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view NoiseFilterGaussian.xml @ 1:e37e8ba1b4b7 draft
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author | bgruening |
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date | Thu, 16 Apr 2015 09:01:52 -0400 |
parents | 3070d71e0e5c |
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<?xml version='1.0' encoding='UTF-8'?> <tool id="NoiseFilterGaussian" name="NoiseFilterGaussian" version="2.0.0"> <description>Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).</description> <macros> <token name="@EXECUTABLE@">NoiseFilterGaussian</token> <import>macros.xml</import> </macros> <expand macro="stdio"/> <expand macro="requirements"/> <command>NoiseFilterGaussian #if $param_in: -in $param_in #end if #if $param_out: -out $param_out #end if -threads \${GALAXY_SLOTS:-24} #if $param_algorithm_gaussian_width: -algorithm:gaussian_width $param_algorithm_gaussian_width #end if #if $param_algorithm_ppm_tolerance: -algorithm:ppm_tolerance $param_algorithm_ppm_tolerance #end if #if $param_algorithm_use_ppm_tolerance: -algorithm:use_ppm_tolerance #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 #end if </command> <inputs> <param name="param_in" type="data" format="mzml" optional="False" label="input raw data file" help="(-in) "/> <param name="param_algorithm_gaussian_width" type="float" value="0.2" label="Use a gaussian filter width which has approximately the same width as your mass peaks (FWHM in m/z)" help="(-gaussian_width) "/> <param name="param_algorithm_ppm_tolerance" type="float" value="10.0" label="Gaussian width, depending on the m/z position" help="(-ppm_tolerance) <br>The higher the value, the wider the peak and therefore the wider the gaussian"/> <param name="param_algorithm_use_ppm_tolerance" type="boolean" truevalue="-algorithm:use_ppm_tolerance" falsevalue="" checked="false" optional="True" label="If true, instead of the gaussian_width value, the ppm_tolerance is used" help="(-use_ppm_tolerance) The gaussian is calculated in each step anew, so this is much slower"/> <expand macro="advanced_options"> <param name="param_processOption" type="select" optional="True" value="inmemory" 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" help="(-processOption) "> <option value="inmemory">inmemory</option> <option value="lowmemory">lowmemory</option> </param> <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> </expand> </inputs> <outputs> <data name="param_out" format="mzml"/> </outputs> <help>**What it does** Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data). For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_NoiseFilterGaussian.html</help> <expand macro="references"/> </tool>