Mercurial > repos > galaxyp > openms_mrmtransitiongrouppicker
diff MRMTransitionGroupPicker.xml @ 14:1c96645cbfbd draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
| author | galaxyp |
|---|---|
| date | Fri, 14 Jun 2024 21:35:06 +0000 |
| parents | 78796b50831b |
| children |
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--- a/MRMTransitionGroupPicker.xml Thu Dec 01 19:11:36 2022 +0000 +++ b/MRMTransitionGroupPicker.xml Fri Jun 14 21:35:06 2024 +0000 @@ -1,8 +1,7 @@ -<?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> -<!--Proposed Tool Section: [Utilities]--> +<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]--> <tool id="MRMTransitionGroupPicker" name="MRMTransitionGroupPicker" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>Picks peaks in SRM/MRM chromatograms.</description> + <description>Picks peaks in SRM/MRM chromatograms</description> <macros> <token name="@EXECUTABLE@">MRMTransitionGroupPicker</token> <import>macros.xml</import> @@ -15,9 +14,9 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir tr && -ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && +cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && mkdir out && ## Main program call @@ -43,18 +42,18 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/> - <param argument="-tr" type="data" format="csv,traml" optional="false" label="transition file ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/> + <param argument="-in" type="data" format="mzml" label="Input file" help=" select mzml data sets(s)"/> + <param argument="-tr" type="data" format="csv,traml" label="transition file ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/> <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> - <param name="stop_after_feature" argument="-algorithm:stop_after_feature" type="integer" optional="true" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/> - <param name="stop_after_intensity_ratio" argument="-algorithm:stop_after_intensity_ratio" type="float" optional="true" value="0.0001" label="Stop after reaching intensity ratio" help=""/> - <param name="min_peak_width" argument="-algorithm:min_peak_width" type="float" optional="true" value="0.001" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/> - <param name="peak_integration" argument="-algorithm:peak_integration" type="select" optional="true" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help=""> + <param name="stop_after_feature" argument="-algorithm:stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/> + <param name="stop_after_intensity_ratio" argument="-algorithm:stop_after_intensity_ratio" type="float" value="0.0001" label="Stop after reaching intensity ratio" help=""/> + <param name="min_peak_width" argument="-algorithm:min_peak_width" type="float" value="0.001" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/> + <param name="peak_integration" argument="-algorithm:peak_integration" type="select" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help=""> <option value="original" selected="true">original</option> <option value="smoothed">smoothed</option> <expand macro="list_string_san" name="peak_integration"/> </param> - <param name="background_subtraction" argument="-algorithm:background_subtraction" type="select" optional="true" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation"> + <param name="background_subtraction" argument="-algorithm:background_subtraction" type="select" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation"> <option value="none" selected="true">none</option> <option value="original">original</option> <option value="exact">exact</option> @@ -63,29 +62,29 @@ <param name="recalculate_peaks" argument="-algorithm:recalculate_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="Tries to use the consensus (median) peak border if the variation within the picked peaks is too large"/> <param name="use_precursors" argument="-algorithm:use_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use precursor chromatogram for peak picking (note that this may lead to precursor signal driving the peak picking)" help=""/> <param name="use_consensus" argument="-algorithm:use_consensus" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use consensus peak boundaries when computing transition group picking (if false, compute independent peak boundaries for each transition)" help=""/> - <param name="recalculate_peaks_max_z" argument="-algorithm:recalculate_peaks_max_z" type="float" optional="true" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/> - <param name="minimal_quality" argument="-algorithm:minimal_quality" type="float" optional="true" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help=""/> - <param name="resample_boundary" argument="-algorithm:resample_boundary" type="float" optional="true" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help=""/> + <param name="recalculate_peaks_max_z" argument="-algorithm:recalculate_peaks_max_z" type="float" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/> + <param name="minimal_quality" argument="-algorithm:minimal_quality" type="float" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help=""/> + <param name="resample_boundary" argument="-algorithm:resample_boundary" type="float" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help=""/> <param name="compute_peak_quality" argument="-algorithm:compute_peak_quality" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/> <param name="compute_peak_shape_metrics" argument="-algorithm:compute_peak_shape_metrics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculates various peak shape metrics" help="(e.g., tailing) that can be used for downstream QC/QA"/> <param name="compute_total_mi" argument="-algorithm:compute_total_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring" help=""/> - <param name="boundary_selection_method" argument="-algorithm:boundary_selection_method" type="select" optional="true" label="Method to use when selecting the best boundaries for peaks" help=""> + <param name="boundary_selection_method" argument="-algorithm:boundary_selection_method" type="select" label="Method to use when selecting the best boundaries for peaks" help=""> <option value="largest" selected="true">largest</option> <option value="widest">widest</option> <expand macro="list_string_san" name="boundary_selection_method"/> </param> <section name="PeakPickerMRM" title="" help="" expanded="false"> - <param name="sgolay_frame_length" argument="-algorithm:PeakPickerMRM:sgolay_frame_length" type="integer" optional="true" value="15" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/> - <param name="sgolay_polynomial_order" argument="-algorithm:PeakPickerMRM:sgolay_polynomial_order" type="integer" optional="true" value="3" label="Order of the polynomial that is fitted" help=""/> - <param name="gauss_width" argument="-algorithm:PeakPickerMRM:gauss_width" type="float" optional="true" value="50.0" label="Gaussian width in seconds, estimated peak size" help=""/> + <param name="sgolay_frame_length" argument="-algorithm:PeakPickerMRM:sgolay_frame_length" type="integer" value="15" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/> + <param name="sgolay_polynomial_order" argument="-algorithm:PeakPickerMRM:sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help=""/> + <param name="gauss_width" argument="-algorithm:PeakPickerMRM:gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help=""/> <param name="use_gauss" argument="-algorithm:PeakPickerMRM:use_gauss" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help=""/> - <param name="peak_width" argument="-algorithm:PeakPickerMRM:peak_width" type="float" optional="true" value="-1.0" label="Force a certain minimal peak_width on the data" help="(e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/> - <param name="signal_to_noise" argument="-algorithm:PeakPickerMRM:signal_to_noise" type="float" optional="true" min="0.0" value="1.0" label="Signal-to-noise threshold at which a peak will not be extended any more" help="Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured"/> - <param name="sn_win_len" argument="-algorithm:PeakPickerMRM:sn_win_len" type="float" optional="true" value="1000.0" label="Signal to noise window length" help=""/> - <param name="sn_bin_count" argument="-algorithm:PeakPickerMRM:sn_bin_count" type="integer" optional="true" value="30" label="Signal to noise bin count" help=""/> + <param name="peak_width" argument="-algorithm:PeakPickerMRM:peak_width" type="float" value="-1.0" label="Force a certain minimal peak_width on the data" help="(e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/> + <param name="signal_to_noise" argument="-algorithm:PeakPickerMRM:signal_to_noise" type="float" min="0.0" value="1.0" label="Signal-to-noise threshold at which a peak will not be extended any more" help="Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured"/> + <param name="sn_win_len" argument="-algorithm:PeakPickerMRM:sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help=""/> + <param name="sn_bin_count" argument="-algorithm:PeakPickerMRM:sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help=""/> <param name="write_sn_log_messages" argument="-algorithm:PeakPickerMRM:write_sn_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" help=""/> <param name="remove_overlapping_peaks" argument="-algorithm:PeakPickerMRM:remove_overlapping_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to remove overlapping peaks during peak picking" help=""/> - <param name="method" argument="-algorithm:PeakPickerMRM:method" type="select" optional="true" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help=""> + <param name="method" argument="-algorithm:PeakPickerMRM:method" type="select" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help=""> <option value="legacy">legacy</option> <option value="corrected" selected="true">corrected</option> <option value="crawdad">crawdad</option> @@ -93,13 +92,13 @@ </param> </section> <section name="PeakIntegrator" title="" help="" expanded="false"> - <param name="integration_type" argument="-algorithm:PeakIntegrator:integration_type" type="select" optional="true" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help=""> + <param name="integration_type" argument="-algorithm:PeakIntegrator:integration_type" type="select" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help=""> <option value="intensity_sum" selected="true">intensity_sum</option> <option value="simpson">simpson</option> <option value="trapezoid">trapezoid</option> <expand macro="list_string_san" name="integration_type"/> </param> - <param name="baseline_type" argument="-algorithm:PeakIntegrator:baseline_type" type="select" optional="true" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)"> + <param name="baseline_type" argument="-algorithm:PeakIntegrator:baseline_type" type="select" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)"> <option value="base_to_base" selected="true">base_to_base</option> <option value="vertical_division">vertical_division</option> <option value="vertical_division_min">vertical_division_min</option> @@ -111,7 +110,7 @@ </section> <expand macro="adv_opts_macro"> <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> <expand macro="list_string_san" name="test"/> </param> </expand> @@ -125,7 +124,8 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- UTILS_MRMTransitionGroupPicker_test_1 --> + <tests> + <!-- TOPP_MRMTransitionGroupPicker_test_1 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> @@ -133,7 +133,7 @@ </section> <param name="in" value="MRMTransitionGroupPicker_1_input.mzML"/> <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/> - <output name="out" file="MRMTransitionGroupPicker_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out" value="MRMTransitionGroupPicker_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <section name="algorithm"> <param name="stop_after_feature" value="-1"/> <param name="stop_after_intensity_ratio" value="0.0001"/> @@ -175,8 +175,11 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> - <!-- UTILS_MRMTransitionGroupPicker_test_2 --> + <!-- TOPP_MRMTransitionGroupPicker_test_2 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> @@ -184,7 +187,7 @@ </section> <param name="in" value="MRMTransitionGroupPicker_1_input.mzML"/> <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/> - <output name="out" file="MRMTransitionGroupPicker_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out" value="MRMTransitionGroupPicker_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <section name="algorithm"> <param name="stop_after_feature" value="-1"/> <param name="stop_after_intensity_ratio" value="0.0001"/> @@ -226,11 +229,14 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> </tests> <help><![CDATA[Picks peaks in SRM/MRM chromatograms. -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MRMTransitionGroupPicker.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MRMTransitionGroupPicker.html]]></help> <expand macro="references"/> </tool>