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comparison NoiseFilterGaussian.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
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3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="NoiseFilterGaussian" name="NoiseFilterGaussian" version="1.12.0"> 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 <description>Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).</description> 3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
4 <macros> 4 <tool id="NoiseFilterGaussian" name="NoiseFilterGaussian" version="2.0.0">
5 <token name="@EXECUTABLE@">NoiseFilterGaussian</token> 5 <description>Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">NoiseFilterGaussian</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>NoiseFilterGaussian 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>NoiseFilterGaussian
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 -processOption inmemory 17 #end if
15 -threads \${GALAXY_SLOTS:-24} 18 #if $param_out:
16 -algorithm:gaussian_width ${param_gaussian_width} 19 -out $param_out
17 -algorithm:ppm_tolerance ${param_ppm_tolerance} 20 #end if
18 ${param_use_ppm_tolerance} 21 -threads \${GALAXY_SLOTS:-24}
22 #if $param_algorithm_gaussian_width:
23 -algorithm:gaussian_width $param_algorithm_gaussian_width
24 #end if
25 #if $param_algorithm_ppm_tolerance:
26 -algorithm:ppm_tolerance $param_algorithm_ppm_tolerance
27 #end if
28 #if $param_algorithm_use_ppm_tolerance:
29 -algorithm:use_ppm_tolerance
30 #end if
31 #if $adv_opts.adv_opts_selector=='advanced':
32 #if $adv_opts.param_processOption:
33 -processOption
34 #if &quot; &quot; in str($adv_opts.param_processOption):
35 &quot;$adv_opts.param_processOption&quot;
36 #else
37 $adv_opts.param_processOption
38 #end if
39 #end if
40 #if $adv_opts.param_force:
41 -force
42 #end if
43 #end if
19 </command> 44 </command>
20 <inputs> 45 <inputs>
21 <param name="param_in" type="data" format="mzML" optional="False" label="input raw data file " help="(-in)"/> 46 <param format="mzml" help="(-in) " label="input raw data file" name="param_in" optional="False" type="data"/>
22 <param name="param_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)"/> 47 <param help="(-gaussian_width) " label="Use a gaussian filter width which has approximately the same width as your mass peaks (FWHM in m/z)" name="param_algorithm_gaussian_width" type="float" value="0.2"/>
23 <param name="param_ppm_tolerance" type="float" value="10.0" label="Gaussian width, depending on the m/z position.#br#The higher the value, the wider the peak and therefore the wider the gaussian." help="(-ppm_tolerance)"/> 48 <param help="(-ppm_tolerance) &lt;br&gt;The higher the value, the wider the peak and therefore the wider the gaussian" label="Gaussian width, depending on the m/z position" name="param_algorithm_ppm_tolerance" type="float" value="10.0"/>
24 <param name="param_use_ppm_tolerance" type="boolean" truevalue="-algorithm:use_ppm_tolerance true" falsevalue="-algorithm:use_ppm_tolerance false" checked="false" optional="True" label="If true, instead of the gaussian_width value, the ppm_tolerance is used. The gaussian is calculated in each step anew, so this is much slower." help="(-use_ppm_tolerance)"/> 49 <param checked="false" falsevalue="" help="(-use_ppm_tolerance) The gaussian is calculated in each step anew, so this is much slower" label="If true, instead of the gaussian_width value, the ppm_tolerance is used" name="param_algorithm_use_ppm_tolerance" optional="True" truevalue="-algorithm:use_ppm_tolerance" type="boolean"/>
25 </inputs> 50 <expand macro="advanced_options">
26 <outputs> 51 <param help="(-processOption) " 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" name="param_processOption" optional="True" type="select" value="inmemory">
27 <data name="param_out" label="output raw data file " format="mzML"/> 52 <option value="inmemory">inmemory</option>
28 </outputs> 53 <option value="lowmemory">lowmemory</option>
29 <help>**What it does** 54 </param>
30 55 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
31 Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data). 56 </expand>
57 </inputs>
58 <outputs>
59 <data format="mzml" name="param_out"/>
60 </outputs>
61 <help>Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).
32 62
33 63
34 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_NoiseFilterGaussian.html 64 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_NoiseFilterGaussian.html</help>
35 65 </tool>
36 @REFERENCES@
37 </help>
38 </tool>