Mercurial > repos > bgruening > openms
view PeakPickerHiRes.xml @ 4:6ead64a594bd draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
| author | bgruening |
|---|---|
| date | Wed, 27 Jan 2016 10:06:49 -0500 |
| parents | 3d84209d3178 |
| children |
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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: [Signal processing and preprocessing]--> <tool id="PeakPickerHiRes" name="PeakPickerHiRes" version="2.0.0"> <description>Finds mass spectrometric peaks in profile mass spectra.</description> <macros> <token name="@EXECUTABLE@">PeakPickerHiRes</token> <import>macros.xml</import> </macros> <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command>PeakPickerHiRes #if $param_in: -in $param_in #end if #if $param_out: -out $param_out #end if -threads \${GALAXY_SLOTS:-24} #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_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 #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_processOption: -processOption #if " " in str($adv_opts.param_processOption): "$adv_opts.param_processOption" #else $adv_opts.param_processOption #end if #end if #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 format="mzml" help="(-in) " label="input profile data file" name="param_in" optional="False" type="data"/> <param help="(-signal_to_noise) " label="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" min="0.0" name="param_algorithm_signal_to_noise" optional="True" type="float" value="1.0"/> <repeat max="1" min="0" name="rep_param_algorithm_ms_levels" title="param_algorithm_ms_levels"> <param help="(-ms_levels) Other scans are copied to the output without changes" label="List of MS levels for which the peak picking is applied" min="1" name="param_algorithm_ms_levels" optional="True" size="30" type="text" value="1 2"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> </repeat> <param help="(-win_len) " label="window length in Thomson" min="1.0" name="param_algorithm_SignalToNoise_win_len" optional="True" type="float" value="200.0"/> <param help="(-bin_count) " label="number of bins for intensity values" min="3" name="param_algorithm_SignalToNoise_bin_count" optional="True" type="integer" value="30"/> <param help="(-min_required_elements) " label="minimum number of elements required in a window (otherwise it is considered sparse)" min="1" name="param_algorithm_SignalToNoise_min_required_elements" optional="True" type="integer" value="10"/> <param checked="true" falsevalue="" help="(-write_log_messages) " label="Write out log messages in case of sparse windows or median in rightmost histogram bin" name="param_algorithm_SignalToNoise_write_log_messages" optional="True" truevalue="-algorithm:SignalToNoise:write_log_messages" type="boolean"/> <expand macro="advanced_options"> <param help="(-processOption) " label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" name="param_processOption" optional="True" type="select" value="inmemory"> <option value="inmemory">inmemory</option> <option value="lowmemory">lowmemory</option> </param> <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/> <param 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" label="The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'" min="0.0" name="param_algorithm_spacing_difference_gap" optional="True" type="float" value="4.0"/> <param 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" label="Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points" min="0.0" name="param_algorithm_spacing_difference" optional="True" type="float" value="1.5"/> <param 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" label="Maximum number of missing points allowed when extending a peak to the left or to the right" min="0" name="param_algorithm_missing" optional="True" type="integer" value="1"/> <param 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" label="maximal intensity considered for histogram construction" min="-1" name="param_algorithm_SignalToNoise_max_intensity" optional="True" type="integer" value="-1"/> <param help="(-auto_max_stdev_factor) " label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" max="999.0" min="0.0" name="param_algorithm_SignalToNoise_auto_max_stdev_factor" optional="True" type="float" value="3.0"/> <param help="(-auto_max_percentile) " label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" max="100" min="0" name="param_algorithm_SignalToNoise_auto_max_percentile" optional="True" type="integer" value="95"/> <param help="(-auto_mode) " label="method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method" max="1" min="-1" name="param_algorithm_SignalToNoise_auto_mode" optional="True" type="integer" value="0"/> <param help="(-noise_for_empty_window) " label="noise value used for sparse windows" name="param_algorithm_SignalToNoise_noise_for_empty_window" type="float" value="1e+20"/> </expand> </inputs> <outputs> <data format="mzml" name="param_out"/> </outputs> <help>Finds mass spectrometric peaks in profile mass spectra. For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeakPickerHiRes.html</help> </tool>