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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="OpenSwathRTNormalizer" name="OpenSwathRTNormalizer" version="1.12.0">
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3 <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>
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4 <macros>
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5 <token name="@EXECUTABLE@">OpenSwathRTNormalizer</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>OpenSwathRTNormalizer
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11
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12 -in ${param_in}
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13 -tr ${param_tr}
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14 -out ${param_out}
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15 -rt_norm ${param_rt_norm}
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16 -min_rsq ${param_min_rsq}
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17 -min_coverage ${param_min_coverage}
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18 ${param_estimateBestPeptides}
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19 -threads \${GALAXY_SLOTS:-24}
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20 -algorithm:stop_report_after_feature ${param_stop_report_after_feature}
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21 -algorithm:rt_extraction_window ${param_rt_extraction_window}
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22 -algorithm:rt_normalization_factor ${param_rt_normalization_factor}
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23 -algorithm:TransitionGroupPicker:stop_after_feature ${param_stop_after_feature}
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24 -algorithm:TransitionGroupPicker:stop_after_intensity_ratio ${param_stop_after_intensity_ratio}
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25 -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length ${param_sgolay_frame_length}
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26 -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order ${param_sgolay_polynomial_order}
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27 -algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width ${param_gauss_width}
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28 -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss ${param_use_gauss}
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29 -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width ${param_peak_width}
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30 -algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise ${param_signal_to_noise}
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31 -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len ${param_sn_win_len}
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32 -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count ${param_sn_bin_count}
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33 ${param_remove_overlapping_peaks}
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34 -algorithm:TransitionGroupPicker:PeakPickerMRM:method ${param_method}
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35 -algorithm:DIAScoring:dia_extraction_window ${param_dia_extraction_window}
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36 ${param_dia_centroided}
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37 -algorithm:DIAScoring:dia_byseries_intensity_min ${param_dia_byseries_intensity_min}
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38 -algorithm:DIAScoring:dia_byseries_ppm_diff ${param_dia_byseries_ppm_diff}
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39 -algorithm:DIAScoring:dia_nr_isotopes ${param_dia_nr_isotopes}
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40 -algorithm:DIAScoring:dia_nr_charges ${param_dia_nr_charges}
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41 -algorithm:DIAScoring:peak_before_mono_max_ppm_diff ${param_peak_before_mono_max_ppm_diff}
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42 -outlierDetection:outlierMethod ${param_outlierMethod}
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43 -outlierDetection:useIterativeChauvenet ${param_useIterativeChauvenet}
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44 -outlierDetection:RANSACMaxIterations ${param_RANSACMaxIterations}
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45 -outlierDetection:RANSACMaxPercentRTThreshold ${param_RANSACMaxPercentRTThreshold}
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46 -outlierDetection:RANSACSamplingSize ${param_RANSACSamplingSize}
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47 -peptideEstimation:InitialQualityCutoff ${param_InitialQualityCutoff}
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48 -peptideEstimation:OverallQualityCutoff ${param_OverallQualityCutoff}
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49 -peptideEstimation:NrRTBins ${param_NrRTBins}
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50 -peptideEstimation:MinPeptidesPerBin ${param_MinPeptidesPerBin}
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51 -peptideEstimation:MinBinsFilled ${param_MinBinsFilled}
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52 #if $adv_opts.adv_opts_selector=='advanced':
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53 -algorithm:quantification_cutoff ${adv_opts.param_quantification_cutoff}
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54 ${adv_opts.param_write_convex_hull}
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55 -algorithm:add_up_spectra ${adv_opts.param_add_up_spectra}
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56 -algorithm:spacing_for_spectra_resampling ${adv_opts.param_spacing_for_spectra_resampling}
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57 -algorithm:TransitionGroupPicker:min_peak_width ${adv_opts.param_min_peak_width}
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58 -algorithm:TransitionGroupPicker:background_subtraction ${adv_opts.param_background_subtraction}
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59 -algorithm:TransitionGroupPicker:recalculate_peaks ${adv_opts.param_recalculate_peaks}
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60 -algorithm:TransitionGroupPicker:recalculate_peaks_max_z ${adv_opts.param_recalculate_peaks_max_z}
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61 -algorithm:TransitionGroupPicker:minimal_quality ${adv_opts.param_minimal_quality}
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62 -algorithm:TransitionGroupPicker:compute_peak_quality ${adv_opts.param_compute_peak_quality}
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63 -algorithm:EMGScoring:interpolation_step ${adv_opts.param_interpolation_step}
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64 -algorithm:EMGScoring:tolerance_stdev_bounding_box ${adv_opts.param_tolerance_stdev_bounding_box}
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65 -algorithm:EMGScoring:max_iteration ${adv_opts.param_max_iteration}
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66 -algorithm:EMGScoring:statistics:mean ${adv_opts.param_mean}
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67 -algorithm:EMGScoring:statistics:variance ${adv_opts.param_variance}
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68 ${adv_opts.param_use_shape_score}
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69 ${adv_opts.param_use_coelution_score}
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70 ${adv_opts.param_use_rt_score}
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71 ${adv_opts.param_use_library_score}
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72 ${adv_opts.param_use_elution_model_score}
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73 ${adv_opts.param_use_intensity_score}
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74 ${adv_opts.param_use_nr_peaks_score}
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75 ${adv_opts.param_use_total_xic_score}
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76 ${adv_opts.param_use_sn_score}
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77 ${adv_opts.param_use_dia_scores}
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78 ${adv_opts.param_use_ms1_correlation}
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79 ${adv_opts.param_use_ms1_fullscan}
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80 #end if
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81 </command>
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82 <inputs>
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83 <param name="param_in" type="data" format="mzML" optional="False" size="20" label="Input files separated by blank" help="(-in)"/>
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84 <param name="param_tr" type="data" format="tabular" optional="False" label="transition file with the RT peptides ('TraML' or 'csv')" help="(-tr)"/>
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85 <param name="param_rt_norm" type="data" format="" optional="True" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help="(-rt_norm)"/>
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86 <param name="param_min_rsq" type="float" value="0.95" label="Minimum r-squared of RT peptides regression" help="(-min_rsq)"/>
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87 <param name="param_min_coverage" type="float" value="0.6" label="Minimum relative amount of RT peptides to keep" help="(-min_coverage)"/>
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88 <param name="param_estimateBestPeptides" type="boolean" truevalue="-estimateBestPeptides true" falsevalue="-estimateBestPeptides false" checked="false" optional="True" label="Whether the algorithms should try to choose the best peptides based on their peak shape for normalization. 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)." help="(-estimateBestPeptides)"/>
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89 <param name="param_stop_report_after_feature" type="integer" value="-1" label="Stop reporting after feature (ordered by quality; -1 means do not stop)." help="(-stop_report_after_feature)"/>
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90 <param name="param_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). For this to work, the TraML input file needs to contain normalized RT values." help="(-rt_extraction_window)"/>
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91 <param name="param_rt_normalization_factor" type="float" value="1.0" label="The normalized RT is expected to be between 0 and 1. If your normalized RT has a different range, pass this here (e.g. it goes from 0 to 100, set this value to 100)" help="(-rt_normalization_factor)"/>
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92 <param name="param_stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)." help="(-stop_after_feature)"/>
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93 <param name="param_stop_after_intensity_ratio" type="float" value="0.0001" label="Stop after reaching intensity ratio" help="(-stop_after_intensity_ratio)"/>
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94 <param name="param_sgolay_frame_length" type="integer" value="15" label="The number of subsequent data points used for smoothing.#br#This number has to be uneven. If it is not, 1 will be added." help="(-sgolay_frame_length)"/>
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95 <param name="param_sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted." help="(-sgolay_polynomial_order)"/>
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96 <param name="param_gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size." help="(-gauss_width)"/>
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97 <param name="param_use_gauss" type="text" size="20" value="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help="(-use_gauss)"/>
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98 <param name="param_peak_width" type="float" value="40.0" label="Force a certain minimal peak_width on the data (e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off." help="(-peak_width)"/>
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99 <param name="param_signal_to_noise" type="float" min="0.0" optional="True" value="1.0" label="Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured." help="(-signal_to_noise)"/>
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100 <param name="param_sn_win_len" type="float" value="1000.0" label="Signal to noise window length." help="(-sn_win_len)"/>
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101 <param name="param_sn_bin_count" type="integer" value="30" label="Signal to noise bin count." help="(-sn_bin_count)"/>
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102 <param name="param_remove_overlapping_peaks" type="boolean" truevalue="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks true" falsevalue="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks false" checked="false" optional="True" label="Try to remove overlapping peaks during peak picking" help="(-remove_overlapping_peaks)"/>
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103 <param name="param_method" type="select" optional="True" value="legacy" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy, corrected picking or Crawdad)." help="(-method)">
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104 <option value="legacy">legacy</option>
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105 <option value="corrected">corrected</option>
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106 <option value="crawdad">crawdad</option>
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107 </param>
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108 <param name="param_dia_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="DIA extraction window in Th." help="(-dia_extraction_window)"/>
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109 <param name="param_dia_centroided" type="boolean" truevalue="-algorithm:DIAScoring:dia_centroided true" falsevalue="-algorithm:DIAScoring:dia_centroided false" checked="false" optional="True" label="Use centroded DIA data." help="(-dia_centroided)"/>
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110 <param name="param_dia_byseries_intensity_min" type="float" min="0.0" optional="True" value="300.0" label="DIA b/y series minimum intensity to consider." help="(-dia_byseries_intensity_min)"/>
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111 <param name="param_dia_byseries_ppm_diff" type="float" min="0.0" optional="True" value="10.0" label="DIA b/y series minimal difference in ppm to consider." help="(-dia_byseries_ppm_diff)"/>
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112 <param name="param_dia_nr_isotopes" type="integer" min="0" optional="True" value="4" label="DIA nr of isotopes to consider." help="(-dia_nr_isotopes)"/>
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113 <param name="param_dia_nr_charges" type="integer" min="0" optional="True" value="4" label="DIA nr of charges to consider." help="(-dia_nr_charges)"/>
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114 <param name="param_peak_before_mono_max_ppm_diff" type="float" min="0.0" optional="True" 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="(-peak_before_mono_max_ppm_diff)"/>
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115 <param name="param_outlierMethod" type="text" size="20" value="iter_residual" label="Which outlier detection method to use (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none'). 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)." help="(-outlierMethod)"/>
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116 <param name="param_useIterativeChauvenet" type="text" size="20" value="false" label="Whether to use Chauvenet's criterion when using iterative methods. This should be used if the algorithm removes too many datapoints but it may lead to true outliers being retained." help="(-useIterativeChauvenet)"/>
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117 <param name="param_RANSACMaxIterations" type="integer" value="1000" label="Maximum iterations for the RANSAC outlier detection algorithm." help="(-RANSACMaxIterations)"/>
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118 <param name="param_RANSACMaxPercentRTThreshold" type="integer" value="3" label="Maximum threshold in RT dimension for the RANSAC outlier detection algorithm (in percent of the total gradient). Default is set to 3% which is around +/- 4 minutes on a 120 gradient." help="(-RANSACMaxPercentRTThreshold)"/>
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119 <param name="param_RANSACSamplingSize" type="integer" value="10" label="Sampling size of data points per iteration for the RANSAC outlier detection algorithm." help="(-RANSACSamplingSize)"/>
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120 <param name="param_InitialQualityCutoff" type="float" value="0.5" label="The initial overall quality cutoff for a peak to be scored (range ca. -2 to 2)" help="(-InitialQualityCutoff)"/>
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121 <param name="param_OverallQualityCutoff" type="float" value="5.5" label="The overall quality cutoff for a peak to go into the retention time estimation (range ca. 0 to 10)" help="(-OverallQualityCutoff)"/>
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122 <param name="param_NrRTBins" type="integer" value="10" label="Number of RT bins to use to compute coverage. 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)" help="(-NrRTBins)"/>
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123 <param name="param_MinPeptidesPerBin" type="integer" value="1" label="Minimal number of peptides that are required for a bin to counted as 'covered'" help="(-MinPeptidesPerBin)"/>
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124 <param name="param_MinBinsFilled" type="integer" value="8" label="Minimal number of bins required to be covered" help="(-MinBinsFilled)"/>
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125 <expand macro="advanced_options">
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126 <param name="param_quantification_cutoff" type="float" min="0.0" optional="True" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help="(-quantification_cutoff)"/>
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127 <param name="param_write_convex_hull" type="boolean" truevalue="-algorithm:write_convex_hull true" falsevalue="-algorithm:write_convex_hull false" checked="false" optional="True" label="Whether to write out all points of all features into the featureXML" help="(-write_convex_hull)"/>
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128 <param name="param_add_up_spectra" type="integer" min="1" optional="True" value="1" label="Add up spectra around the peak apex (needs to be a non-even integer)" help="(-add_up_spectra)"/>
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129 <param name="param_spacing_for_spectra_resampling" type="float" min="0.0" optional="True" value="0.005" label="If spectra are to be added, use this spacing to add them up" help="(-spacing_for_spectra_resampling)"/>
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130 <param name="param_min_peak_width" type="float" value="-1.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)." help="(-min_peak_width)"/>
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131 <param name="param_background_subtraction" type="select" optional="True" value="none" label="Try to apply a background subtraction to the peak (experimental). The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that." help="(-background_subtraction)">
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132 <option value="none">none</option>
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133 <option value="smoothed">smoothed</option>
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134 <option value="original">original</option>
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135 </param>
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136 <param name="param_recalculate_peaks" type="text" size="20" value="false" label="Tries to get better peak picking by looking at peak consistency of all picked peaks. Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large." help="(-recalculate_peaks)"/>
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137 <param name="param_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. If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)." help="(-recalculate_peaks_max_z)"/>
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138 <param name="param_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="(-minimal_quality)"/>
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139 <param name="param_compute_peak_quality" type="text" size="20" value="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions. The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad." help="(-compute_peak_quality)"/>
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140 <param name="param_interpolation_step" type="float" value="0.2" label="Sampling rate for the interpolation of the model function." help="(-interpolation_step)"/>
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141 <param name="param_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="(-tolerance_stdev_bounding_box)"/>
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142 <param name="param_max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm." help="(-max_iteration)"/>
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143 <param name="param_mean" type="float" value="1.0" label="Centroid position of the model." help="(-mean)"/>
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144 <param name="param_variance" type="float" value="1.0" label="Variance of the model." help="(-variance)"/>
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145 <param name="param_use_shape_score" type="boolean" truevalue="-algorithm:Scores:use_shape_score true" falsevalue="-algorithm:Scores:use_shape_score false" checked="true" optional="True" label="Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)" help="(-use_shape_score)"/>
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146 <param name="param_use_coelution_score" type="boolean" truevalue="-algorithm:Scores:use_coelution_score true" falsevalue="-algorithm:Scores:use_coelution_score false" checked="true" optional="True" label="Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation)" help="(-use_coelution_score)"/>
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147 <param name="param_use_rt_score" type="boolean" truevalue="-algorithm:Scores:use_rt_score true" falsevalue="-algorithm:Scores:use_rt_score false" checked="true" optional="True" label="Use the retention time score (this score measure the difference in retention time)" help="(-use_rt_score)"/>
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148 <param name="param_use_library_score" type="boolean" truevalue="-algorithm:Scores:use_library_score true" falsevalue="-algorithm:Scores:use_library_score false" checked="true" optional="True" label="Use the library score" help="(-use_library_score)"/>
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149 <param name="param_use_elution_model_score" type="boolean" truevalue="-algorithm:Scores:use_elution_model_score true" falsevalue="-algorithm:Scores:use_elution_model_score false" checked="true" optional="True" label="Use the elution model (EMG) score (this score fits a gaussian model to the peak and checks the fit)" help="(-use_elution_model_score)"/>
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150 <param name="param_use_intensity_score" type="boolean" truevalue="-algorithm:Scores:use_intensity_score true" falsevalue="-algorithm:Scores:use_intensity_score false" checked="true" optional="True" label="Use the intensity score" help="(-use_intensity_score)"/>
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151 <param name="param_use_nr_peaks_score" type="boolean" truevalue="-algorithm:Scores:use_nr_peaks_score true" falsevalue="-algorithm:Scores:use_nr_peaks_score false" checked="true" optional="True" label="Use the number of peaks score" help="(-use_nr_peaks_score)"/>
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152 <param name="param_use_total_xic_score" type="boolean" truevalue="-algorithm:Scores:use_total_xic_score true" falsevalue="-algorithm:Scores:use_total_xic_score false" checked="true" optional="True" label="Use the total XIC score" help="(-use_total_xic_score)"/>
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153 <param name="param_use_sn_score" type="boolean" truevalue="-algorithm:Scores:use_sn_score true" falsevalue="-algorithm:Scores:use_sn_score false" checked="true" optional="True" label="Use the SN (signal to noise) score" help="(-use_sn_score)"/>
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154 <param name="param_use_dia_scores" type="boolean" truevalue="-algorithm:Scores:use_dia_scores true" falsevalue="-algorithm:Scores:use_dia_scores false" checked="true" optional="True" label="Use the DIA (SWATH) scores" help="(-use_dia_scores)"/>
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155 <param name="param_use_ms1_correlation" type="boolean" truevalue="-algorithm:Scores:use_ms1_correlation true" falsevalue="-algorithm:Scores:use_ms1_correlation false" checked="false" optional="True" label="Use the correlation scores with the MS1 elution profiles" help="(-use_ms1_correlation)"/>
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156 <param name="param_use_ms1_fullscan" type="boolean" truevalue="-algorithm:Scores:use_ms1_fullscan true" falsevalue="-algorithm:Scores:use_ms1_fullscan false" checked="false" optional="True" label="Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)" help="(-use_ms1_fullscan)"/>
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157 </expand>
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158 </inputs>
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159 <outputs>
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160 <data name="param_out" label="output file" format="data"/>
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161 </outputs>
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162 <help>**What it does**
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163
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164 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.
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165
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166
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167 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathRTNormalizer.html
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168
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169 @REFERENCES@
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170 </help>
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171 </tool>
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