Mercurial > repos > galaxyp > openms_peakpickerwavelet

comparison PeakPickerWavelet.xml @ 12:81ab5441f18c draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 05:54:59 -0400
parents b05ee1050b5e
children 22f988ca1de4
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equal deleted inserted replaced
11:755fb2fe06a3 12:81ab5441f18c
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Signal processing and preprocessing]--> 3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
4 <tool id="PeakPickerWavelet" name="PeakPickerWavelet" version="2.2.0"> 4 <tool id="PeakPickerWavelet" name="PeakPickerWavelet" version="2.3.0">
5 <description>Finds mass spectrometric peaks in profile mass spectra.</description> 5 <description>Finds mass spectrometric peaks in profile mass spectra.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">PeakPickerWavelet</token> 7 <token name="@EXECUTABLE@">PeakPickerWavelet</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
10 <expand macro="references"/> 10 <expand macro="references"/>
11 <expand macro="stdio"/> 11 <expand macro="stdio"/>
12 <expand macro="requirements"/> 12 <expand macro="requirements"/>
13 <command>PeakPickerWavelet 13 <command detect_errors="aggressive"><![CDATA[PeakPickerWavelet
14 14
15 #if $param_in: 15 #if $param_in:
16 -in $param_in 16 -in $param_in
17 #end if 17 #end if
18 #if $param_out: 18 #if $param_out:
147 #end if 147 #end if
148 #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_noise_for_empty_window: 148 #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_noise_for_empty_window:
149 -algorithm:SignalToNoiseEstimationParameter:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_noise_for_empty_window 149 -algorithm:SignalToNoiseEstimationParameter:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_noise_for_empty_window
150 #end if 150 #end if
151 #end if 151 #end if
152 </command> 152 ]]></command>
153 <inputs> 153 <inputs>
154 <param name="param_in" type="data" format="mzml" optional="False" label="input profile data file" help="(-in) "/> 154 <param name="param_in" type="data" format="mzml" optional="False" label="input profile data file" help="(-in) "/>
155 <param name="param_algorithm_signal_to_noise" type="float" min="0.0" optional="True" value="1.0" label="Minimal signal to noise ratio for a peak to be picked" help="(-signal_to_noise) "/> 155 <param name="param_algorithm_signal_to_noise" type="float" min="0.0" optional="True" value="1.0" label="Minimal signal to noise ratio for a peak to be picked" help="(-signal_to_noise) "/>
156 <param name="param_algorithm_peak_width" type="float" min="0.0" optional="True" value="0.15" label="Approximate fwhm of the peaks" help="(-peak_width) "/> 156 <param name="param_algorithm_peak_width" type="float" min="0.0" optional="True" value="0.15" label="Approximate fwhm of the peaks" help="(-peak_width) "/>
157 <param name="param_algorithm_estimate_peak_width" display="radio" type="boolean" truevalue="-algorithm:estimate_peak_width" falsevalue="" checked="false" optional="True" label="Flag if the average peak width shall be estimated" help="(-estimate_peak_width) Attention: when this flag is set, the peak_width is ignored"/> 157 <param name="param_algorithm_estimate_peak_width" display="radio" type="boolean" truevalue="-algorithm:estimate_peak_width" falsevalue="" checked="false" optional="True" label="Flag if the average peak width shall be estimated" help="(-estimate_peak_width) Attention: when this flag is set, the peak_width is ignored"/>
202 <data name="param_out" format="mzml"/> 202 <data name="param_out" format="mzml"/>
203 </outputs> 203 </outputs>
204 <help>Finds mass spectrometric peaks in profile mass spectra. 204 <help>Finds mass spectrometric peaks in profile mass spectra.
205 205
206 206
207 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeakPickerWavelet.html</help> 207 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_PeakPickerWavelet.html</help>
208 </tool> 208 </tool>