Mercurial > repos > galaxyp > openms_noisefiltersgolay
comparison 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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-1:000000000000 | 0:2b7b288f2d2a |
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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.--> | |
3 <!--Proposed Tool Section: [Signal processing and preprocessing]--> | |
4 <tool id="NoiseFilterSGolay" name="NoiseFilterSGolay" version="2.1.0"> | |
5 <description>Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.</description> | |
6 <macros> | |
7 <token name="@EXECUTABLE@">NoiseFilterSGolay</token> | |
8 <import>macros.xml</import> | |
9 </macros> | |
10 <expand macro="references"/> | |
11 <expand macro="stdio"/> | |
12 <expand macro="requirements"/> | |
13 <command>NoiseFilterSGolay | |
14 | |
15 #if $param_in: | |
16 -in $param_in | |
17 #end if | |
18 #if $param_out: | |
19 -out $param_out | |
20 #end if | |
21 #if $param_algorithm_frame_length: | |
22 -algorithm:frame_length $param_algorithm_frame_length | |
23 #end if | |
24 #if $param_algorithm_polynomial_order: | |
25 -algorithm:polynomial_order $param_algorithm_polynomial_order | |
26 #end if | |
27 #if $adv_opts.adv_opts_selector=='advanced': | |
28 #if $adv_opts.param_processOption: | |
29 -processOption $adv_opts.param_processOption | |
30 #end if | |
31 #if $adv_opts.param_force: | |
32 -force | |
33 #end if | |
34 #end if | |
35 </command> | |
36 <inputs> | |
37 <param name="param_in" type="data" format="mzml" optional="False" label="input raw data file" help="(-in) "/> | |
38 <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"/> | |
39 <param name="param_algorithm_polynomial_order" type="integer" value="4" label="Order or the polynomial that is fitted" help="(-polynomial_order) "/> | |
40 <expand macro="advanced_options"> | |
41 <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) "> | |
42 <option value="inmemory" selected="true">inmemory</option> | |
43 <option value="lowmemory">lowmemory</option> | |
44 </param> | |
45 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
46 </expand> | |
47 </inputs> | |
48 <outputs> | |
49 <data name="param_out" format="mzml"/> | |
50 </outputs> | |
51 <help>Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data. | |
52 | |
53 | |
54 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_NoiseFilterSGolay.html</help> | |
55 </tool> |