openms_openswathanalyzer: OpenSwathAnalyzer.xml comparison

comparison OpenSwathAnalyzer.xml @ 14:9cdf469a3241 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906

author	galaxyp
date	Fri, 14 Jun 2024 21:38:17 +0000
parents	08488066d588
children

comparison

equal deleted inserted replaced

-:08488066d588
+:9cdf469a3241
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Targeted Experiments]-->
+<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
 <tool id="OpenSwathAnalyzer" name="OpenSwathAnalyzer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-<description>Picks peaks and finds features in an SWATH-MS or SRM experiment.</description>
+<description>Picks peaks and finds features in an SWATH-MS or SRM experiment</description>
 <macros>
 <token name="@EXECUTABLE@">OpenSwathAnalyzer</token>
 <import>macros.xml</import>
 </macros>
 <expand macro="requirements"/>
 @EXT_FOO@
 #import re
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir tr &&
-ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
+cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
 #if $rt_norm:
 mkdir rt_norm &&
-ln -s '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' &&
+cp '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' &&
 #end if
 mkdir out &&
 #if $swath_files_cond.swath_files:
 mkdir swath_files_cond.swath_files &&
 #if $swath_files_cond.swath_files_select == "no"
 mkdir ${' '.join(["'swath_files_cond.swath_files/%s'" % (i) for i, f in enumerate($swath_files_cond.swath_files) if f])} &&
-${' '.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])}
+${' '.join(["cp '%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])}
 #else
-ln -s '$swath_files_cond.swath_files' 'swath_files_cond.swath_files/${re.sub("[^\w\-_]", "_", $swath_files_cond.swath_files.element_identifier)}.$gxy2omsext($swath_files_cond.swath_files.ext)' &&
+cp '$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)' &&
 #end if
 #end if
 ## Main program call
 <configfiles>
 <inputs name="args_json" data_style="paths"/>
 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
 </configfiles>
 <inputs>
-<param argument="-in" type="data" format="mzml" optional="false" label="input file containing the chromatograms" help=" select mzml data sets(s)"/>
+<param argument="-in" type="data" format="mzml" label="input file containing the chromatograms" help=" select mzml data sets(s)"/>
-<param argument="-tr" type="data" format="traml" optional="false" label="transition file" help=" select traml data sets(s)"/>
+<param argument="-tr" type="data" format="traml" label="transition file" help=" select traml data sets(s)"/>
 <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)"/>
-<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=""/>
+<param 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=""/>
 <conditional name="swath_files_cond">
 <param name="swath_files_select" type="select" label="Run tool in batch mode for -swath_files">
 <option value="no">No: process all datasets jointly</option>
 <option value="yes">Yes: process each dataset in an independent job</option>
 </param>
 <when value="no">
 <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)"/>
 </when>
 <when value="yes">
-<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)"/>
+<param argument="-swath_files" type="data" format="mzml" 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)"/>
 </when>
 </conditional>
-<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=""/>
+<param argument="-min_upper_edge_dist" type="float" 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=""/>
 <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
-<param name="type" argument="-model:type" type="select" optional="true" label="Type of model" help="">
+<param name="type" argument="-model:type" type="select" label="Type of model" help="">
 <option value="linear" selected="true">linear</option>
 <option value="b_spline">b_spline</option>
 <option value="interpolated">interpolated</option>
 <option value="lowess">lowess</option>
 <expand macro="list_string_san" name="type"/>
 </param>
 <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'"/>
 </section>
 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-<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=""/>
+<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=""/>
-<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"/>
+<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"/>
-<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)"/>
+<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)"/>
-<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=""/>
+<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=""/>
 <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=""/>
-<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="">
+<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="">
 <option value="simple" selected="true">simple</option>
 <option value="resample">resample</option>
 <expand macro="list_string_san" name="spectrum_addition_method"/>
 </param>
-<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=""/>
+<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=""/>
-<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=""/>
+<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=""/>
-<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=""/>
+<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=""/>
-<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=""/>
+<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=""/>
-<param name="scoring_model" argument="-algorithm:scoring_model" type="select" optional="true" label="Scoring model to use" help="">
+<param name="scoring_model" argument="-algorithm:scoring_model" type="select" label="Scoring model to use" help="">
 <option value="default" selected="true">default</option>
 <option value="single_transition">single_transition</option>
 <expand macro="list_string_san" name="scoring_model"/>
 </param>
-<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)"/>
+<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)"/>
 <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=""/>
 <section name="TransitionGroupPicker" title="" help="" expanded="false">
-<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=""/>
+<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=""/>
-<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=""/>
+<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=""/>
-<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=""/>
+<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=""/>
-<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="">
+<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="">
 <option value="original" selected="true">original</option>
 <option value="smoothed">smoothed</option>
 <expand macro="list_string_san" name="peak_integration"/>
 </param>
-<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">
+<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">
 <option value="none" selected="true">none</option>
 <option value="original">original</option>
 <option value="exact">exact</option>
 <expand macro="list_string_san" name="background_subtraction"/>
 </param>
 <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"/>
 <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=""/>
 <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=""/>
-<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)"/>
+<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)"/>
-<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=""/>
+<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=""/>
-<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=""/>
+<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=""/>
 <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"/>
 <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"/>
 <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=""/>
-<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="">
+<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="">
 <option value="largest" selected="true">largest</option>
 <option value="widest">widest</option>
 <expand macro="list_string_san" name="boundary_selection_method"/>
 </param>
 <section name="PeakPickerMRM" title="" help="" expanded="false">
-<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"/>
+<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"/>
-<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=""/>
+<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=""/>
-<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=""/>
+<param name="gauss_width" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help=""/>
 <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=""/>
-<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"/>
+<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"/>
-<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"/>
+<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"/>
-<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=""/>
+<param name="sn_win_len" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help=""/>
-<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=""/>
+<param name="sn_bin_count" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help=""/>
 <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=""/>
 <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=""/>
-<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="">
+<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="">
 <option value="legacy">legacy</option>
 <option value="corrected" selected="true">corrected</option>
 <option value="crawdad">crawdad</option>
 <expand macro="list_string_san" name="method"/>
 </param>
 </section>
 <section name="PeakIntegrator" title="" help="" expanded="false">
-<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="">
+<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="">
 <option value="intensity_sum" selected="true">intensity_sum</option>
 <option value="simpson">simpson</option>
 <option value="trapezoid">trapezoid</option>
 <expand macro="list_string_san" name="integration_type"/>
 </param>
-<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)">
+<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)">
 <option value="base_to_base" selected="true">base_to_base</option>
 <option value="vertical_division">vertical_division</option>
 <option value="vertical_division_min">vertical_division_min</option>
 <option value="vertical_division_max">vertical_division_max</option>
 <expand macro="list_string_san" name="baseline_type"/>
 </param>
 <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=""/>
 </section>
 </section>
 <section name="DIAScoring" title="" help="" expanded="false">
-<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=""/>
+<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=""/>
-<param name="dia_extraction_unit" argument="-algorithm:DIAScoring:dia_extraction_unit" type="select" optional="true" label="DIA extraction window unit" help="">
+<param name="dia_extraction_unit" argument="-algorithm:DIAScoring:dia_extraction_unit" type="select" label="DIA extraction window unit" help="">
 <option value="Th" selected="true">Th</option>
 <option value="ppm">ppm</option>
 <expand macro="list_string_san" name="dia_extraction_unit"/>
 </param>
 <param name="dia_centroided" argument="-algorithm:DIAScoring:dia_centroided" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use centroided DIA data" help=""/>
-<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=""/>
+<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=""/>
-<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=""/>
+<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=""/>
-<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=""/>
+<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=""/>
-<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=""/>
+<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=""/>
-<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=""/>
+<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=""/>
 </section>
 <section name="EMGScoring" title="" help="" expanded="false">
-<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=""/>
+<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=""/>
-<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=""/>
+<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=""/>
-<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=""/>
+<param name="max_iteration" argument="-algorithm:EMGScoring:max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help=""/>
 <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=""/>
 <section name="statistics" title="" help="" expanded="false">
-<param name="mean" argument="-algorithm:EMGScoring:statistics:mean" type="float" optional="true" value="1.0" label="Centroid position of the model" help=""/>
+<param name="mean" argument="-algorithm:EMGScoring:statistics:mean" type="float" value="1.0" label="Centroid position of the model" help=""/>
-<param name="variance" argument="-algorithm:EMGScoring:statistics:variance" type="float" optional="true" value="1.0" label="Variance of the model" help=""/>
+<param name="variance" argument="-algorithm:EMGScoring:statistics:variance" type="float" value="1.0" label="Variance of the model" help=""/>
 </section>
 </section>
 <section name="Scores" title="" help="" expanded="false">
 <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=""/>
 <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=""/>
 <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=""/>
 </section>
 </section>
 <expand macro="adv_opts_macro">
 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-<param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+<param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
 <expand macro="list_string_san" name="test"/>
 </param>
 </expand>
 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
 </data>
 </outputs>
-<tests><!-- TOPP_OpenSwathAnalyzer_test_1 -->
+<tests>
+<!-- TOPP_OpenSwathAnalyzer_test_1 -->
 <test expect_num_outputs="2">
 <section name="adv_opts">
 <param name="force" value="false"/>
 <param name="test" value="true"/>
 </section>
 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
-<output name="out" file="OpenSwathAnalyzer_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+<output name="out" value="OpenSwathAnalyzer_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
 <param name="no_strict" value="false"/>
 <param name="min_upper_edge_dist" value="0.0"/>
 <section name="model">
 <param name="type" value="linear"/>
 <param name="symmetric_regression" value="false"/>
 <output name="ctd_out" ftype="xml">
 <assert_contents>
 <is_valid_xml/>
 </assert_contents>
 </output>
+<assert_stdout>
+<has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+</assert_stdout>
 </test>
 <!-- TOPP_OpenSwathAnalyzer_test_2 -->
 <test expect_num_outputs="2">
 <section name="adv_opts">
 <param name="force" value="false"/>
 <param name="test" value="true"/>
 </section>
 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
-<output name="out" file="OpenSwathAnalyzer_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+<output name="out" value="OpenSwathAnalyzer_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
 <param name="no_strict" value="false"/>
 <conditional name="swath_files_cond">
 <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
 </conditional>
 <param name="min_upper_edge_dist" value="0.0"/>
 <output name="ctd_out" ftype="xml">
 <assert_contents>
 <is_valid_xml/>
 </assert_contents>
 </output>
+<assert_stdout>
+<has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+</assert_stdout>
 </test>
 <!-- TOPP_OpenSwathAnalyzer_test_5_mod -->
 <test expect_num_outputs="2">
 <section name="adv_opts">
 <param name="force" value="false"/>
 <param name="test" value="true"/>
 </section>
 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
 <param name="tr" value="OpenSwathAnalyzer_mod_input.TraML"/>
-<output name="out" file="OpenSwathAnalyzer_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+<output name="out" value="OpenSwathAnalyzer_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
 <param name="no_strict" value="false"/>
 <conditional name="swath_files_cond">
 <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
 </conditional>
 <param name="min_upper_edge_dist" value="0.0"/>
 <output name="ctd_out" ftype="xml">
 <assert_contents>
 <is_valid_xml/>
 </assert_contents>
 </output>
+<assert_stdout>
+<has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+</assert_stdout>
 </test>
 <!-- TOPP_OpenSwathAnalyzer_test_6_nomod -->
 <test expect_num_outputs="2">
 <section name="adv_opts">
 <param name="force" value="false"/>
 <param name="test" value="true"/>
 </section>
 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
-<output name="out" file="OpenSwathAnalyzer_6_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+<output name="out" value="OpenSwathAnalyzer_6_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
 <param name="no_strict" value="false"/>
 <conditional name="swath_files_cond">
 <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
 </conditional>
 <param name="min_upper_edge_dist" value="0.0"/>
 <output name="ctd_out" ftype="xml">
 <assert_contents>
 <is_valid_xml/>
 </assert_contents>
 </output>
+<assert_stdout>
+<has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+</assert_stdout>
 </test>
 <!-- TOPP_OpenSwathAnalyzer_test_7_backgroundSubtraction -->
 <test expect_num_outputs="2">
 <section name="adv_opts">
 <param name="force" value="false"/>
 <param name="test" value="true"/>
 </section>
 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
-<output name="out" file="OpenSwathAnalyzer_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+<output name="out" value="OpenSwathAnalyzer_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
 <param name="no_strict" value="false"/>
 <param name="min_upper_edge_dist" value="0.0"/>
 <section name="model">
 <param name="type" value="linear"/>
 <param name="symmetric_regression" value="false"/>
 <output name="ctd_out" ftype="xml">
 <assert_contents>
 <is_valid_xml/>
 </assert_contents>
 </output>
+<assert_stdout>
+<has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+</assert_stdout>
 </test>
 <!-- TOPP_OpenSwathAnalyzer_test_8 -->
 <test expect_num_outputs="2">
 <section name="adv_opts">
 <param name="force" value="false"/>
 <param name="test" value="true"/>
 </section>
 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
-<output name="out" file="OpenSwathAnalyzer_8_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+<output name="out" value="OpenSwathAnalyzer_8_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
 <param name="no_strict" value="false"/>
 <param name="min_upper_edge_dist" value="0.0"/>
 <section name="model">
 <param name="type" value="linear"/>
 <param name="symmetric_regression" value="false"/>
 <output name="ctd_out" ftype="xml">
 <assert_contents>
 <is_valid_xml/>
 </assert_contents>
 </output>
+<assert_stdout>
+<has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+</assert_stdout>
 </test>
 <!-- TOPP_OpenSwathAnalyzer_test_9 -->
 <test expect_num_outputs="2">
 <section name="adv_opts">
 <param name="force" value="false"/>
 <param name="test" value="true"/>
 </section>
 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
-<output name="out" file="OpenSwathAnalyzer_9_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+<output name="out" value="OpenSwathAnalyzer_9_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
 <param name="no_strict" value="false"/>
 <param name="min_upper_edge_dist" value="0.0"/>
 <section name="model">
 <param name="type" value="linear"/>
 <param name="symmetric_regression" value="false"/>
 <output name="ctd_out" ftype="xml">
 <assert_contents>
 <is_valid_xml/>
 </assert_contents>
 </output>
+<assert_stdout>
+<has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+</assert_stdout>
 </test>
 <!-- TOPP_OpenSwathAnalyzer_test_10 -->
 <test expect_num_outputs="2">
 <section name="adv_opts">
 <param name="force" value="false"/>
 <param name="test" value="true"/>
 </section>
 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
-<output name="out" file="OpenSwathAnalyzer_10_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+<output name="out" value="OpenSwathAnalyzer_10_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
 <param name="no_strict" value="false"/>
 <param name="min_upper_edge_dist" value="0.0"/>
 <section name="model">
 <param name="type" value="linear"/>
 <param name="symmetric_regression" value="false"/>
 <output name="ctd_out" ftype="xml">
 <assert_contents>
 <is_valid_xml/>
 </assert_contents>
 </output>
+<assert_stdout>
+<has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+</assert_stdout>
 </test>
 <!-- TOPP_OpenSwathAnalyzer_test_11 -->
 <test expect_num_outputs="2">
 <section name="adv_opts">
 <param name="force" value="false"/>
 <param name="test" value="true"/>
 </section>
 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
-<output name="out" file="OpenSwathAnalyzer_11_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+<output name="out" value="OpenSwathAnalyzer_11_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
 <param name="no_strict" value="false"/>
 <param name="min_upper_edge_dist" value="0.0"/>
 <section name="model">
 <param name="type" value="linear"/>
 <param name="symmetric_regression" value="false"/>
 <output name="ctd_out" ftype="xml">
 <assert_contents>
 <is_valid_xml/>
 </assert_contents>
 </output>
+<assert_stdout>
+<has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+</assert_stdout>
 </test>
 </tests>
 <help><![CDATA[Picks peaks and finds features in an SWATH-MS or SRM experiment.
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathAnalyzer.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathAnalyzer.html]]></help>
 <expand macro="references"/>
 </tool>

Mercurial > repos > galaxyp > openms_openswathanalyzer

comparison OpenSwathAnalyzer.xml @ 14:9cdf469a3241 draft default tip