Mercurial > repos > galaxyp > openms_openswathrtnormalizer
diff OpenSwathRTNormalizer.xml @ 13:d31426ef20f6 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:19:38 +0000 |
| parents | 7d73049c05c0 |
| children | 0eaf3d4219cf |
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--- a/OpenSwathRTNormalizer.xml Fri Nov 06 20:21:59 2020 +0000 +++ b/OpenSwathRTNormalizer.xml Thu Dec 01 19:19:38 2022 +0000 @@ -1,13 +1,11 @@ <?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]--> -<tool id="OpenSwathRTNormalizer" name="OpenSwathRTNormalizer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="OpenSwathRTNormalizer" name="OpenSwathRTNormalizer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <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> <macros> <token name="@EXECUTABLE@">OpenSwathRTNormalizer</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -16,8 +14,13 @@ #import re ## Preprocessing -mkdir in && -${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } +mkdir in_cond.in && +#if $in_cond.in_select == "no" +mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && +${' '.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])} +#else +ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +#end if mkdir tr && ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && mkdir out && @@ -33,7 +36,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && @EXECUTABLE@ -ini @EXECUTABLE@.ctd -in -${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} +#if $in_cond.in_select == "no" +${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +#else +'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' +#end if -tr 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' -out @@ -53,19 +60,30 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param name="in" argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input files separated by blank" help=" select mzml data sets(s)"/> - <param name="tr" 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)"/> - <param name="rt_norm" argument="-rt_norm" type="data" format="trafoxml" optional="true" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help=" select trafoxml data sets(s)"/> - <param name="min_rsq" argument="-min_rsq" type="float" optional="true" value="0.95" label="Minimum r-squared of RT peptides regression" help=""/> - <param name="min_coverage" argument="-min_coverage" type="float" optional="true" value="0.6" label="Minimum relative amount of RT peptides to keep" help=""/> - <param name="estimateBestPeptides" 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)"/> + <conditional name="in_cond"> + <param name="in_select" type="select" label="Run tool in batch mode for -in"> + <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="-in" type="data" format="mzml" multiple="true" optional="false" label="Input files separated by blank" help=" select mzml data sets(s)"/> + </when> + <when value="yes"> + <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="Input files separated by blank" help=" select mzml data sets(s)"/> + </when> + </conditional> + <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)"/> + <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 argument="-min_rsq" type="float" optional="true" value="0.95" label="Minimum r-squared of RT peptides regression" help=""/> + <param argument="-min_coverage" type="float" optional="true" value="0.6" label="Minimum relative amount of RT peptides to keep" help=""/> + <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)"/> <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"> - <param name="outlierMethod" argument="-RTNormalization:outlierMethod" display="radio" type="select" optional="false" 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)"> + <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)"> <option value="iter_residual" selected="true">iter_residual</option> <option value="iter_jackknife">iter_jackknife</option> <option value="ransac">ransac</option> <option value="none">none</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="outlierMethod"/> </param> <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"/> <param name="RANSACMaxIterations" argument="-RTNormalization:RANSACMaxIterations" type="integer" optional="true" value="1000" label="Maximum iterations for the RANSAC outlier detection algorithm" help=""/> @@ -78,38 +96,36 @@ <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="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="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" display="radio" type="select" optional="false" 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" optional="true" 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"/> + <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="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="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_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="scoring_model" argument="-algorithm:scoring_model" display="radio" type="select" optional="false" label="Scoring model to use" help=""> + <param name="scoring_model" argument="-algorithm:scoring_model" type="select" optional="true" 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"/> + <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="strict" argument="-algorithm:strict" type="text" optional="true" value="true" label="Whether to error (true) or skip (false) if a transition in a transition group does not have a corresponding chromatogram" help=""> - <expand macro="list_string_san"/> - </param> + <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_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="min_peak_width" argument="-algorithm:TransitionGroupPicker:min_peak_width" type="float" optional="true" value="-1.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/> - <param name="peak_integration" argument="-algorithm:TransitionGroupPicker:peak_integration" display="radio" type="select" optional="false" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help=""> + <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="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=""> <option value="original" selected="true">original</option> <option value="smoothed">smoothed</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="peak_integration"/> </param> - <param name="background_subtraction" argument="-algorithm:TransitionGroupPicker:background_subtraction" display="radio" type="select" optional="false" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation"> + <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"> <option value="none" selected="true">none</option> <option value="original">original</option> <option value="exact">exact</option> - <expand macro="list_string_san"/> + <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=""/> @@ -120,10 +136,10 @@ <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" display="radio" type="select" optional="false" 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" optional="true" 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"/> + <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"/> @@ -136,36 +152,36 @@ <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="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" display="radio" type="select" optional="false" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help=""> + <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=""> <option value="legacy">legacy</option> <option value="corrected" selected="true">corrected</option> <option value="crawdad">crawdad</option> - <expand macro="list_string_san"/> + <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" display="radio" type="select" optional="false" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help=""> + <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=""> <option value="intensity_sum" selected="true">intensity_sum</option> <option value="simpson">simpson</option> <option value="trapezoid">trapezoid</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="integration_type"/> </param> - <param name="baseline_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:baseline_type" display="radio" type="select" optional="false" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)"> + <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)"> <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"/> + <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_unit" argument="-algorithm:DIAScoring:dia_extraction_unit" display="radio" type="select" optional="false" label="DIA extraction window unit" help=""> + <param name="dia_extraction_unit" argument="-algorithm:DIAScoring:dia_extraction_unit" type="select" optional="true" label="DIA extraction window unit" help=""> <option value="Th" selected="true">Th</option> <option value="ppm">ppm</option> - <expand macro="list_string_san"/> + <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=""/> @@ -178,6 +194,7 @@ <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="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="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="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="variance" argument="-algorithm:EMGScoring:statistics:variance" type="float" optional="true" value="1.0" label="Variance of the model" help=""/> @@ -202,6 +219,8 @@ <param name="use_ms1_fullscan" argument="-algorithm:Scores:use_ms1_fullscan" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)" help=""/> <param name="use_ms1_mi" argument="-algorithm:Scores:use_ms1_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the MS1 MI score" help=""/> <param name="use_uis_scores" argument="-algorithm:Scores:use_uis_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use UIS scores for peptidoform identification" help=""/> + <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=""/> + <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 & manhattan) across product transitions (based on ID if annotated or averagine)" help=""/> </section> </section> <section name="peptideEstimation" title="Parameters for the peptide estimation (use -estimateBestPeptides to enable)" help="" expanded="false"> @@ -212,9 +231,9 @@ <param name="MinBinsFilled" argument="-peptideEstimation:MinBinsFilled" type="integer" optional="true" value="8" label="Minimal number of bins required to be covered" help=""/> </section> <expand macro="adv_opts_macro"> - <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> - <expand macro="list_string_san"/> + <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=""> + <expand macro="list_string_san" name="test"/> </param> </expand> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> @@ -227,13 +246,391 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_OpenSwathRTNormalizer"/> - <expand macro="manutest_OpenSwathRTNormalizer"/> + <tests><!-- TOPP_OpenSwathRTNormalizer_test_1 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <conditional name="in_cond"> + <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/> + </conditional> + <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/> + <output name="out" file="OpenSwathRTNormalizer_1_output.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="estimateBestPeptides" value="false"/> + <section name="RTNormalization"> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + </section> + <section name="algorithm"> + <param name="stop_report_after_feature" value="-1"/> + <param name="rt_extraction_window" value="-1.0"/> + <param name="rt_normalization_factor" value="1.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="stop_after_intensity_ratio" value="0.0001"/> + <param name="min_peak_width" value="0.001"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="false"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="1.0"/> + <param name="minimal_quality" value="-10000.0"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="15"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="50.0"/> + <param name="use_gauss" value="true"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="1.0"/> + <param name="sn_win_len" value="1000.0"/> + <param name="sn_bin_count" value="30"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="false"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="interpolation_step" value="0.2"/> + <param name="tolerance_stdev_bounding_box" value="3.0"/> + <param name="max_iteration" value="500"/> + <param name="init_mom" value="false"/> + <section name="statistics"> + <param name="mean" value="1.0"/> + <param name="variance" value="1.0"/> + </section> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_elution_model_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="false"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="false"/> + <param name="use_uis_scores" value="false"/> + <param name="use_ionseries_scores" value="true"/> + <param name="use_ms2_isotope_scores" value="true"/> + </section> + </section> + <section name="peptideEstimation"> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_OpenSwathRTNormalizer_test_3 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <conditional name="in_cond"> + <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/> + </conditional> + <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/> + <output name="out" file="OpenSwathRTNormalizer_3_output.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="estimateBestPeptides" value="true"/> + <section name="RTNormalization"> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + </section> + <section name="algorithm"> + <param name="stop_report_after_feature" value="-1"/> + <param name="rt_extraction_window" value="-1.0"/> + <param name="rt_normalization_factor" value="1.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="stop_after_intensity_ratio" value="0.0001"/> + <param name="min_peak_width" value="0.001"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="false"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="1.0"/> + <param name="minimal_quality" value="-10000.0"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="15"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="50.0"/> + <param name="use_gauss" value="true"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="1.0"/> + <param name="sn_win_len" value="1000.0"/> + <param name="sn_bin_count" value="30"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="false"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="interpolation_step" value="0.2"/> + <param name="tolerance_stdev_bounding_box" value="3.0"/> + <param name="max_iteration" value="500"/> + <param name="init_mom" value="false"/> + <section name="statistics"> + <param name="mean" value="1.0"/> + <param name="variance" value="1.0"/> + </section> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_elution_model_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="false"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="false"/> + <param name="use_uis_scores" value="false"/> + <param name="use_ionseries_scores" value="true"/> + <param name="use_ms2_isotope_scores" value="true"/> + </section> + </section> + <section name="peptideEstimation"> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="3"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="3"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_OpenSwathRTNormalizer_test_4 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <conditional name="in_cond"> + <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/> + </conditional> + <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/> + <output name="out" file="OpenSwathRTNormalizer_4_output.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/> + <param name="min_rsq" value="0.95"/> + <param name="min_coverage" value="0.6"/> + <param name="estimateBestPeptides" value="false"/> + <section name="RTNormalization"> + <param name="outlierMethod" value="iter_residual"/> + <param name="useIterativeChauvenet" value="false"/> + <param name="RANSACMaxIterations" value="1000"/> + <param name="RANSACMaxPercentRTThreshold" value="3"/> + <param name="RANSACSamplingSize" value="10"/> + </section> + <section name="algorithm"> + <param name="stop_report_after_feature" value="-1"/> + <param name="rt_extraction_window" value="-1.0"/> + <param name="rt_normalization_factor" value="1.0"/> + <param name="quantification_cutoff" value="0.0"/> + <param name="write_convex_hull" value="false"/> + <param name="spectrum_addition_method" value="simple"/> + <param name="add_up_spectra" value="1"/> + <param name="spacing_for_spectra_resampling" value="0.005"/> + <param name="uis_threshold_sn" value="-1"/> + <param name="uis_threshold_peak_area" value="0"/> + <param name="scoring_model" value="default"/> + <param name="im_extra_drift" value="0.0"/> + <param name="strict" value="true"/> + <section name="TransitionGroupPicker"> + <param name="stop_after_feature" value="-1"/> + <param name="stop_after_intensity_ratio" value="0.0001"/> + <param name="min_peak_width" value="0.001"/> + <param name="peak_integration" value="original"/> + <param name="background_subtraction" value="none"/> + <param name="recalculate_peaks" value="false"/> + <param name="use_precursors" value="false"/> + <param name="use_consensus" value="true"/> + <param name="recalculate_peaks_max_z" value="1.0"/> + <param name="minimal_quality" value="-10000.0"/> + <param name="resample_boundary" value="15.0"/> + <param name="compute_peak_quality" value="false"/> + <param name="compute_peak_shape_metrics" value="false"/> + <param name="compute_total_mi" value="false"/> + <param name="boundary_selection_method" value="largest"/> + <section name="PeakPickerMRM"> + <param name="sgolay_frame_length" value="15"/> + <param name="sgolay_polynomial_order" value="3"/> + <param name="gauss_width" value="50.0"/> + <param name="use_gauss" value="true"/> + <param name="peak_width" value="-1.0"/> + <param name="signal_to_noise" value="1.0"/> + <param name="sn_win_len" value="1000.0"/> + <param name="sn_bin_count" value="30"/> + <param name="write_sn_log_messages" value="false"/> + <param name="remove_overlapping_peaks" value="false"/> + <param name="method" value="corrected"/> + </section> + <section name="PeakIntegrator"> + <param name="integration_type" value="intensity_sum"/> + <param name="baseline_type" value="base_to_base"/> + <param name="fit_EMG" value="false"/> + </section> + </section> + <section name="DIAScoring"> + <param name="dia_extraction_window" value="0.05"/> + <param name="dia_extraction_unit" value="Th"/> + <param name="dia_centroided" value="false"/> + <param name="dia_byseries_intensity_min" value="300.0"/> + <param name="dia_byseries_ppm_diff" value="10.0"/> + <param name="dia_nr_isotopes" value="4"/> + <param name="dia_nr_charges" value="4"/> + <param name="peak_before_mono_max_ppm_diff" value="20.0"/> + </section> + <section name="EMGScoring"> + <param name="interpolation_step" value="0.2"/> + <param name="tolerance_stdev_bounding_box" value="3.0"/> + <param name="max_iteration" value="500"/> + <param name="init_mom" value="false"/> + <section name="statistics"> + <param name="mean" value="1.0"/> + <param name="variance" value="1.0"/> + </section> + </section> + <section name="Scores"> + <param name="use_shape_score" value="true"/> + <param name="use_coelution_score" value="true"/> + <param name="use_rt_score" value="true"/> + <param name="use_library_score" value="true"/> + <param name="use_elution_model_score" value="true"/> + <param name="use_intensity_score" value="true"/> + <param name="use_nr_peaks_score" value="true"/> + <param name="use_total_xic_score" value="true"/> + <param name="use_total_mi_score" value="false"/> + <param name="use_sn_score" value="true"/> + <param name="use_mi_score" value="false"/> + <param name="use_dia_scores" value="true"/> + <param name="use_ms1_correlation" value="false"/> + <param name="use_sonar_scores" value="false"/> + <param name="use_ion_mobility_scores" value="false"/> + <param name="use_ms1_fullscan" value="false"/> + <param name="use_ms1_mi" value="false"/> + <param name="use_uis_scores" value="false"/> + <param name="use_ionseries_scores" value="true"/> + <param name="use_ms2_isotope_scores" value="true"/> + </section> + </section> + <section name="peptideEstimation"> + <param name="InitialQualityCutoff" value="0.5"/> + <param name="OverallQualityCutoff" value="5.5"/> + <param name="NrRTBins" value="10"/> + <param name="MinPeptidesPerBin" value="1"/> + <param name="MinBinsFilled" value="8"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> </tests> <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. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_OpenSwathRTNormalizer.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathRTNormalizer.html]]></help> <expand macro="references"/> </tool>