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view OpenSwathWorkflow.xml @ 4:60a33af52042 draft default tip
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| author | galaxyp |
|---|---|
| date | Wed, 13 May 2015 21:19:44 -0400 |
| parents | 3070d71e0e5c |
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<?xml version='1.0' encoding='UTF-8'?> <tool id="OpenSwathWorkflow" name="OpenSwathWorkflow" version="2.0.0"> <description>Complete workflow to run OpenSWATH</description> <macros> <token name="@EXECUTABLE@">OpenSwathWorkflow</token> <import>macros.xml</import> </macros> <expand macro="stdio"/> <expand macro="requirements"/> <command>OpenSwathWorkflow -in #for token in $param_in: $token #end for #if $param_tr: -tr $param_tr #end if #if $param_tr_type: -tr_type #if " " in str($param_tr_type): "$param_tr_type" #else $param_tr_type #end if #end if #if $param_tr_irt: -tr_irt $param_tr_irt #end if #if $output_fmt == 'tsv': -out_tsv "$out_tsv" #else: -out_features "$out_features" #end if #if $param_out_chrom: -out_chrom $param_out_chrom #end if #if $param_rt_extraction_window: -rt_extraction_window $param_rt_extraction_window #end if #if $param_mz_extraction_window: -mz_extraction_window $param_mz_extraction_window #end if #if $param_ppm: -ppm #end if -threads \${GALAXY_SLOTS:-24} #if $param_Scoring_stop_report_after_feature: -Scoring:stop_report_after_feature $param_Scoring_stop_report_after_feature #end if #if $param_Scoring_rt_normalization_factor: -Scoring:rt_normalization_factor $param_Scoring_rt_normalization_factor #end if #if $param_Scoring_TransitionGroupPicker_stop_after_feature: -Scoring:TransitionGroupPicker:stop_after_feature $param_Scoring_TransitionGroupPicker_stop_after_feature #end if #if $param_Scoring_TransitionGroupPicker_min_peak_width: -Scoring:TransitionGroupPicker:min_peak_width $param_Scoring_TransitionGroupPicker_min_peak_width #end if #if $param_Scoring_TransitionGroupPicker_recalculate_peaks: -Scoring:TransitionGroupPicker:recalculate_peaks "$param_Scoring_TransitionGroupPicker_recalculate_peaks" #end if #if $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z: -Scoring:TransitionGroupPicker:recalculate_peaks_max_z $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z #end if #if $param_Scoring_TransitionGroupPicker_minimal_quality: -Scoring:TransitionGroupPicker:minimal_quality $param_Scoring_TransitionGroupPicker_minimal_quality #end if #if $param_Scoring_TransitionGroupPicker_compute_peak_quality: -Scoring:TransitionGroupPicker:compute_peak_quality "$param_Scoring_TransitionGroupPicker_compute_peak_quality" #end if #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length: -Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length #end if #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order: -Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order #end if #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width: -Scoring:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width #end if #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_use_gauss: -Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss "$param_Scoring_TransitionGroupPicker_PeakPickerMRM_use_gauss" #end if #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_peak_width: -Scoring:TransitionGroupPicker:PeakPickerMRM:peak_width $param_Scoring_TransitionGroupPicker_PeakPickerMRM_peak_width #end if #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_signal_to_noise: -Scoring:TransitionGroupPicker:PeakPickerMRM:signal_to_noise $param_Scoring_TransitionGroupPicker_PeakPickerMRM_signal_to_noise #end if #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks: -Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks #end if #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method: -Scoring:TransitionGroupPicker:PeakPickerMRM:method #if " " in str($param_Scoring_TransitionGroupPicker_PeakPickerMRM_method): "$param_Scoring_TransitionGroupPicker_PeakPickerMRM_method" #else $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method #end if #end if #if $param_Scoring_DIAScoring_dia_extraction_window: -Scoring:DIAScoring:dia_extraction_window $param_Scoring_DIAScoring_dia_extraction_window #end if #if $param_Scoring_DIAScoring_dia_centroided: -Scoring:DIAScoring:dia_centroided #end if #if $param_Scoring_DIAScoring_dia_byseries_intensity_min: -Scoring:DIAScoring:dia_byseries_intensity_min $param_Scoring_DIAScoring_dia_byseries_intensity_min #end if #if $param_Scoring_DIAScoring_dia_byseries_ppm_diff: -Scoring:DIAScoring:dia_byseries_ppm_diff $param_Scoring_DIAScoring_dia_byseries_ppm_diff #end if #if $param_Scoring_DIAScoring_dia_nr_isotopes: -Scoring:DIAScoring:dia_nr_isotopes $param_Scoring_DIAScoring_dia_nr_isotopes #end if #if $param_Scoring_DIAScoring_dia_nr_charges: -Scoring:DIAScoring:dia_nr_charges $param_Scoring_DIAScoring_dia_nr_charges #end if #if $param_Scoring_DIAScoring_peak_before_mono_max_ppm_diff: -Scoring:DIAScoring:peak_before_mono_max_ppm_diff $param_Scoring_DIAScoring_peak_before_mono_max_ppm_diff #end if #if $param_Scoring_EMGScoring_max_iteration: -Scoring:EMGScoring:max_iteration $param_Scoring_EMGScoring_max_iteration #end if #if $param_Scoring_EMGScoring_deltaRelError: -Scoring:EMGScoring:deltaRelError $param_Scoring_EMGScoring_deltaRelError #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_rt_norm: -rt_norm $adv_opts.param_rt_norm #end if #if $adv_opts.param_swath_windows_file: -swath_windows_file $adv_opts.param_swath_windows_file #end if #if $adv_opts.param_sort_swath_maps: -sort_swath_maps #end if #if $adv_opts.param_use_ms1_traces: -use_ms1_traces #end if #if $adv_opts.param_min_upper_edge_dist: -min_upper_edge_dist $adv_opts.param_min_upper_edge_dist #end if #if $adv_opts.param_extra_rt_extraction_window: -extra_rt_extraction_window $adv_opts.param_extra_rt_extraction_window #end if #if $adv_opts.param_min_rsq: -min_rsq $adv_opts.param_min_rsq #end if #if $adv_opts.param_min_coverage: -min_coverage $adv_opts.param_min_coverage #end if #if $adv_opts.param_split_file_input: -split_file_input #end if #if $adv_opts.param_use_elution_model_score: -use_elution_model_score #end if #if $adv_opts.param_readOptions: -readOptions #if " " in str($adv_opts.param_readOptions): "$adv_opts.param_readOptions" #else $adv_opts.param_readOptions #end if #end if #if $adv_opts.param_tempDirectory: -tempDirectory "$adv_opts.param_tempDirectory" #end if #if $adv_opts.param_extraction_function: -extraction_function #if " " in str($adv_opts.param_extraction_function): "$adv_opts.param_extraction_function" #else $adv_opts.param_extraction_function #end if #end if #if $adv_opts.param_batchSize: -batchSize $adv_opts.param_batchSize #end if #if $adv_opts.param_force: -force #end if #if $adv_opts.param_Scoring_quantification_cutoff: -Scoring:quantification_cutoff $adv_opts.param_Scoring_quantification_cutoff #end if #if $adv_opts.param_Scoring_write_convex_hull: -Scoring:write_convex_hull #end if #if $adv_opts.param_Scoring_Scores_use_shape_score: -Scoring:Scores:use_shape_score #end if #if $adv_opts.param_Scoring_Scores_use_coelution_score: -Scoring:Scores:use_coelution_score #end if #if $adv_opts.param_Scoring_Scores_use_rt_score: -Scoring:Scores:use_rt_score #end if #if $adv_opts.param_Scoring_Scores_use_library_score: -Scoring:Scores:use_library_score #end if #if $adv_opts.param_Scoring_Scores_use_intensity_score: -Scoring:Scores:use_intensity_score #end if #if $adv_opts.param_Scoring_Scores_use_nr_peaks_score: -Scoring:Scores:use_nr_peaks_score #end if #if $adv_opts.param_Scoring_Scores_use_total_xic_score: -Scoring:Scores:use_total_xic_score #end if #if $adv_opts.param_Scoring_Scores_use_sn_score: -Scoring:Scores:use_sn_score #end if #if $adv_opts.param_Scoring_Scores_use_dia_scores: -Scoring:Scores:use_dia_scores #end if #if $adv_opts.param_Scoring_Scores_use_ms1_correlation: -Scoring:Scores:use_ms1_correlation #end if #if $adv_opts.param_Scoring_Scores_use_ms1_fullscan: -Scoring:Scores:use_ms1_fullscan #end if #end if </command> <inputs> <param name="param_in" type="data" format="mzxml,mzml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) "> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file ('TraML','tsv' or 'csv')" help="(-tr) "/> <param name="param_tr_type" type="select" optional="True" label="input file type -- default: determined from file extension or content" help="(-tr_type) "> <option value="traML">traML</option> <option value="tsv">tsv</option> <option value="csv">csv</option> </param> <param name="param_tr_irt" type="data" format="traml" optional="True" label="transition file ('TraML')" help="(-tr_irt) "/> <param name="output_fmt" type="select" label="Select feature list output format"> <option value="featurexml">FeatureXML</option> <option value="tsv">TSV output file (mProphet compatible)</option> </param> <param name="param_rt_extraction_window" type="float" 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="(-rt_extraction_window) "/> <param name="param_mz_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="Extraction window used (in Thomson, to use ppm see -ppm flag)" help="(-mz_extraction_window) "/> <param name="param_ppm" type="boolean" truevalue="-ppm" falsevalue="" checked="false" optional="True" label="m/z extraction_window is in ppm" help="(-ppm) "/> <param name="param_Scoring_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) "/> <param name="param_Scoring_rt_normalization_factor" type="float" value="100.0" label="The normalized RT is expected to be between 0 and 1. If your normalized RT has a different range, pass this here (" help="(-rt_normalization_factor) e.g. it goes from 0 to 100, set this value to 100)"/> <param name="param_Scoring_TransitionGroupPicker_stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help="(-stop_after_feature) "/> <param name="param_Scoring_TransitionGroupPicker_min_peak_width" type="float" value="14.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help="(-min_peak_width) "/> <param name="param_Scoring_TransitionGroupPicker_recalculate_peaks" type="text" size="30" value="true" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param name="param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z" type="float" value="0.75" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="(-recalculate_peaks_max_z) If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/> <param name="param_Scoring_TransitionGroupPicker_minimal_quality" type="float" value="-1.5" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality) "/> <param name="param_Scoring_TransitionGroupPicker_compute_peak_quality" type="text" size="30" value="true" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length" type="integer" value="11" label="The number of subsequent data points used for smoothing" help="(-sgolay_frame_length) <br>This number has to be uneven. If it is not, 1 will be added"/> <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help="(-sgolay_polynomial_order) "/> <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width" type="float" value="30.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/> <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_use_gauss" type="text" size="30" value="false" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help="(-use_gauss) "> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_peak_width" type="float" value="-1.0" label="Force a certain minimal peak_width on the data (" help="(-peak_width) e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/> <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_signal_to_noise" type="float" min="0.0" optional="True" value="0.1" label="Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (" help="(-signal_to_noise) e.g. 1.0) can lead to peaks whose flanks are not fully captured"/> <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks" type="boolean" truevalue="-Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" falsevalue="" checked="true" optional="True" label="Try to remove overlapping peaks during peak picking" help="(-remove_overlapping_peaks) "/> <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_method" type="select" optional="True" value="corrected" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy, corrected picking or Crawdad)" help="(-method) "> <option value="legacy">legacy</option> <option value="corrected">corrected</option> <option value="crawdad">crawdad</option> </param> <param name="param_Scoring_DIAScoring_dia_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="DIA extraction window in Th" help="(-dia_extraction_window) "/> <param name="param_Scoring_DIAScoring_dia_centroided" type="boolean" truevalue="-Scoring:DIAScoring:dia_centroided" falsevalue="" checked="false" optional="True" label="Use centroded DIA data" help="(-dia_centroided) "/> <param name="param_Scoring_DIAScoring_dia_byseries_intensity_min" type="float" min="0.0" optional="True" value="300.0" label="DIA b/y series minimum intensity to conside" help="(-dia_byseries_intensity_min) "/> <param name="param_Scoring_DIAScoring_dia_byseries_ppm_diff" type="float" min="0.0" optional="True" value="10.0" label="DIA b/y series minimal difference in ppm to conside" help="(-dia_byseries_ppm_diff) "/> <param name="param_Scoring_DIAScoring_dia_nr_isotopes" type="integer" min="0" optional="True" value="4" label="DIA nr of isotopes to conside" help="(-dia_nr_isotopes) "/> <param name="param_Scoring_DIAScoring_dia_nr_charges" type="integer" min="0" optional="True" value="4" label="DIA nr of charges to conside" help="(-dia_nr_charges) "/> <param name="param_Scoring_DIAScoring_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) "/> <param name="param_Scoring_EMGScoring_max_iteration" type="integer" value="10" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/> <param name="param_Scoring_EMGScoring_deltaRelError" type="float" value="0.1" label="" help="(-deltaRelError) "/> <expand macro="advanced_options"> <param name="param_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="(-rt_norm) If set, tr_irt may be omitted"/> <param name="param_swath_windows_file" type="data" format="text" label="Optional, tab separated file containing the SWATH windows: lower_offset upper_offset \newline 400 425 \newline .." help="(-swath_windows_file) Note that the first line is a header and will be skipped"/> <param name="param_sort_swath_maps" type="boolean" truevalue="-sort_swath_maps" falsevalue="" checked="false" optional="True" label="Sort of input SWATH files when matching to SWATH windows from swath_windows_file" help="(-sort_swath_maps) "/> <param name="param_use_ms1_traces" type="boolean" truevalue="-use_ms1_traces" falsevalue="" checked="false" optional="True" label="Extract the precursor ion trace(s) and use for scoring" help="(-use_ms1_traces) "/> <param name="param_min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help="(-min_upper_edge_dist) "/> <param name="param_extra_rt_extraction_window" type="float" min="0.0" optional="True" value="0.0" label="Output an XIC with a RT-window that by this much larger (" help="(-extra_rt_extraction_window) e.g. to visually inspect a larger area of the chromatogram)"/> <param name="param_min_rsq" type="float" value="0.95" label="Minimum r-squared of RT peptides regression" help="(-min_rsq) "/> <param name="param_min_coverage" type="float" value="0.6" label="Minimum relative amount of RT peptides to keep" help="(-min_coverage) "/> <param name="param_split_file_input" type="boolean" truevalue="-split_file_input" falsevalue="" checked="false" optional="True" label="The input files each contain one single SWATH (alternatively: all SWATH are in separate files)" help="(-split_file_input) "/> <param name="param_use_elution_model_score" type="boolean" truevalue="-use_elution_model_score" falsevalue="" checked="false" optional="True" label="Turn on elution model score (EMG fit to peak)" help="(-use_elution_model_score) "/> <param name="param_readOptions" type="select" optional="True" value="normal" label="Whether to run OpenSWATH directly on the input data, cache data to disk first or to perform a datareduction step first" help="(-readOptions) If you choose cache, make sure to also set tempDirectory"> <option value="normal">normal</option> <option value="cache">cache</option> </param> <param name="param_tempDirectory" type="text" size="30" value="/tmp/" label="Temporary directory to store cached files for example" help="(-tempDirectory) "> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param name="param_extraction_function" type="select" optional="True" value="tophat" label="Function used to extract the signal" help="(-extraction_function) "> <option value="tophat">tophat</option> <option value="bartlett">bartlett</option> </param> <param name="param_batchSize" type="integer" min="0" optional="True" value="0" label="The batch size of chromatograms to process (0 means to only have one batch, sensible values are around 500-1000)" help="(-batchSize) "/> <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> <param name="param_Scoring_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) "/> <param name="param_Scoring_write_convex_hull" type="boolean" truevalue="-Scoring:write_convex_hull" falsevalue="" checked="false" optional="True" label="Whether to write out all points of all features into the featureXML" help="(-write_convex_hull) "/> <param name="param_Scoring_Scores_use_shape_score" type="boolean" truevalue="-Scoring:Scores:use_shape_score" falsevalue="" 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) "/> <param name="param_Scoring_Scores_use_coelution_score" type="boolean" truevalue="-Scoring:Scores:use_coelution_score" falsevalue="" 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) "/> <param name="param_Scoring_Scores_use_rt_score" type="boolean" truevalue="-Scoring:Scores:use_rt_score" falsevalue="" checked="true" optional="True" label="Use the retention time score (this score measure the difference in retention time)" help="(-use_rt_score) "/> <param name="param_Scoring_Scores_use_library_score" type="boolean" truevalue="-Scoring:Scores:use_library_score" falsevalue="" checked="true" optional="True" label="Use the library score" help="(-use_library_score) "/> <param name="param_Scoring_Scores_use_intensity_score" type="boolean" truevalue="-Scoring:Scores:use_intensity_score" falsevalue="" checked="true" optional="True" label="Use the intensity score" help="(-use_intensity_score) "/> <param name="param_Scoring_Scores_use_nr_peaks_score" type="boolean" truevalue="-Scoring:Scores:use_nr_peaks_score" falsevalue="" checked="true" optional="True" label="Use the number of peaks score" help="(-use_nr_peaks_score) "/> <param name="param_Scoring_Scores_use_total_xic_score" type="boolean" truevalue="-Scoring:Scores:use_total_xic_score" falsevalue="" checked="true" optional="True" label="Use the total XIC score" help="(-use_total_xic_score) "/> <param name="param_Scoring_Scores_use_sn_score" type="boolean" truevalue="-Scoring:Scores:use_sn_score" falsevalue="" checked="true" optional="True" label="Use the SN (signal to noise) score" help="(-use_sn_score) "/> <param name="param_Scoring_Scores_use_dia_scores" type="boolean" truevalue="-Scoring:Scores:use_dia_scores" falsevalue="" checked="true" optional="True" label="Use the DIA (SWATH) scores" help="(-use_dia_scores) "/> <param name="param_Scoring_Scores_use_ms1_correlation" type="boolean" truevalue="-Scoring:Scores:use_ms1_correlation" falsevalue="" checked="false" optional="True" label="Use the correlation scores with the MS1 elution profiles" help="(-use_ms1_correlation) "/> <param name="param_Scoring_Scores_use_ms1_fullscan" type="boolean" truevalue="-Scoring:Scores:use_ms1_fullscan" falsevalue="" 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) "/> </expand> </inputs> <outputs> <data name="out_features" format="featurexml"> <filter>output_fmt == 'featurexml'</filter> </data> <data name="out_tsv" format="tabular"> <filter>output_fmt == 'tsv'</filter> </data> <data name="param_out_chrom" format="mzml"/> </outputs> <help>**What it does** Complete workflow to run OpenSWATH For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_OpenSwathWorkflow.html</help> <expand macro="references"/> </tool>