Mercurial > repos > galaxyp > openms_noisefiltergaussian
comparison NoiseFilterGaussian.xml @ 13:47982606f542 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:19:06 +0000 |
parents | 038c7525527e |
children | 464f7877215b |
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12:da0add7a8abd | 13:47982606f542 |
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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> |