|
0
|
1 <?xml version='1.0' encoding='UTF-8'?>
|
|
|
2 <tool id="NoiseFilterGaussian" name="NoiseFilterGaussian" version="2.0.0">
|
|
|
3 <description>Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).</description>
|
|
|
4 <macros>
|
|
|
5 <token name="@EXECUTABLE@">NoiseFilterGaussian</token>
|
|
|
6 <import>macros.xml</import>
|
|
|
7 </macros>
|
|
|
8 <expand macro="stdio"/>
|
|
|
9 <expand macro="requirements"/>
|
|
|
10 <command>NoiseFilterGaussian
|
|
|
11
|
|
|
12 #if $param_in:
|
|
|
13 -in $param_in
|
|
|
14 #end if
|
|
|
15 #if $param_out:
|
|
|
16 -out $param_out
|
|
|
17 #end if
|
|
|
18 -threads \${GALAXY_SLOTS:-24}
|
|
|
19 #if $param_algorithm_gaussian_width:
|
|
|
20 -algorithm:gaussian_width $param_algorithm_gaussian_width
|
|
|
21 #end if
|
|
|
22 #if $param_algorithm_ppm_tolerance:
|
|
|
23 -algorithm:ppm_tolerance $param_algorithm_ppm_tolerance
|
|
|
24 #end if
|
|
|
25 #if $param_algorithm_use_ppm_tolerance:
|
|
|
26 -algorithm:use_ppm_tolerance
|
|
|
27 #end if
|
|
|
28 #if $adv_opts.adv_opts_selector=='advanced':
|
|
|
29 #if $adv_opts.param_processOption:
|
|
|
30 -processOption
|
|
|
31 #if " " in str($adv_opts.param_processOption):
|
|
|
32 "$adv_opts.param_processOption"
|
|
|
33 #else
|
|
|
34 $adv_opts.param_processOption
|
|
|
35 #end if
|
|
|
36 #end if
|
|
|
37 #if $adv_opts.param_force:
|
|
|
38 -force
|
|
|
39 #end if
|
|
|
40 #end if
|
|
|
41 </command>
|
|
|
42 <inputs>
|
|
|
43 <param name="param_in" type="data" format="mzml" optional="False" label="input raw data file" help="(-in) "/>
|
|
|
44 <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) "/>
|
|
|
45 <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"/>
|
|
|
46 <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"/>
|
|
|
47 <expand macro="advanced_options">
|
|
|
48 <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) ">
|
|
|
49 <option value="inmemory">inmemory</option>
|
|
|
50 <option value="lowmemory">lowmemory</option>
|
|
|
51 </param>
|
|
|
52 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
|
|
|
53 </expand>
|
|
|
54 </inputs>
|
|
|
55 <outputs>
|
|
|
56 <data name="param_out" format="mzml"/>
|
|
|
57 </outputs>
|
|
|
58 <help>**What it does**
|
|
|
59
|
|
|
60 Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).
|
|
|
61
|
|
|
62
|
|
|
63 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_NoiseFilterGaussian.html</help>
|
|
|
64 <expand macro="references"/>
|
|
|
65 </tool>
|
