Mercurial > repos > galaxyp > openms_noisefiltergaussian

comparison NoiseFilterGaussian.xml @ 13:47982606f542 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:19:06 +0000
parents 038c7525527e
children 464f7877215b
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12:da0add7a8abd 13:47982606f542
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="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="NoiseFilterGaussian" name="NoiseFilterGaussian" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
39 <configfiles> 37 <configfiles>
40 <inputs name="args_json" data_style="paths"/> 38 <inputs name="args_json" data_style="paths"/>
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles> 40 </configfiles>
43 <inputs> 41 <inputs>
44 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input raw data file" help=" select mzml data sets(s)"/> 42 <param argument="-in" type="data" format="mzml" optional="false" label="input raw data file" help=" select mzml data sets(s)"/>
45 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> 43 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
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=""/> 44 <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=""/>
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"/> 45 <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"/>
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"/> 46 <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"/>
47 <param name="write_log_messages" argument="-algorithm:write_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="false" label="true: Warn if no signal was found by the Gauss filter algorithm" help=""/>
49 </section> 48 </section>
50 <expand macro="adv_opts_macro"> 49 <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=""> 50 <param argument="-processOption" type="select" optional="true" 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="">
52 <option value="inmemory" selected="true">inmemory</option> 51 <option value="inmemory" selected="true">inmemory</option>
53 <option value="lowmemory">lowmemory</option> 52 <option value="lowmemory">lowmemory</option>
54 <expand macro="list_string_san"/> 53 <expand macro="list_string_san" name="processOption"/>
55 </param> 54 </param>
56 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 55 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides 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=""> 56 <param 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"/> 57 <expand macro="list_string_san" name="test"/>
59 </param> 58 </param>
60 </expand> 59 </expand>
61 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 60 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
62 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 61 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
63 </param> 62 </param>
66 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 65 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
67 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 66 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
68 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 67 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
69 </data> 68 </data>
70 </outputs> 69 </outputs>
71 <tests> 70 <tests><!-- TOPP_NoiseFilterGaussian_1 -->
72 <expand macro="autotest_NoiseFilterGaussian"/> 71 <test expect_num_outputs="2">
73 <expand macro="manutest_NoiseFilterGaussian"/> 72 <section name="adv_opts">
73 <param name="processOption" value="inmemory"/>
74 <param name="force" value="false"/>
75 <param name="test" value="true"/>
76 </section>
77 <param name="in" value="NoiseFilterGaussian_1_input.mzML"/>
78 <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
79 <section name="algorithm">
80 <param name="gaussian_width" value="1.0"/>
81 <param name="ppm_tolerance" value="10.0"/>
82 <param name="use_ppm_tolerance" value="false"/>
83 <param name="write_log_messages" value="false"/>
84 </section>
85 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
86 <output name="ctd_out" ftype="xml">
87 <assert_contents>
88 <is_valid_xml/>
89 </assert_contents>
90 </output>
91 </test>
92 <!-- TOPP_NoiseFilterGaussian_2 -->
93 <test expect_num_outputs="2">
94 <section name="adv_opts">
95 <param name="processOption" value="inmemory"/>
96 <param name="force" value="false"/>
97 <param name="test" value="true"/>
98 </section>
99 <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/>
100 <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
101 <section name="algorithm">
102 <param name="gaussian_width" value="50.0"/>
103 <param name="ppm_tolerance" value="10.0"/>
104 <param name="use_ppm_tolerance" value="false"/>
105 <param name="write_log_messages" value="false"/>
106 </section>
107 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
108 <output name="ctd_out" ftype="xml">
109 <assert_contents>
110 <is_valid_xml/>
111 </assert_contents>
112 </output>
113 </test>
114 <!-- TOPP_NoiseFilterGaussian_3 -->
115 <test expect_num_outputs="2">
116 <section name="adv_opts">
117 <param name="processOption" value="lowmemory"/>
118 <param name="force" value="false"/>
119 <param name="test" value="true"/>
120 </section>
121 <param name="in" value="NoiseFilterGaussian_1_input.mzML"/>
122 <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
123 <section name="algorithm">
124 <param name="gaussian_width" value="1.0"/>
125 <param name="ppm_tolerance" value="10.0"/>
126 <param name="use_ppm_tolerance" value="false"/>
127 <param name="write_log_messages" value="false"/>
128 </section>
129 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
130 <output name="ctd_out" ftype="xml">
131 <assert_contents>
132 <is_valid_xml/>
133 </assert_contents>
134 </output>
135 </test>
136 <!-- TOPP_NoiseFilterGaussian_4 -->
137 <test expect_num_outputs="2">
138 <section name="adv_opts">
139 <param name="processOption" value="lowmemory"/>
140 <param name="force" value="false"/>
141 <param name="test" value="true"/>
142 </section>
143 <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/>
144 <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
145 <section name="algorithm">
146 <param name="gaussian_width" value="50.0"/>
147 <param name="ppm_tolerance" value="10.0"/>
148 <param name="use_ppm_tolerance" value="false"/>
149 <param name="write_log_messages" value="false"/>
150 </section>
151 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
152 <output name="ctd_out" ftype="xml">
153 <assert_contents>
154 <is_valid_xml/>
155 </assert_contents>
156 </output>
157 </test>
74 </tests> 158 </tests>
75 <help><![CDATA[Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data). 159 <help><![CDATA[Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).
76 160
77 161
78 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_NoiseFilterGaussian.html]]></help> 162 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_NoiseFilterGaussian.html]]></help>
79 <expand macro="references"/> 163 <expand macro="references"/>
80 </tool> 164 </tool>