Mercurial > repos > galaxyp > openms_openswathworkflow

comparison OpenSwathWorkflow.xml @ 11:48e2d8b51c8a draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:19:13 +0000
parents 887be35bc42e
children 4a7b96835140
comparison
equal deleted inserted replaced
10:887be35bc42e 11:48e2d8b51c8a
26 #end if 26 #end if
27 #if $tr_irt_nonlinear: 27 #if $tr_irt_nonlinear:
28 mkdir tr_irt_nonlinear && 28 mkdir tr_irt_nonlinear &&
29 ln -s '$tr_irt_nonlinear' 'tr_irt_nonlinear/${re.sub("[^\w\-_]", "_", $tr_irt_nonlinear.element_identifier)}.$gxy2omsext($tr_irt_nonlinear.ext)' && 29 ln -s '$tr_irt_nonlinear' 'tr_irt_nonlinear/${re.sub("[^\w\-_]", "_", $tr_irt_nonlinear.element_identifier)}.$gxy2omsext($tr_irt_nonlinear.ext)' &&
30 #end if 30 #end if
31 #if $swath_windows_file:
32 mkdir swath_windows_file &&
33 ln -s '$swath_windows_file' 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)' &&
34 #end if
31 #if "out_features_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 35 #if "out_features_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
32 mkdir out_features && 36 mkdir out_features &&
33 #end if 37 #end if
34 #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 38 #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
35 mkdir out_tsv && 39 mkdir out_tsv &&
51 #end if 55 #end if
52 #if $adv_opts_cond.adv_opts_selector=='advanced': 56 #if $adv_opts_cond.adv_opts_selector=='advanced':
53 #if $adv_opts_cond.rt_norm: 57 #if $adv_opts_cond.rt_norm:
54 mkdir adv_opts_cond.rt_norm && 58 mkdir adv_opts_cond.rt_norm &&
55 ln -s '$adv_opts_cond.rt_norm' 'adv_opts_cond.rt_norm/${re.sub("[^\w\-_]", "_", $adv_opts_cond.rt_norm.element_identifier)}.$gxy2omsext($adv_opts_cond.rt_norm.ext)' && 59 ln -s '$adv_opts_cond.rt_norm' 'adv_opts_cond.rt_norm/${re.sub("[^\w\-_]", "_", $adv_opts_cond.rt_norm.element_identifier)}.$gxy2omsext($adv_opts_cond.rt_norm.ext)' &&
56 #end if
57 #if $adv_opts_cond.swath_windows_file:
58 mkdir adv_opts_cond.swath_windows_file &&
59 ln -s '$adv_opts_cond.swath_windows_file' 'adv_opts_cond.swath_windows_file/${re.sub("[^\w\-_]", "_", $adv_opts_cond.swath_windows_file.element_identifier)}.$gxy2omsext($adv_opts_cond.swath_windows_file.ext)' &&
60 #end if 60 #end if
61 #end if 61 #end if
62 62
63 ## Main program call 63 ## Main program call
64 64
76 #end if 76 #end if
77 #if $tr_irt_nonlinear: 77 #if $tr_irt_nonlinear:
78 -tr_irt_nonlinear 78 -tr_irt_nonlinear
79 'tr_irt_nonlinear/${re.sub("[^\w\-_]", "_", $tr_irt_nonlinear.element_identifier)}.$gxy2omsext($tr_irt_nonlinear.ext)' 79 'tr_irt_nonlinear/${re.sub("[^\w\-_]", "_", $tr_irt_nonlinear.element_identifier)}.$gxy2omsext($tr_irt_nonlinear.ext)'
80 #end if 80 #end if
81 #if $swath_windows_file:
82 -swath_windows_file
83 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)'
84 #end if
81 #if "out_features_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 85 #if "out_features_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
82 -out_features 86 -out_features
83 'out_features/output.${gxy2omsext("featurexml")}' 87 'out_features/output.${gxy2omsext("featurexml")}'
84 #end if 88 #end if
85 #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 89 #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
108 #end if 112 #end if
109 #if $adv_opts_cond.adv_opts_selector=='advanced': 113 #if $adv_opts_cond.adv_opts_selector=='advanced':
110 #if $adv_opts_cond.rt_norm: 114 #if $adv_opts_cond.rt_norm:
111 -rt_norm 115 -rt_norm
112 'adv_opts_cond.rt_norm/${re.sub("[^\w\-_]", "_", $adv_opts_cond.rt_norm.element_identifier)}.$gxy2omsext($adv_opts_cond.rt_norm.ext)' 116 'adv_opts_cond.rt_norm/${re.sub("[^\w\-_]", "_", $adv_opts_cond.rt_norm.element_identifier)}.$gxy2omsext($adv_opts_cond.rt_norm.ext)'
113 #end if
114 #if $adv_opts_cond.swath_windows_file:
115 -swath_windows_file
116 'adv_opts_cond.swath_windows_file/${re.sub("[^\w\-_]", "_", $adv_opts_cond.swath_windows_file.element_identifier)}.$gxy2omsext($adv_opts_cond.swath_windows_file.ext)'
117 #end if 117 #end if
118 #end if 118 #end if
119 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 119 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
120 | tee '$stdout' 120 | tee '$stdout'
121 #end if 121 #end if
152 <inputs> 152 <inputs>
153 <param name="in" argument="-in" type="data" format="mzml,mzxml,sqmass" optional="false" label="Input files separated by blank" help=" select mzml,mzxml,sqmass data sets(s)"/> 153 <param name="in" argument="-in" type="data" format="mzml,mzxml,sqmass" optional="false" label="Input files separated by blank" help=" select mzml,mzxml,sqmass data sets(s)"/>
154 <param name="tr" argument="-tr" type="data" format="pqp,tabular,traml" optional="false" label="transition file ('TraML','tsv','pqp')" help=" select pqp,tabular,traml data sets(s)"/> 154 <param name="tr" argument="-tr" type="data" format="pqp,tabular,traml" optional="false" label="transition file ('TraML','tsv','pqp')" help=" select pqp,tabular,traml data sets(s)"/>
155 <param name="tr_irt" argument="-tr_irt" type="data" format="pqp,tabular,traml" optional="true" label="transition file ('TraML')" help=" select pqp,tabular,traml data sets(s)"/> 155 <param name="tr_irt" argument="-tr_irt" type="data" format="pqp,tabular,traml" optional="true" label="transition file ('TraML')" help=" select pqp,tabular,traml data sets(s)"/>
156 <param name="tr_irt_nonlinear" argument="-tr_irt_nonlinear" type="data" format="pqp,tabular,traml" optional="true" label="additional nonlinear transition file ('TraML')" help=" select pqp,tabular,traml data sets(s)"/> 156 <param name="tr_irt_nonlinear" argument="-tr_irt_nonlinear" type="data" format="pqp,tabular,traml" optional="true" label="additional nonlinear transition file ('TraML')" help=" select pqp,tabular,traml data sets(s)"/>
157 <param name="swath_windows_file" argument="-swath_windows_file" type="data" format="txt" optional="true" label="Optional, tab-separated file containing the SWATH windows for extraction: lower_offset upper_offset" help="Note that the first line is a header and will be skipped select txt data sets(s)"/>
157 <param name="sonar" argument="-sonar" type="boolean" truevalue="true" falsevalue="false" checked="false" label="data is scanning SWATH data" help=""/> 158 <param name="sonar" argument="-sonar" type="boolean" truevalue="true" falsevalue="false" checked="false" label="data is scanning SWATH data" help=""/>
158 <param name="rt_extraction_window" argument="-rt_extraction_window" type="float" optional="true" value="600.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 600 means to extract around +/- 300 s of the expected elution)" help=""/> 159 <param name="rt_extraction_window" argument="-rt_extraction_window" type="float" optional="true" value="600.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 600 means to extract around +/- 300 s of the expected elution)" help=""/>
159 <param name="ion_mobility_window" argument="-ion_mobility_window" type="float" optional="true" value="-1.0" label="Extraction window in ion mobility dimension (in milliseconds)" help="This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side"/> 160 <param name="ion_mobility_window" argument="-ion_mobility_window" type="float" optional="true" value="-1.0" label="Extraction window in ion mobility dimension (in milliseconds)" help="This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side"/>
160 <param name="mz_extraction_window" argument="-mz_extraction_window" type="float" optional="true" min="0.0" value="0.05" label="Extraction window in Thomson or ppm (see mz_extraction_window_unit)" help=""/> 161 <param name="mz_extraction_window" argument="-mz_extraction_window" type="float" optional="true" min="0.0" value="50.0" label="Extraction window in Thomson or ppm (see mz_extraction_window_unit)" help=""/>
161 <param name="mz_extraction_window_ms1" argument="-mz_extraction_window_ms1" type="float" optional="true" min="0.0" value="0.05" label="Extraction window used in MS1 in Thomson or ppm (see mz_extraction_window_ms1_unit)" help=""/> 162 <param name="mz_extraction_window_ms1" argument="-mz_extraction_window_ms1" type="float" optional="true" min="0.0" value="50.0" label="Extraction window used in MS1 in Thomson or ppm (see mz_extraction_window_ms1_unit)" help=""/>
162 <param name="im_extraction_window_ms1" argument="-im_extraction_window_ms1" type="float" optional="true" value="-1.0" label="Extraction window in ion mobility dimension for MS1 (in milliseconds)" help=""/> 163 <param name="im_extraction_window_ms1" argument="-im_extraction_window_ms1" type="float" optional="true" value="-1.0" label="Extraction window in ion mobility dimension for MS1 (in milliseconds)" help=""/>
163 <section name="Calibration" title="Parameters for the m/z and ion mobility calibration" help="" expanded="false"> 164 <section name="Calibration" title="Parameters for the m/z and ion mobility calibration" help="" expanded="false">
164 <param name="ms1_im_calibration" argument="-Calibration:ms1_im_calibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to use MS1 precursor data for the ion mobility calibration (default = false, uses MS2 / fragment ions for calibration)" help=""/> 165 <param name="ms1_im_calibration" argument="-Calibration:ms1_im_calibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to use MS1 precursor data for the ion mobility calibration (default = false, uses MS2 / fragment ions for calibration)" help=""/>
165 <param name="im_correction_function" argument="-Calibration:im_correction_function" display="radio" type="select" optional="false" label="Type of normalization function for IM calibration" help=""> 166 <param name="im_correction_function" argument="-Calibration:im_correction_function" display="radio" type="select" optional="false" label="Type of normalization function for IM calibration" help="">
166 <option value="none">none</option> 167 <option value="none">none</option>
208 <param name="OverallQualityCutoff" argument="-RTNormalization:OverallQualityCutoff" type="float" optional="true" value="5.5" label="The overall quality cutoff for a peak to go into the retention time estimation (range ca" help="0 to 10)"/> 209 <param name="OverallQualityCutoff" argument="-RTNormalization:OverallQualityCutoff" type="float" optional="true" value="5.5" label="The overall quality cutoff for a peak to go into the retention time estimation (range ca" help="0 to 10)"/>
209 <param name="NrRTBins" argument="-RTNormalization:NrRTBins" type="integer" optional="true" value="10" label="Number of RT bins to use to compute coverage" help="This option should be used to ensure that there is a complete coverage of the RT space (this should detect cases where only a part of the RT gradient is actually covered by normalization peptides)"/> 210 <param name="NrRTBins" argument="-RTNormalization:NrRTBins" type="integer" optional="true" value="10" label="Number of RT bins to use to compute coverage" help="This option should be used to ensure that there is a complete coverage of the RT space (this should detect cases where only a part of the RT gradient is actually covered by normalization peptides)"/>
210 <param name="MinPeptidesPerBin" argument="-RTNormalization:MinPeptidesPerBin" type="integer" optional="true" value="1" label="Minimal number of peptides that are required for a bin to counted as 'covered'" help=""/> 211 <param name="MinPeptidesPerBin" argument="-RTNormalization:MinPeptidesPerBin" type="integer" optional="true" value="1" label="Minimal number of peptides that are required for a bin to counted as 'covered'" help=""/>
211 <param name="MinBinsFilled" argument="-RTNormalization:MinBinsFilled" type="integer" optional="true" value="8" label="Minimal number of bins required to be covered" help=""/> 212 <param name="MinBinsFilled" argument="-RTNormalization:MinBinsFilled" type="integer" optional="true" value="8" label="Minimal number of bins required to be covered" help=""/>
212 <section name="lowess" title="" help="" expanded="false"> 213 <section name="lowess" title="" help="" expanded="false">
213 <param name="span" argument="-RTNormalization:lowess:span" type="float" optional="true" min="0.0" max="1.0" value="0.666666666666667" label="Span parameter for lowess" help=""/> 214 <param name="span" argument="-RTNormalization:lowess:span" type="float" optional="true" min="0.0" max="1.0" value="0.05" label="Span parameter for lowess" help=""/>
214 </section> 215 </section>
215 <section name="b_spline" title="" help="" expanded="false"> 216 <section name="b_spline" title="" help="" expanded="false">
216 <param name="num_nodes" argument="-RTNormalization:b_spline:num_nodes" type="integer" optional="true" min="0" value="5" label="Number of nodes for b spline" help=""/> 217 <param name="num_nodes" argument="-RTNormalization:b_spline:num_nodes" type="integer" optional="true" min="0" value="5" label="Number of nodes for b spline" help=""/>
217 </section> 218 </section>
218 </section> 219 </section>
226 <option value="resample">resample</option> 227 <option value="resample">resample</option>
227 <expand macro="list_string_san"/> 228 <expand macro="list_string_san"/>
228 </param> 229 </param>
229 <param name="add_up_spectra" argument="-Scoring: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=""/> 230 <param name="add_up_spectra" argument="-Scoring: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=""/>
230 <param name="spacing_for_spectra_resampling" argument="-Scoring: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=""/> 231 <param name="spacing_for_spectra_resampling" argument="-Scoring: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=""/>
231 <param name="uis_threshold_sn" argument="-Scoring:uis_threshold_sn" type="integer" optional="true" value="0" label="S/N threshold to consider identification transition (set to -1 to consider all)" help=""/> 232 <param name="uis_threshold_sn" argument="-Scoring:uis_threshold_sn" type="integer" optional="true" value="-1" label="S/N threshold to consider identification transition (set to -1 to consider all)" help=""/>
232 <param name="uis_threshold_peak_area" argument="-Scoring: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=""/> 233 <param name="uis_threshold_peak_area" argument="-Scoring: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=""/>
233 <param name="scoring_model" argument="-Scoring:scoring_model" display="radio" type="select" optional="false" label="Scoring model to use" help=""> 234 <param name="scoring_model" argument="-Scoring:scoring_model" display="radio" type="select" optional="false" label="Scoring model to use" help="">
234 <option value="default" selected="true">default</option> 235 <option value="default" selected="true">default</option>
235 <option value="single_transition">single_transition</option> 236 <option value="single_transition">single_transition</option>
236 <expand macro="list_string_san"/> 237 <expand macro="list_string_san"/>
237 </param> 238 </param>
238 <param name="im_extra_drift" argument="-Scoring: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)"/> 239 <param name="im_extra_drift" argument="-Scoring: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)"/>
240 <param name="strict" argument="-Scoring: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="">
241 <expand macro="list_string_san"/>
242 </param>
239 <section name="TransitionGroupPicker" title="" help="" expanded="false"> 243 <section name="TransitionGroupPicker" title="" help="" expanded="false">
240 <param name="stop_after_feature" argument="-Scoring:TransitionGroupPicker:stop_after_feature" type="integer" optional="true" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/> 244 <param name="stop_after_feature" argument="-Scoring:TransitionGroupPicker:stop_after_feature" type="integer" optional="true" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
241 <param name="min_peak_width" argument="-Scoring: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=""/> 245 <param name="min_peak_width" argument="-Scoring: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=""/>
242 <param name="peak_integration" argument="-Scoring: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=""> 246 <param name="peak_integration" argument="-Scoring: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="">
243 <option value="original" selected="true">original</option> 247 <option value="original" selected="true">original</option>
254 <param name="use_precursors" argument="-Scoring: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=""/> 258 <param name="use_precursors" argument="-Scoring: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=""/>
255 <param name="use_consensus" argument="-Scoring: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=""/> 259 <param name="use_consensus" argument="-Scoring: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=""/>
256 <param name="recalculate_peaks_max_z" argument="-Scoring:TransitionGroupPicker:recalculate_peaks_max_z" type="float" optional="true" value="0.75" 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)"/> 260 <param name="recalculate_peaks_max_z" argument="-Scoring:TransitionGroupPicker:recalculate_peaks_max_z" type="float" optional="true" value="0.75" 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)"/>
257 <param name="minimal_quality" argument="-Scoring:TransitionGroupPicker:minimal_quality" type="float" optional="true" value="-1.5" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help=""/> 261 <param name="minimal_quality" argument="-Scoring:TransitionGroupPicker:minimal_quality" type="float" optional="true" value="-1.5" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help=""/>
258 <param name="resample_boundary" argument="-Scoring: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=""/> 262 <param name="resample_boundary" argument="-Scoring: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=""/>
259 <param name="compute_peak_quality" argument="-Scoring:TransitionGroupPicker:compute_peak_quality" type="boolean" truevalue="true" falsevalue="false" checked="true" 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"/> 263 <param name="compute_peak_quality" argument="-Scoring: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"/>
260 <param name="compute_peak_shape_metrics" argument="-Scoring: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"/> 264 <param name="compute_peak_shape_metrics" argument="-Scoring: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"/>
261 <param name="compute_total_mi" argument="-Scoring: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=""/> 265 <param name="compute_total_mi" argument="-Scoring: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=""/>
262 <param name="boundary_selection_method" argument="-Scoring:TransitionGroupPicker:boundary_selection_method" display="radio" type="select" optional="false" label="Method to use when selecting the best boundaries for peaks" help=""> 266 <param name="boundary_selection_method" argument="-Scoring:TransitionGroupPicker:boundary_selection_method" display="radio" type="select" optional="false" label="Method to use when selecting the best boundaries for peaks" help="">
263 <option value="largest" selected="true">largest</option> 267 <option value="largest" selected="true">largest</option>
264 <option value="widest">widest</option> 268 <option value="widest">widest</option>
322 <param name="use_intensity_score" argument="-Scoring:Scores:use_intensity_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the intensity score" help=""/> 326 <param name="use_intensity_score" argument="-Scoring:Scores:use_intensity_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the intensity score" help=""/>
323 <param name="use_nr_peaks_score" argument="-Scoring:Scores:use_nr_peaks_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the number of peaks score" help=""/> 327 <param name="use_nr_peaks_score" argument="-Scoring:Scores:use_nr_peaks_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the number of peaks score" help=""/>
324 <param name="use_total_xic_score" argument="-Scoring:Scores:use_total_xic_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the total XIC score" help=""/> 328 <param name="use_total_xic_score" argument="-Scoring:Scores:use_total_xic_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the total XIC score" help=""/>
325 <param name="use_total_mi_score" argument="-Scoring:Scores:use_total_mi_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the total MI score" help=""/> 329 <param name="use_total_mi_score" argument="-Scoring:Scores:use_total_mi_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the total MI score" help=""/>
326 <param name="use_sn_score" argument="-Scoring:Scores:use_sn_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the SN (signal to noise) score" help=""/> 330 <param name="use_sn_score" argument="-Scoring:Scores:use_sn_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the SN (signal to noise) score" help=""/>
327 <param name="use_mi_score" argument="-Scoring:Scores:use_mi_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the MI (mutual information) score" help=""/> 331 <param name="use_mi_score" argument="-Scoring:Scores:use_mi_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the MI (mutual information) score" help=""/>
328 <param name="use_dia_scores" argument="-Scoring:Scores:use_dia_scores" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the DIA (SWATH) scores" help="If turned off, will not use fragment ion spectra for scoring"/> 332 <param name="use_dia_scores" argument="-Scoring:Scores:use_dia_scores" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the DIA (SWATH) scores" help="If turned off, will not use fragment ion spectra for scoring"/>
329 <param name="use_ms1_correlation" argument="-Scoring:Scores:use_ms1_correlation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the correlation scores with the MS1 elution profiles" help=""/> 333 <param name="use_ms1_correlation" argument="-Scoring:Scores:use_ms1_correlation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the correlation scores with the MS1 elution profiles" help=""/>
330 <param name="use_sonar_scores" argument="-Scoring:Scores:use_sonar_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the scores for SONAR scans (scanning swath)" help=""/> 334 <param name="use_sonar_scores" argument="-Scoring:Scores:use_sonar_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the scores for SONAR scans (scanning swath)" help=""/>
331 <param name="use_ion_mobility_scores" argument="-Scoring:Scores:use_ion_mobility_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the scores for Ion Mobility scans" help=""/> 335 <param name="use_ion_mobility_scores" argument="-Scoring:Scores:use_ion_mobility_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the scores for Ion Mobility scans" help=""/>
332 <param name="use_ms1_fullscan" argument="-Scoring: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=""/> 336 <param name="use_ms1_fullscan" argument="-Scoring: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=""/>
333 <param name="use_ms1_mi" argument="-Scoring:Scores:use_ms1_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the MS1 MI score" help=""/> 337 <param name="use_ms1_mi" argument="-Scoring:Scores:use_ms1_mi" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the MS1 MI score" help=""/>
334 <param name="use_uis_scores" argument="-Scoring:Scores:use_uis_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use UIS scores for peptidoform identification" help=""/> 338 <param name="use_uis_scores" argument="-Scoring:Scores:use_uis_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use UIS scores for peptidoform identification" help=""/>
335 </section> 339 </section>
336 </section> 340 </section>
337 <expand macro="adv_opts_macro"> 341 <expand macro="adv_opts_macro">
338 <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="If set, tr_irt may be omitted select trafoxml data sets(s)"/> 342 <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="If set, tr_irt may be omitted select trafoxml data sets(s)"/>
339 <param name="swath_windows_file" argument="-swath_windows_file" type="data" format="txt" optional="true" label="Optional, tab-separated file containing the SWATH windows for extraction: lower_offset upper_offset" help="Note that the first line is a header and will be skipped select txt data sets(s)"/>
340 <param name="sort_swath_maps" argument="-sort_swath_maps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Sort input SWATH files when matching to SWATH windows from swath_windows_file" help=""/> 343 <param name="sort_swath_maps" argument="-sort_swath_maps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Sort input SWATH files when matching to SWATH windows from swath_windows_file" help=""/>
341 <param name="use_ms1_traces" argument="-use_ms1_traces" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Extract the precursor ion trace(s) and use for scoring" help=""/> 344 <param name="enable_ms1" argument="-enable_ms1" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Extract the precursor ion trace(s) and use for scoring if present" help=""/>
342 <param name="enable_uis_scoring" argument="-enable_uis_scoring" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable additional scoring of identification assays" help=""/> 345 <param name="enable_ipf" argument="-enable_ipf" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enable additional scoring of identification assays using IPF (see online documentation)" help=""/>
343 <param name="out_chrom_type" type="select" optional="false" label="File type of output out_chrom (Also output all computed chromatograms output in mzML (chrom.mzML) or sqMass (SQLite format))"> 346 <param name="out_chrom_type" type="select" optional="false" label="File type of output out_chrom (Also output all computed chromatograms output in mzML (chrom.mzML) or sqMass (SQLite format))">
344 <option value="mzML">mzml</option> 347 <option value="mzML">mzml</option>
345 <option value="sqMass">sqmass</option> 348 <option value="sqMass">sqmass</option>
346 </param> 349 </param>
347 <param name="min_upper_edge_dist" argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="Minimal distance to the upper edge of a Swath window to still consider a precursor, in Thomson" help=""/> 350 <param name="min_upper_edge_dist" argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="Minimal distance to the upper edge of a Swath window to still consider a precursor, in Thomson" help=""/>
348 <param name="extra_rt_extraction_window" argument="-extra_rt_extraction_window" type="float" optional="true" min="0.0" value="0.0" label="Output an XIC with a RT-window by this much large" help="(e.g. to visually inspect a larger area of the chromatogram)"/> 351 <param name="extra_rt_extraction_window" argument="-extra_rt_extraction_window" type="float" optional="true" min="0.0" value="0.0" label="Output an XIC with a RT-window by this much large" help="(e.g. to visually inspect a larger area of the chromatogram)"/>
349 <param name="mz_extraction_window_unit" argument="-mz_extraction_window_unit" display="radio" type="select" optional="false" label="Unit for mz extraction" help=""> 352 <param name="mz_extraction_window_unit" argument="-mz_extraction_window_unit" display="radio" type="select" optional="false" label="Unit for mz extraction" help="">
350 <option value="Th" selected="true">Th</option> 353 <option value="Th">Th</option>
351 <option value="ppm">ppm</option> 354 <option value="ppm" selected="true">ppm</option>
352 <expand macro="list_string_san"/> 355 <expand macro="list_string_san"/>
353 </param> 356 </param>
354 <param name="mz_extraction_window_ms1_unit" argument="-mz_extraction_window_ms1_unit" display="radio" type="select" optional="false" label="Unit of the MS1 m/z extraction window" help=""> 357 <param name="mz_extraction_window_ms1_unit" argument="-mz_extraction_window_ms1_unit" display="radio" type="select" optional="false" label="Unit of the MS1 m/z extraction window" help="">
355 <option value="ppm">ppm</option> 358 <option value="ppm" selected="true">ppm</option>
356 <option value="Th" selected="true">Th</option> 359 <option value="Th">Th</option>
357 <expand macro="list_string_san"/> 360 <expand macro="list_string_san"/>
358 </param> 361 </param>
359 <param name="use_ms1_ion_mobility" argument="-use_ms1_ion_mobility" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Also perform precursor extraction using the same ion mobility window as for fragment ion extraction" help=""/> 362 <param name="use_ms1_ion_mobility" argument="-use_ms1_ion_mobility" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Also perform precursor extraction using the same ion mobility window as for fragment ion extraction" help=""/>
360 <param name="matching_window_only" argument="-matching_window_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assume the input data is targeted / PRM-like data with potentially overlapping DIA windows" help="Will only attempt to extract each assay from the *best* matching DIA window (instead of all matching windows)"/> 363 <param name="matching_window_only" argument="-matching_window_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assume the input data is targeted / PRM-like data with potentially overlapping DIA windows" help="Will only attempt to extract each assay from the *best* matching DIA window (instead of all matching windows)"/>
361 <param name="irt_mz_extraction_window" argument="-irt_mz_extraction_window" type="float" optional="true" min="0.0" value="0.05" label="Extraction window used for iRT and m/z correction in Thomson or ppm (see irt_mz_extraction_window_unit)" help=""/> 364 <param name="irt_mz_extraction_window" argument="-irt_mz_extraction_window" type="float" optional="true" min="0.0" value="50.0" label="Extraction window used for iRT and m/z correction in Thomson or ppm (see irt_mz_extraction_window_unit)" help=""/>
362 <param name="irt_mz_extraction_window_unit" argument="-irt_mz_extraction_window_unit" display="radio" type="select" optional="false" label="Unit for mz extraction" help=""> 365 <param name="irt_mz_extraction_window_unit" argument="-irt_mz_extraction_window_unit" display="radio" type="select" optional="false" label="Unit for mz extraction" help="">
363 <option value="Th" selected="true">Th</option> 366 <option value="Th">Th</option>
364 <option value="ppm">ppm</option> 367 <option value="ppm" selected="true">ppm</option>
365 <expand macro="list_string_san"/> 368 <expand macro="list_string_san"/>
366 </param> 369 </param>
367 <param name="irt_im_extraction_window" argument="-irt_im_extraction_window" type="float" optional="true" value="-1.0" label="Ion mobility extraction window used for iRT (in 1/K0 or milliseconds)" help=""/> 370 <param name="irt_im_extraction_window" argument="-irt_im_extraction_window" type="float" optional="true" value="-1.0" label="Ion mobility extraction window used for iRT (in 1/K0 or milliseconds)" help=""/>
368 <param name="min_rsq" argument="-min_rsq" type="float" optional="true" value="0.95" label="Minimum r-squared of RT peptides regression" help=""/> 371 <param name="min_rsq" argument="-min_rsq" type="float" optional="true" value="0.95" label="Minimum r-squared of RT peptides regression" help=""/>
369 <param name="min_coverage" argument="-min_coverage" type="float" optional="true" value="0.6" label="Minimum relative amount of RT peptides to keep" help=""/> 372 <param name="min_coverage" argument="-min_coverage" type="float" optional="true" value="0.6" label="Minimum relative amount of RT peptides to keep" help=""/>
390 <param name="extraction_function" argument="-extraction_function" display="radio" type="select" optional="false" label="Function used to extract the signal" help=""> 393 <param name="extraction_function" argument="-extraction_function" display="radio" type="select" optional="false" label="Function used to extract the signal" help="">
391 <option value="tophat" selected="true">tophat</option> 394 <option value="tophat" selected="true">tophat</option>
392 <option value="bartlett">bartlett</option> 395 <option value="bartlett">bartlett</option>
393 <expand macro="list_string_san"/> 396 <expand macro="list_string_san"/>
394 </param> 397 </param>
395 <param name="batchSize" argument="-batchSize" type="integer" optional="true" min="0" value="250" label="The batch size of chromatograms to process (0 means to only have one batch, sensible values are around 250-1000)" help=""/> 398 <param name="batchSize" argument="-batchSize" type="integer" optional="true" min="0" value="1000" label="The batch size of chromatograms to process (0 means to only have one batch, sensible values are around 250-1000)" help=""/>
396 <param name="ms1_isotopes" argument="-ms1_isotopes" type="integer" optional="true" min="0" value="0" label="The number of MS1 isotopes used for extraction" help=""/> 399 <param name="ms1_isotopes" argument="-ms1_isotopes" type="integer" optional="true" min="0" value="3" label="The number of MS1 isotopes used for extraction" help=""/>
397 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 400 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
398 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 401 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
399 <expand macro="list_string_san"/> 402 <expand macro="list_string_san"/>
400 </param> 403 </param>
401 </expand> 404 </expand>
402 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false"> 405 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
403 <option value="out_features_FLAG">out_features (Use UIS scores for peptidoform identification)</option> 406 <option value="out_features_FLAG">out_features (output file)</option>
404 <option value="out_tsv_FLAG">out_tsv (Use UIS scores for peptidoform identification)</option> 407 <option value="out_tsv_FLAG">out_tsv (TSV output file (mProphet-compatible TSV file))</option>
405 <option value="out_osw_FLAG">out_osw (Use UIS scores for peptidoform identification)</option> 408 <option value="out_osw_FLAG">out_osw (OSW output file (PyProphet-compatible SQLite file))</option>
406 <option value="out_chrom_FLAG">out_chrom (Use UIS scores for peptidoform identification)</option> 409 <option value="out_chrom_FLAG">out_chrom (Also output all computed chromatograms output in mzML (chrom.mzML) or sqMass (SQLite format))</option>
407 <option value="out_qc_FLAG">out_qc (Use UIS scores for peptidoform identification)</option> 410 <option value="out_qc_FLAG">out_qc (Optional QC meta data (charge distribution in MS1))</option>
408 <option value="irt_mzml_FLAG">irt_mzml (Use UIS scores for peptidoform identification)</option> 411 <option value="irt_mzml_FLAG">irt_mzml (Chromatogram mzML containing the iRT peptides)</option>
409 <option value="irt_trafo_FLAG">irt_trafo (Use UIS scores for peptidoform identification)</option> 412 <option value="irt_trafo_FLAG">irt_trafo (Transformation file for RT transform)</option>
410 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 413 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
411 </param> 414 </param>
412 </inputs> 415 </inputs>
413 <outputs> 416 <outputs>
414 <data name="out_features" label="${tool.name} on ${on_string}: out_features" format="featurexml"> 417 <data name="out_features" label="${tool.name} on ${on_string}: out_features" format="featurexml">
448 <expand macro="manutest_OpenSwathWorkflow"/> 451 <expand macro="manutest_OpenSwathWorkflow"/>
449 </tests> 452 </tests>
450 <help><![CDATA[Complete workflow to run OpenSWATH 453 <help><![CDATA[Complete workflow to run OpenSWATH
451 454
452 455
453 For more information, visit http://www.openms.de/documentation/UTILS_OpenSwathWorkflow.html]]></help> 456 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_OpenSwathWorkflow.html]]></help>
454 <expand macro="references"/> 457 <expand macro="references"/>
455 </tool> 458 </tool>