Mercurial > repos > galaxyp > openms_noisefiltersgolay
diff NoiseFilterSGolay.xml @ 0:2b7b288f2d2a draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author | galaxyp |
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date | Wed, 01 Mar 2017 12:21:55 -0500 |
parents | |
children | 1dd7a72aa16c |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NoiseFilterSGolay.xml Wed Mar 01 12:21:55 2017 -0500 @@ -0,0 +1,55 @@ +<?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="NoiseFilterSGolay" name="NoiseFilterSGolay" version="2.1.0"> + <description>Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.</description> + <macros> + <token name="@EXECUTABLE@">NoiseFilterSGolay</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>NoiseFilterSGolay + +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_algorithm_frame_length: + -algorithm:frame_length $param_algorithm_frame_length +#end if +#if $param_algorithm_polynomial_order: + -algorithm:polynomial_order $param_algorithm_polynomial_order +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_processOption: + -processOption $adv_opts.param_processOption +#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_frame_length" type="integer" value="11" label="The number of subsequent data points used for smoothing" help="(-frame_length) <br>This number has to be uneven. If it is not, 1 will be added"/> + <param name="param_algorithm_polynomial_order" type="integer" value="4" label="Order or the polynomial that is fitted" help="(-polynomial_order) "/> + <expand macro="advanced_options"> + <param name="param_processOption" display="radio" type="select" optional="False" 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" selected="true">inmemory</option> + <option value="lowmemory">lowmemory</option> + </param> + <param name="param_force" display="radio" 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>Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_NoiseFilterSGolay.html</help> +</tool>