Mercurial > repos > galaxyp > openms_lowmempeakpickerhires
view LowMemPeakPickerHiRes.xml @ 3:f36f545e6ce4 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d4b74e94ddabaccec6b1c5f9540d074c39207600
author | galaxyp |
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date | Sat, 28 Oct 2017 05:16:04 -0400 |
parents | c9c2a39c94de |
children | afb20fdaec5e |
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<?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 CTD2Galaxy.--> <!--Proposed Tool Section: [Utilities]--> <tool id="LowMemPeakPickerHiRes" name="LowMemPeakPickerHiRes" version="2.2.0"> <description>Finds mass spectrometric peaks in profile mass spectra.</description> <macros> <token name="@EXECUTABLE@">LowMemPeakPickerHiRes</token> <import>macros.xml</import> </macros> <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command>LowMemPeakPickerHiRes #if $param_in: -in $param_in #end if #if $param_out: -out $param_out #end if #if $param_algorithm_signal_to_noise: -algorithm:signal_to_noise $param_algorithm_signal_to_noise #end if #if $rep_param_algorithm_ms_levels: -algorithm:ms_levels #for token in $rep_param_algorithm_ms_levels: #if " " in str(token): "$token.param_algorithm_ms_levels" #else $token.param_algorithm_ms_levels #end if #end for #end if #if $param_algorithm_report_FWHM: -algorithm:report_FWHM #end if #if $param_algorithm_report_FWHM_unit: -algorithm:report_FWHM_unit #if " " in str($param_algorithm_report_FWHM_unit): "$param_algorithm_report_FWHM_unit" #else $param_algorithm_report_FWHM_unit #end if #end if #if $param_algorithm_SignalToNoise_win_len: -algorithm:SignalToNoise:win_len $param_algorithm_SignalToNoise_win_len #end if #if $param_algorithm_SignalToNoise_bin_count: -algorithm:SignalToNoise:bin_count $param_algorithm_SignalToNoise_bin_count #end if #if $param_algorithm_SignalToNoise_min_required_elements: -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements #end if #if $param_algorithm_SignalToNoise_write_log_messages: -algorithm:SignalToNoise:write_log_messages #if " " in str($param_algorithm_SignalToNoise_write_log_messages): "$param_algorithm_SignalToNoise_write_log_messages" #else $param_algorithm_SignalToNoise_write_log_messages #end if #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force: -force #end if #if $adv_opts.param_algorithm_spacing_difference_gap: -algorithm:spacing_difference_gap $adv_opts.param_algorithm_spacing_difference_gap #end if #if $adv_opts.param_algorithm_spacing_difference: -algorithm:spacing_difference $adv_opts.param_algorithm_spacing_difference #end if #if $adv_opts.param_algorithm_missing: -algorithm:missing $adv_opts.param_algorithm_missing #end if #if $adv_opts.param_algorithm_SignalToNoise_max_intensity: -algorithm:SignalToNoise:max_intensity $adv_opts.param_algorithm_SignalToNoise_max_intensity #end if #if $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor: -algorithm:SignalToNoise:auto_max_stdev_factor $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor #end if #if $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile: -algorithm:SignalToNoise:auto_max_percentile $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile #end if #if $adv_opts.param_algorithm_SignalToNoise_auto_mode: -algorithm:SignalToNoise:auto_mode $adv_opts.param_algorithm_SignalToNoise_auto_mode #end if #if $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window: -algorithm:SignalToNoise:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window #end if #end if </command> <inputs> <param name="param_in" type="data" format="mzml" optional="False" label="input profile data file" help="(-in) "/> <param name="param_algorithm_signal_to_noise" type="float" min="0.0" optional="True" value="0.0" label="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" help="(-signal_to_noise) "/> <repeat name="rep_param_algorithm_ms_levels" min="0" max="1" title="param_algorithm_ms_levels"> <param name="param_algorithm_ms_levels" type="text" min="1" optional="True" size="30" value="1" label="List of MS levels for which the peak picking is applied" help="(-ms_levels) Other scans are copied to the output without changes"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> </repeat> <param name="param_algorithm_report_FWHM" display="radio" type="boolean" truevalue="-algorithm:report_FWHM" falsevalue="" checked="false" optional="True" label="Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak" help="(-report_FWHM) "/> <param name="param_algorithm_report_FWHM_unit" display="radio" type="select" optional="False" value="relative" label="Unit of FWHM. Either absolute in the unit of input," help="(-report_FWHM_unit) e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms)"> <option value="relative" selected="true">relative</option> <option value="absolute">absolute</option> </param> <param name="param_algorithm_SignalToNoise_win_len" type="float" min="1.0" optional="True" value="200.0" label="window length in Thomson" help="(-win_len) "/> <param name="param_algorithm_SignalToNoise_bin_count" type="integer" min="3" optional="True" value="30" label="number of bins for intensity values" help="(-bin_count) "/> <param name="param_algorithm_SignalToNoise_min_required_elements" type="integer" min="1" optional="True" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help="(-min_required_elements) "/> <param name="param_algorithm_SignalToNoise_write_log_messages" display="radio" type="select" optional="False" value="true" label="Write out log messages in case of sparse windows or median in rightmost histogram bin" help="(-write_log_messages) "> <option value="true" selected="true">true</option> <option value="false">false</option> </param> <expand macro="advanced_options"> <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> <param name="param_algorithm_spacing_difference_gap" type="float" min="0.0" optional="True" value="4.0" label="The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'" help="(-spacing_difference_gap) 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. '0' to disable the constraint. Not applicable to chromatograms"/> <param name="param_algorithm_spacing_difference" type="float" min="0.0" optional="True" value="1.5" label="Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points" help="(-spacing_difference) If this difference is exceeded a missing point is assumed (see parameter 'missing'). A higher value implies a less stringent peak definition, since individual signals within the peak are allowed to be further apart. '0' to disable the constraint. Not applicable to chromatograms"/> <param name="param_algorithm_missing" type="integer" min="0" optional="True" value="1" label="Maximum number of missing points allowed when extending a peak to the left or to the right" help="(-missing) A missing data point occurs if the spacing between two subsequent data points exceeds 'spacing_difference * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. Not applicable to chromatograms"/> <param name="param_algorithm_SignalToNoise_max_intensity" type="integer" min="-1" optional="True" value="-1" label="maximal intensity considered for histogram construction" help="(-max_intensity) By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N"/> <param name="param_algorithm_SignalToNoise_auto_max_stdev_factor" type="float" min="0.0" max="999.0" optional="True" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help="(-auto_max_stdev_factor) "/> <param name="param_algorithm_SignalToNoise_auto_max_percentile" type="integer" min="0" max="100" optional="True" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help="(-auto_max_percentile) "/> <param name="param_algorithm_SignalToNoise_auto_mode" type="integer" min="-1" max="1" optional="True" value="0" label="method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method" help="(-auto_mode) "/> <param name="param_algorithm_SignalToNoise_noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help="(-noise_for_empty_window) "/> </expand> </inputs> <outputs> <data name="param_out" format="mzml"/> </outputs> <help>Finds mass spectrometric peaks in profile mass spectra. For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_LowMemPeakPickerHiRes.html</help> </tool>