Mercurial > repos > galaxyp > openms_noisefiltergaussian

comparison NoiseFilterGaussian.xml @ 9:4b6ea1de6dc4 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 20:06:56 +0000
parents f3524fcfb491
children 038c7525527e
comparison
equal deleted inserted replaced
8:26f04cb8795b 9:4b6ea1de6dc4
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 CTDConverter.--> 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="NoiseFilterGaussian" name="NoiseFilterGaussian" version="2.3.0"> 4 <tool id="NoiseFilterGaussian" name="NoiseFilterGaussian" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).</description> 5 <description>Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">NoiseFilterGaussian</token> 7 <token name="@EXECUTABLE@">NoiseFilterGaussian</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[NoiseFilterGaussian 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
17 #end if 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
18 #if $param_out: 21 mkdir out &&
19 -out $param_out 22
20 #end if 23 ## Main program call
21 #if $param_algorithm_gaussian_width: 24
22 -algorithm:gaussian_width $param_algorithm_gaussian_width 25 set -o pipefail &&
23 #end if 26 @EXECUTABLE@ -write_ctd ./ &&
24 #if $param_algorithm_ppm_tolerance: 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
25 -algorithm:ppm_tolerance $param_algorithm_ppm_tolerance 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
26 #end if 29 -in
27 #if $param_algorithm_use_ppm_tolerance: 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
28 -algorithm:use_ppm_tolerance 31 -out
29 #end if 32 'out/output.${gxy2omsext("mzml")}'
30 #if $adv_opts.adv_opts_selector=='advanced': 33
31 #if $adv_opts.param_processOption: 34 ## Postprocessing
32 -processOption 35 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
33 #if " " in str($adv_opts.param_processOption): 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
34 "$adv_opts.param_processOption" 37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
35 #else 38 #end if]]></command>
36 $adv_opts.param_processOption 39 <configfiles>
37 #end if 40 <inputs name="args_json" data_style="paths"/>
38 #end if 41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
39 #if $adv_opts.param_force: 42 </configfiles>
40 -force
41 #end if
42 #end if
43 ]]></command>
44 <inputs> 43 <inputs>
45 <param name="param_in" type="data" format="mzml" optional="False" label="input raw data file" help="(-in) "/> 44 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input raw data file" help=" select mzml data sets(s)"/>
46 <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 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
47 <param name="param_algorithm_ppm_tolerance" type="float" value="10.0" label="Gaussian width, depending on the m/z position" help="(-ppm_tolerance) &lt;br&gt;The higher the value, the wider the peak and therefore the wider the gaussian"/> 46 <param name="gaussian_width" argument="-algorithm:gaussian_width" type="float" optional="true" value="0.2" label="Use a gaussian filter width which has approximately the same width as your mass peaks (FWHM in m/z)" help=""/>
48 <param name="param_algorithm_use_ppm_tolerance" display="radio" 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 <param name="ppm_tolerance" argument="-algorithm:ppm_tolerance" type="float" optional="true" value="10.0" label="Gaussian width, depending on the m/z position" help="The higher the value, the wider the peak and therefore the wider the gaussian"/>
49 <expand macro="advanced_options"> 48 <param name="use_ppm_tolerance" argument="-algorithm:use_ppm_tolerance" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, instead of the gaussian_width value, the ppm_tolerance is used" help="The gaussian is calculated in each step anew, so this is much slower"/>
50 <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) "> 49 </section>
50 <expand macro="adv_opts_macro">
51 <param name="processOption" argument="-processOption" display="radio" type="select" optional="false" 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="">
51 <option value="inmemory" selected="true">inmemory</option> 52 <option value="inmemory" selected="true">inmemory</option>
52 <option value="lowmemory">lowmemory</option> 53 <option value="lowmemory">lowmemory</option>
54 <expand macro="list_string_san"/>
53 </param> 55 </param>
54 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 56 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
57 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
58 <expand macro="list_string_san"/>
59 </param>
55 </expand> 60 </expand>
61 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
62 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
63 </param>
56 </inputs> 64 </inputs>
57 <outputs> 65 <outputs>
58 <data name="param_out" format="mzml"/> 66 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
67 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
68 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
69 </data>
59 </outputs> 70 </outputs>
60 <help>Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data). 71 <tests>
72 <expand macro="autotest_NoiseFilterGaussian"/>
73 <expand macro="manutest_NoiseFilterGaussian"/>
74 </tests>
75 <help><![CDATA[Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).
61 76
62 77
63 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_NoiseFilterGaussian.html</help> 78 For more information, visit http://www.openms.de/documentation/TOPP_NoiseFilterGaussian.html]]></help>
79 <expand macro="references"/>
64 </tool> 80 </tool>