == "no"
19 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 18 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
20 ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} 19 ${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
21 #else 20 #else
22 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && 21 cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
23 #end if 22 #end if
24 mkdir tr && 23 mkdir tr &&
25 ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && 24 cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
26 mkdir out && 25 mkdir out &&
27 #if $rt_norm: 26 #if $rt_norm:
28 mkdir rt_norm && 27 mkdir rt_norm &&
29 ln -s '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' && 28 cp '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' &&
30 #end if 29 #end if
31 30
32 ## Main program call 31 ## Main program call
33 32
34 set -o pipefail && 33 set -o pipefail &&
64 <param name="in_select" type="select" label="Run tool in batch mode for -in"> 63 <param name="in_select" type="select" label="Run tool in batch mode for -in">
65 <option value="no">No: process all datasets jointly</option> 64 <option value="no">No: process all datasets jointly</option>
66 <option value="yes">Yes: process each dataset in an independent job</option> 65 <option value="yes">Yes: process each dataset in an independent job</option>
67 </param> 66 </param>
68 <when value="no"> 67 <when value="no">
69 <param argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input files separated by blank" help=" select mzml data sets(s)"/> 68 <param argument="-in" type="data" format="mzml" multiple="true" label="Input files separated by blank" help=" select mzml data sets(s)"/>
70 </when> 69 </when>
71 <when value="yes"> 70 <when value="yes">
72 <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="Input files separated by blank" help=" select mzml data sets(s)"/> 71 <param argument="-in" type="data" format="mzml" label="Input files separated by blank" help=" select mzml data sets(s)"/>
73 </when> 72 </when>
74 </conditional> 73 </conditional>
75 <param argument="-tr" type="data" format="csv,traml" optional="false" label="transition file with the RT peptides ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/> 74 <param argument="-tr" type="data" format="csv,traml" label="transition file with the RT peptides ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/>
76 <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)"/> 75 <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)"/>
77 <param argument="-min_rsq" type="float" optional="true" value="0.95" label="Minimum r-squared of RT peptides regression" help=""/> 76 <param argument="-min_rsq" type="float" value="0.95" label="Minimum r-squared of RT peptides regression" help=""/>
78 <param argument="-min_coverage" type="float" optional="true" value="0.6" label="Minimum relative amount of RT peptides to keep" help=""/> 77 <param argument="-min_coverage" type="float" value="0.6" label="Minimum relative amount of RT peptides to keep" help=""/>
79 <param argument="-estimateBestPeptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether the algorithms should try to choose the best peptides based on their peak shape for normalization" help="Use this option you do not expect all your peptides to be detected in a sample and too many 'bad' peptides enter the outlier removal step (e.g. due to them being endogenous peptides or using a less curated list of peptides)"/> 78 <param argument="-estimateBestPeptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether the algorithms should try to choose the best peptides based on their peak shape for normalization" help="Use this option you do not expect all your peptides to be detected in a sample and too many 'bad' peptides enter the outlier removal step (e.g. due to them being endogenous peptides or using a less curated list of peptides)"/>
80 <section name="RTNormalization" title="Parameters for the RTNormalization" help="RT normalization and outlier detection can be done iteratively (by default) which removes one outlier per iteration or using the RANSAC algorithm" expanded="false"> 79 <section name="RTNormalization" title="Parameters for the RTNormalization" help="RT normalization and outlier detection can be done iteratively (by default) which removes one outlier per iteration or using the RANSAC algorithm" expanded="false">
81 <param name="outlierMethod" argument="-RTNormalization:outlierMethod" type="select" optional="true" label="Which outlier detection method to use (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none')" help="Iterative methods remove one outlier at a time. Jackknife approach optimizes for maximum r-squared improvement while 'iter_residual' removes the datapoint with the largest residual error (removal by residual is computationally cheaper, use this with lots of peptides)"> 80 <param name="outlierMethod" argument="-RTNormalization:outlierMethod" type="select" label="Which outlier detection method to use (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none')" help="Iterative methods remove one outlier at a time. Jackknife approach optimizes for maximum r-squared improvement while 'iter_residual' removes the datapoint with the largest residual error (removal by residual is computationally cheaper, use this with lots of peptides)">
82 <option value="iter_residual" selected="true">iter_residual</option> 81 <option value="iter_residual" selected="true">iter_residual</option>
83 <option value="iter_jackknife">iter_jackknife</option> 82 <option value="iter_jackknife">iter_jackknife</option>
84 <option value="ransac">ransac</option> 83 <option value="ransac">ransac</option>
85 <option value="none">none</option> 84 <option value="none">none</option>
86 <expand macro="list_string_san" name="outlierMethod"/> 85 <expand macro="list_string_san" name="outlierMethod"/>
87 </param> 86 </param>
88 <param name="useIterativeChauvenet" argument="-RTNormalization:useIterativeChauvenet" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to use Chauvenet's criterion when using iterative methods" help="This should be used if the algorithm removes too many datapoints but it may lead to true outliers being retained"/> 87 <param name="useIterativeChauvenet" argument="-RTNormalization:useIterativeChauvenet" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to use Chauvenet's criterion when using iterative methods" help="This should be used if the algorithm removes too many datapoints but it may lead to true outliers being retained"/>
89 <param name="RANSACMaxIterations" argument="-RTNormalization:RANSACMaxIterations" type="integer" optional="true" value="1000" label="Maximum iterations for the RANSAC outlier detection algorithm" help=""/> 88 <param name="RANSACMaxIterations" argument="-RTNormalization:RANSACMaxIterations" type="integer" value="1000" label="Maximum iterations for the RANSAC outlier detection algorithm" help=""/>
90 <param name="RANSACMaxPercentRTThreshold" argument="-RTNormalization:RANSACMaxPercentRTThreshold" type="integer" optional="true" value="3" label="Maximum threshold in RT dimension for the RANSAC outlier detection algorithm (in percent of the total gradient)" help="Default is set to 3% which is around +/- 4 minutes on a 120 gradient"/> 89 <param name="RANSACMaxPercentRTThreshold" argument="-RTNormalization:RANSACMaxPercentRTThreshold" type="integer" value="3" label="Maximum threshold in RT dimension for the RANSAC outlier detection algorithm (in percent of the total gradient)" help="Default is set to 3% which is around +/- 4 minutes on a 120 gradient"/>
91 <param name="RANSACSamplingSize" argument="-RTNormalization:RANSACSamplingSize" type="integer" optional="true" value="10" label="Sampling size of data points per iteration for the RANSAC outlier detection algorithm" help=""/> 90 <param name="RANSACSamplingSize" argument="-RTNormalization:RANSACSamplingSize" type="integer" value="10" label="Sampling size of data points per iteration for the RANSAC outlier detection algorithm" help=""/>
92 </section> 91 </section>
93 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> 92 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
94 <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=""/> 93 <param name="stop_report_after_feature" argument="-algorithm:stop_report_after_feature" type="integer" value="-1" label="Stop reporting after feature (ordered by quality; -1 means do not stop)" help=""/>
95 <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"/> 94 <param name="rt_extraction_window" argument="-algorithm:rt_extraction_window" type="float" 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"/>
96 <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)"/> 95 <param name="rt_normalization_factor" argument="-algorithm:rt_normalization_factor" type="float" 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)"/>
97 <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=""/> 96 <param name="quantification_cutoff" argument="-algorithm:quantification_cutoff" type="float" min="0.0" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help=""/>
98 <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=""/> 97 <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=""/>
99 <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=""> 98 <param name="spectrum_addition_method" argument="-algorithm:spectrum_addition_method" type="select" label="For spectrum addition, either use simple concatenation or use peak resampling" help="">
100 <option value="simple" selected="true">simple</option> 99 <option value="simple" selected="true">simple</option>
101 <option value="resample">resample</option> 100 <option value="resample">resample</option>
102 <expand macro="list_string_san" name="spectrum_addition_method"/> 101 <expand macro="list_string_san" name="spectrum_addition_method"/>
103 </param> 102 </param>
104 <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=""/> 103 <param name="add_up_spectra" argument="-algorithm:add_up_spectra" type="integer" min="1" value="1" label="Add up spectra around the peak apex (needs to be a non-even integer)" help=""/>
105 <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=""/> 104 <param name="spacing_for_spectra_resampling" argument="-algorithm:spacing_for_spectra_resampling" type="float" min="0.0" value="0.005" label="If spectra are to be added, use this spacing to add them up" help=""/>
106 <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=""/> 105 <param name="uis_threshold_sn" argument="-algorithm:uis_threshold_sn" type="integer" value="-1" label="S/N threshold to consider identification transition (set to -1 to consider all)" help=""/>
107 <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=""/> 106 <param name="uis_threshold_peak_area" argument="-algorithm:uis_threshold_peak_area" type="integer" value="0" label="Peak area threshold to consider identification transition (set to -1 to consider all)" help=""/>
108 <param name="scoring_model" argument="-algorithm:scoring_model" type="select" optional="true" label="Scoring model to use" help=""> 107 <param name="scoring_model" argument="-algorithm:scoring_model" type="select" label="Scoring model to use" help="">
109 <option value="default" selected="true">default</option> 108 <option value="default" selected="true">default</option>
110 <option value="single_transition">single_transition</option> 109 <option value="single_transition">single_transition</option>
111 <expand macro="list_string_san" name="scoring_model"/> 110 <expand macro="list_string_san" name="scoring_model"/>
112 </param> 111 </param>
113 <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)"/> 112 <param name="im_extra_drift" argument="-algorithm:im_extra_drift" type="float" 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)"/>
114 <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=""/> 113 <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=""/>
115 <section name="TransitionGroupPicker" title="" help="" expanded="false"> 114 <section name="TransitionGroupPicker" title="" help="" expanded="false">
116 <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=""/> 115 <param name="stop_after_feature" argument="-algorithm:TransitionGroupPicker:stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
117 <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=""/> 116 <param name="stop_after_intensity_ratio" argument="-algorithm:TransitionGroupPicker:stop_after_intensity_ratio" type="float" value="0.0001" label="Stop after reaching intensity ratio" help=""/>
118 <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=""/> 117 <param name="min_peak_width" argument="-algorithm:TransitionGroupPicker:min_peak_width" type="float" value="0.001" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
119 <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=""> 118 <param name="peak_integration" argument="-algorithm:TransitionGroupPicker:peak_integration" type="select" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
120 <option value="original" selected="true">original</option> 119 <option value="original" selected="true">original</option>
121 <option value="smoothed">smoothed</option> 120 <option value="smoothed">smoothed</option>
122 <expand macro="list_string_san" name="peak_integration"/> 121 <expand macro="list_string_san" name="peak_integration"/>
123 </param> 122 </param>
124 <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"> 123 <param name="background_subtraction" argument="-algorithm:TransitionGroupPicker:background_subtraction" type="select" 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">
125 <option value="none" selected="true">none</option> 124 <option value="none" selected="true">none</option>
126 <option value="original">original</option> 125 <option value="original">original</option>
127 <option value="exact">exact</option> 126 <option value="exact">exact</option>
128 <expand macro="list_string_san" name="background_subtraction"/> 127 <expand macro="list_string_san" name="background_subtraction"/>
129 </param> 128 </param>
130 <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"/> 129 <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"/>
131 <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=""/> 130 <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=""/>
132 <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=""/> 131 <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=""/>
133 <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)"/> 132 <param name="recalculate_peaks_max_z" argument="-algorithm:TransitionGroupPicker:recalculate_peaks_max_z" type="float" 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)"/>
134 <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=""/> 133 <param name="minimal_quality" argument="-algorithm:TransitionGroupPicker:minimal_quality" type="float" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help=""/>
135 <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=""/> 134 <param name="resample_boundary" argument="-algorithm:TransitionGroupPicker:resample_boundary" type="float" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help=""/>
136 <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"/> 135 <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"/>
137 <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"/> 136 <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"/>
138 <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=""/> 137 <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=""/>
139 <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=""> 138 <param name="boundary_selection_method" argument="-algorithm:TransitionGroupPicker:boundary_selection_method" type="select" label="Method to use when selecting the best boundaries for peaks" help="">
140 <option value="largest" selected="true">largest</option> 139 <option value="largest" selected="true">largest</option>
141 <option value="widest">widest</option> 140 <option value="widest">widest</option>
142 <expand macro="list_string_san" name="boundary_selection_method"/> 141 <expand macro="list_string_san" name="boundary_selection_method"/>
143 </param> 142 </param>
144 <section name="PeakPickerMRM" title="" help="" expanded="false"> 143 <section name="PeakPickerMRM" title="" help="" expanded="false">
145 <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"/> 144 <param name="sgolay_frame_length" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length" type="integer" 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"/>
146 <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=""/> 145 <param name="sgolay_polynomial_order" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help=""/>
147 <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=""/> 146 <param name="gauss_width" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help=""/>
148 <param name="use_gauss" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help=""/> 147 <param name="use_gauss" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help=""/>
149 <param name="peak_width" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width" type="float" optional="true" value="-1.0" label="Force a certain minimal peak_width on the data" help="(e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/> 148 <param name="peak_width" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width" type="float" value="-1.0" label="Force a certain minimal peak_width on the data" help="(e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
150 <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"/> 149 <param name="signal_to_noise" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise" type="float" 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"/>
151 <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=""/> 150 <param name="sn_win_len" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help=""/>
152 <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=""/> 151 <param name="sn_bin_count" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help=""/>
153 <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=""/> 152 <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=""/>
154 <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=""/> 153 <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=""/>
155 <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=""> 154 <param name="method" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:method" type="select" 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="">
156 <option value="legacy">legacy</option> 155 <option value="legacy">legacy</option>
157 <option value="corrected" selected="true">corrected</option> 156 <option value="corrected" selected="true">corrected</option>
158 <option value="crawdad">crawdad</option> 157 <option value="crawdad">crawdad</option>
159 <expand macro="list_string_san" name="method"/> 158 <expand macro="list_string_san" name="method"/>
160 </param> 159 </param>
161 </section> 160 </section>
162 <section name="PeakIntegrator" title="" help="" expanded="false"> 161 <section name="PeakIntegrator" title="" help="" expanded="false">
163 <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=""> 162 <param name="integration_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:integration_type" type="select" 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="">
164 <option value="intensity_sum" selected="true">intensity_sum</option> 163 <option value="intensity_sum" selected="true">intensity_sum</option>
165 <option value="simpson">simpson</option> 164 <option value="simpson">simpson</option>
166 <option value="trapezoid">trapezoid</option> 165 <option value="trapezoid">trapezoid</option>
167 <expand macro="list_string_san" name="integration_type"/> 166 <expand macro="list_string_san" name="integration_type"/>
168 </param> 167 </param>
169 <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)"> 168 <param name="baseline_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:baseline_type" type="select" 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)">
170 <option value="base_to_base" selected="true">base_to_base</option> 169 <option value="base_to_base" selected="true">base_to_base</option>
171 <option value="vertical_division">vertical_division</option> 170 <option value="vertical_division">vertical_division</option>
172 <option value="vertical_division_min">vertical_division_min</option> 171 <option value="vertical_division_min">vertical_division_min</option>
173 <option value="vertical_division_max">vertical_division_max</option> 172 <option value="vertical_division_max">vertical_division_max</option>
174 <expand macro="list_string_san" name="baseline_type"/> 173 <expand macro="list_string_san" name="baseline_type"/>
175 </param> 174 </param>
176 <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=""/> 175 <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=""/>
177 </section> 176 </section>
178 </section> 177 </section>
179 <section name="DIAScoring" title="" help="" expanded="false"> 178 <section name="DIAScoring" title="" help="" expanded="false">
180 <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=""/> 179 <param name="dia_extraction_window" argument="-algorithm:DIAScoring:dia_extraction_window" type="float" min="0.0" value="0.05" label="DIA extraction window in Th or ppm" help=""/>
181 <param name="dia_extraction_unit" argument="-algorithm:DIAScoring:dia_extraction_unit" type="select" optional="true" label="DIA extraction window unit" help=""> 180 <param name="dia_extraction_unit" argument="-algorithm:DIAScoring:dia_extraction_unit" type="select" label="DIA extraction window unit" help="">
182 <option value="Th" selected="true">Th</option> 181 <option value="Th" selected="true">Th</option>
183 <option value="ppm">ppm</option> 182 <option value="ppm">ppm</option>
184 <expand macro="list_string_san" name="dia_extraction_unit"/> 183 <expand macro="list_string_san" name="dia_extraction_unit"/>
185 </param> 184 </param>
186 <param name="dia_centroided" argument="-algorithm:DIAScoring:dia_centroided" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use centroided DIA data" help=""/> 185 <param name="dia_centroided" argument="-algorithm:DIAScoring:dia_centroided" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use centroided DIA data" help=""/>
187 <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=""/> 186 <param name="dia_byseries_intensity_min" argument="-algorithm:DIAScoring:dia_byseries_intensity_min" type="float" min="0.0" value="300.0" label="DIA b/y series minimum intensity to conside" help=""/>
188 <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=""/> 187 <param name="dia_byseries_ppm_diff" argument="-algorithm:DIAScoring:dia_byseries_ppm_diff" type="float" min="0.0" value="10.0" label="DIA b/y series minimal difference in ppm to conside" help=""/>
189 <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=""/> 188 <param name="dia_nr_isotopes" argument="-algorithm:DIAScoring:dia_nr_isotopes" type="integer" min="0" value="4" label="DIA number of isotopes to conside" help=""/>
190 <param name="dia_nr_charges" argument="-algorithm:DIAScoring:dia_nr_charges" type="integer" optional="true" min="0" value="4" label="DIA number of charges to conside" help=""/> 189 <param name="dia_nr_charges" argument="-algorithm:DIAScoring:dia_nr_charges" type="integer" min="0" value="4" label="DIA number of charges to conside" help=""/>
191 <param name="peak_before_mono_max_ppm_diff" argument="-algorithm:DIAScoring:peak_before_mono_max_ppm_diff" type="float" optional="true" min="0.0" value="20.0" label="DIA maximal difference in ppm to count a peak at lower m/z when searching for evidence that a peak might not be monoisotopic" help=""/> 190 <param name="peak_before_mono_max_ppm_diff" argument="-algorithm:DIAScoring:peak_before_mono_max_ppm_diff" type="float" min="0.0" value="20.0" label="DIA maximal difference in ppm to count a peak at lower m/z when searching for evidence that a peak might not be monoisotopic" help=""/>
192 </section> 191 </section>
193 <section name="EMGScoring" title="" help="" expanded="false"> 192 <section name="EMGScoring" title="" help="" expanded="false">
194 <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=""/> 193 <param name="interpolation_step" argument="-algorithm:EMGScoring:interpolation_step" type="float" value="0.2" label="Sampling rate for the interpolation of the model function" help=""/>
195 <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=""/> 194 <param name="tolerance_stdev_bounding_box" argument="-algorithm:EMGScoring:tolerance_stdev_bounding_box" type="float" 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=""/>
196 <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=""/> 195 <param name="max_iteration" argument="-algorithm:EMGScoring:max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help=""/>
197 <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=""/> 196 <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=""/>
198 <section name="statistics" title="" help="" expanded="false"> 197 <section name="statistics" title="" help="" expanded="false">
199 <param name="mean" argument="-algorithm:EMGScoring:statistics:mean" type="float" optional="true" value="1.0" label="Centroid position of the model" help=""/> 198 <param name="mean" argument="-algorithm:EMGScoring:statistics:mean" type="float" value="1.0" label="Centroid position of the model" help=""/>
200 <param name="variance" argument="-algorithm:EMGScoring:statistics:variance" type="float" optional="true" value="1.0" label="Variance of the model" help=""/> 199 <param name="variance" argument="-algorithm:EMGScoring:statistics:variance" type="float" value="1.0" label="Variance of the model" help=""/>
201 </section> 200 </section>
202 </section> 201 </section>
203 <section name="Scores" title="" help="" expanded="false"> 202 <section name="Scores" title="" help="" expanded="false">
204 <param name="use_shape_score" argument="-algorithm:Scores:use_shape_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)" help=""/> 203 <param name="use_shape_score" argument="-algorithm:Scores:use_shape_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)" help=""/>
205 <param name="use_coelution_score" argument="-algorithm:Scores:use_coelution_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation)" help=""/> 204 <param name="use_coelution_score" argument="-algorithm:Scores:use_coelution_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation)" help=""/>
222 <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=""/> 221 <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=""/>
223 <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=""/> 222 <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=""/>
224 </section> 223 </section>
225 </section> 224 </section>
226 <section name="peptideEstimation" title="Parameters for the peptide estimation (use -estimateBestPeptides to enable)" help="" expanded="false"> 225 <section name="peptideEstimation" title="Parameters for the peptide estimation (use -estimateBestPeptides to enable)" help="" expanded="false">
227 <param name="InitialQualityCutoff" argument="-peptideEstimation:InitialQualityCutoff" type="float" optional="true" value="0.5" label="The initial overall quality cutoff for a peak to be scored (range ca" help="-2 to 2)"/> 226 <param name="InitialQualityCutoff" argument="-peptideEstimation:InitialQualityCutoff" type="float" value="0.5" label="The initial overall quality cutoff for a peak to be scored (range ca" help="-2 to 2)"/>
228 <param name="OverallQualityCutoff" argument="-peptideEstimation:OverallQualityCutoff" type="float" optional="true" value="5.5" label="The overall quality cutoff for a peak to go into the retention time estimation (range ca" help="0 to 10)"/> 227 <param name="OverallQualityCutoff" argument="-peptideEstimation:OverallQualityCutoff" type="float" value="5.5" label="The overall quality cutoff for a peak to go into the retention time estimation (range ca" help="0 to 10)"/>
229 <param name="NrRTBins" argument="-peptideEstimation:NrRTBins" type="integer" optional="true" value="10" label="Number of RT bins to use to compute coverage" help="This option should be used to ensure that there is a complete coverage of the RT space (this should detect cases where only a part of the RT gradient is actually covered by normalization peptides)"/> 228 <param name="NrRTBins" argument="-peptideEstimation:NrRTBins" type="integer" value="10" label="Number of RT bins to use to compute coverage" help="This option should be used to ensure that there is a complete coverage of the RT space (this should detect cases where only a part of the RT gradient is actually covered by normalization peptides)"/>
230 <param name="MinPeptidesPerBin" argument="-peptideEstimation:MinPeptidesPerBin" type="integer" optional="true" value="1" label="Minimal number of peptides that are required for a bin to counted as 'covered'" help=""/> 229 <param name="MinPeptidesPerBin" argument="-peptideEstimation:MinPeptidesPerBin" type="integer" value="1" label="Minimal number of peptides that are required for a bin to counted as 'covered'" help=""/>
231 <param name="MinBinsFilled" argument="-peptideEstimation:MinBinsFilled" type="integer" optional="true" value="8" label="Minimal number of bins required to be covered" help=""/> 230 <param name="MinBinsFilled" argument="-peptideEstimation:MinBinsFilled" type="integer" value="8" label="Minimal number of bins required to be covered" help=""/>
232 </section> 231 </section>
233 <expand macro="adv_opts_macro"> 232 <expand macro="adv_opts_macro">
234 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 233 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
235 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 234 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
236 <expand macro="list_string_san" name="test"/> 235 <expand macro="list_string_san" name="test"/>
237 </param> 236 </param>
238 </expand> 237 </expand>
239 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 238 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
240 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 239 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
244 <data name="out" label="${tool.name} on ${on_string}: out" format="trafoxml"/> 243 <data name="out" label="${tool.name} on ${on_string}: out" format="trafoxml"/>
245 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 244 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
246 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 245 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
247 </data> 246 </data>
248 </outputs> 247 </outputs>
249 <tests><!-- TOPP_OpenSwathRTNormalizer_test_1 --> 248 <tests>
249 <!-- TOPP_OpenSwathRTNormalizer_test_1 -->
250 <test expect_num_outputs="2"> 250 <test expect_num_outputs="2">
251 <section name="adv_opts"> 251 <section name="adv_opts">
252 <param name="force" value="false"/> 252 <param name="force" value="false"/>
253 <param name="test" value="true"/> 253 <param name="test" value="true"/>
254 </section> 254 </section>
255 <conditional name="in_cond"> 255 <conditional name="in_cond">
256 <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/> 256 <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/>
257 </conditional> 257 </conditional>
258 <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/> 258 <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/>
259 <output name="out" file="OpenSwathRTNormalizer_1_output.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/> 259 <output name="out" value="OpenSwathRTNormalizer_1_output.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/>
260 <param name="min_rsq" value="0.95"/> 260 <param name="min_rsq" value="0.95"/>
261 <param name="min_coverage" value="0.6"/> 261 <param name="min_coverage" value="0.6"/>
262 <param name="estimateBestPeptides" value="false"/> 262 <param name="estimateBestPeptides" value="false"/>
263 <section name="RTNormalization"> 263 <section name="RTNormalization">
264 <param name="outlierMethod" value="iter_residual"/> 264 <param name="outlierMethod" value="iter_residual"/>
370 <output name="ctd_out" ftype="xml"> 370 <output name="ctd_out" ftype="xml">
371 <assert_contents> 371 <assert_contents>
372 <is_valid_xml/> 372 <is_valid_xml/>
373 </assert_contents> 373 </assert_contents>
374 </output> 374 </output>
375 <assert_stdout>
376 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
377 </assert_stdout>
375 </test> 378 </test>
376 <!-- TOPP_OpenSwathRTNormalizer_test_3 --> 379 <!-- TOPP_OpenSwathRTNormalizer_test_3 -->
377 <test expect_num_outputs="2"> 380 <test expect_num_outputs="2">
378 <section name="adv_opts"> 381 <section name="adv_opts">
379 <param name="force" value="false"/> 382 <param name="force" value="false"/>
381 </section> 384 </section>
382 <conditional name="in_cond"> 385 <conditional name="in_cond">
383 <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/> 386 <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/>
384 </conditional> 387 </conditional>
385 <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/> 388 <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/>
386 <output name="out" file="OpenSwathRTNormalizer_3_output.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/> 389 <output name="out" value="OpenSwathRTNormalizer_3_output.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/>
387 <param name="min_rsq" value="0.95"/> 390 <param name="min_rsq" value="0.95"/>
388 <param name="min_coverage" value="0.6"/> 391 <param name="min_coverage" value="0.6"/>
389 <param name="estimateBestPeptides" value="true"/> 392 <param name="estimateBestPeptides" value="true"/>
390 <section name="RTNormalization"> 393 <section name="RTNormalization">
391 <param name="outlierMethod" value="iter_residual"/> 394 <param name="outlierMethod" value="iter_residual"/>
497 <output name="ctd_out" ftype="xml"> 500 <output name="ctd_out" ftype="xml">
498 <assert_contents> 501 <assert_contents>
499 <is_valid_xml/> 502 <is_valid_xml/>
500 </assert_contents> 503 </assert_contents>
501 </output> 504 </output>
505 <assert_stdout>
506 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
507 </assert_stdout>
502 </test> 508 </test>
503 <!-- TOPP_OpenSwathRTNormalizer_test_4 --> 509 <!-- TOPP_OpenSwathRTNormalizer_test_4 -->
504 <test expect_num_outputs="2"> 510 <test expect_num_outputs="2">
505 <section name="adv_opts"> 511 <section name="adv_opts">
506 <param name="force" value="false"/> 512 <param name="force" value="false"/>
508 </section> 514 </section>
509 <conditional name="in_cond"> 515 <conditional name="in_cond">
510 <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/> 516 <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/>
511 </conditional> 517 </conditional>
512 <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/> 518 <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/>
513 <output name="out" file="OpenSwathRTNormalizer_4_output.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/> 519 <output name="out" value="OpenSwathRTNormalizer_4_output.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/>
514 <param name="min_rsq" value="0.95"/> 520 <param name="min_rsq" value="0.95"/>
515 <param name="min_coverage" value="0.6"/> 521 <param name="min_coverage" value="0.6"/>
516 <param name="estimateBestPeptides" value="false"/> 522 <param name="estimateBestPeptides" value="false"/>
517 <section name="RTNormalization"> 523 <section name="RTNormalization">
518 <param name="outlierMethod" value="iter_residual"/> 524 <param name="outlierMethod" value="iter_residual"/>
624 <output name="ctd_out" ftype="xml"> 630 <output name="ctd_out" ftype="xml">
625 <assert_contents> 631 <assert_contents>
626 <is_valid_xml/> 632 <is_valid_xml/>
627 </assert_contents> 633 </assert_contents>
628 </output> 634 </output>
635 <assert_stdout>
636 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
637 </assert_stdout>
629 </test> 638 </test>
630 </tests> 639 </tests>
631 <help><![CDATA[This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space. 640 <help><![CDATA[This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space.
632 641
633 642
634 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathRTNormalizer.html]]></help> 643 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathRTNormalizer.html]]></help>
635 <expand macro="references"/> 644 <expand macro="references"/>
636 </tool> 645 </tool>