Mercurial > repos > galaxyp > openms_noisefiltergaussian
comparison NoiseFilterGaussian.xml @ 14:464f7877215b draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author | galaxyp |
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date | Fri, 14 Jun 2024 21:37:30 +0000 |
parents | 47982606f542 |
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13:47982606f542 | 14:464f7877215b |
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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.--> | 1 <!--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]--> | 2 <!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]--> |
4 <tool id="NoiseFilterGaussian" name="NoiseFilterGaussian" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | 3 <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> | 4 <description>Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data)</description> |
6 <macros> | 5 <macros> |
7 <token name="@EXECUTABLE@">NoiseFilterGaussian</token> | 6 <token name="@EXECUTABLE@">NoiseFilterGaussian</token> |
8 <import>macros.xml</import> | 7 <import>macros.xml</import> |
9 </macros> | 8 </macros> |
10 <expand macro="requirements"/> | 9 <expand macro="requirements"/> |
13 @EXT_FOO@ | 12 @EXT_FOO@ |
14 #import re | 13 #import re |
15 | 14 |
16 ## Preprocessing | 15 ## Preprocessing |
17 mkdir in && | 16 mkdir in && |
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && | 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && |
19 mkdir out && | 18 mkdir out && |
20 | 19 |
21 ## Main program call | 20 ## Main program call |
22 | 21 |
23 set -o pipefail && | 22 set -o pipefail && |
37 <configfiles> | 36 <configfiles> |
38 <inputs name="args_json" data_style="paths"/> | 37 <inputs name="args_json" data_style="paths"/> |
39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | 38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
40 </configfiles> | 39 </configfiles> |
41 <inputs> | 40 <inputs> |
42 <param argument="-in" type="data" format="mzml" optional="false" label="input raw data file" help=" select mzml data sets(s)"/> | 41 <param argument="-in" type="data" format="mzml" label="input raw data file" help=" select mzml data sets(s)"/> |
43 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> | 42 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> |
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=""/> | 43 <param name="gaussian_width" argument="-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=""/> |
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"/> | 44 <param name="ppm_tolerance" argument="-algorithm:ppm_tolerance" type="float" 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"/> |
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"/> | 45 <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=""/> | 46 <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=""/> |
48 </section> | 47 </section> |
49 <expand macro="adv_opts_macro"> | 48 <expand macro="adv_opts_macro"> |
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=""> | 49 <param argument="-processOption" type="select" 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> | 50 <option value="inmemory" selected="true">inmemory</option> |
52 <option value="lowmemory">lowmemory</option> | 51 <option value="lowmemory">lowmemory</option> |
53 <expand macro="list_string_san" name="processOption"/> | 52 <expand macro="list_string_san" name="processOption"/> |
54 </param> | 53 </param> |
55 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 54 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
56 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 55 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> |
57 <expand macro="list_string_san" name="test"/> | 56 <expand macro="list_string_san" name="test"/> |
58 </param> | 57 </param> |
59 </expand> | 58 </expand> |
60 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 59 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
61 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 60 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
65 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> | 64 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> |
66 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 65 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
67 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 66 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
68 </data> | 67 </data> |
69 </outputs> | 68 </outputs> |
70 <tests><!-- TOPP_NoiseFilterGaussian_1 --> | 69 <tests> |
70 <!-- TOPP_NoiseFilterGaussian_1 --> | |
71 <test expect_num_outputs="2"> | 71 <test expect_num_outputs="2"> |
72 <section name="adv_opts"> | 72 <section name="adv_opts"> |
73 <param name="processOption" value="inmemory"/> | 73 <param name="processOption" value="inmemory"/> |
74 <param name="force" value="false"/> | 74 <param name="force" value="false"/> |
75 <param name="test" value="true"/> | 75 <param name="test" value="true"/> |
76 </section> | 76 </section> |
77 <param name="in" value="NoiseFilterGaussian_1_input.mzML"/> | 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"/> | 78 <output name="out" value="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
79 <section name="algorithm"> | 79 <section name="algorithm"> |
80 <param name="gaussian_width" value="1.0"/> | 80 <param name="gaussian_width" value="1.0"/> |
81 <param name="ppm_tolerance" value="10.0"/> | 81 <param name="ppm_tolerance" value="10.0"/> |
82 <param name="use_ppm_tolerance" value="false"/> | 82 <param name="use_ppm_tolerance" value="false"/> |
83 <param name="write_log_messages" value="false"/> | 83 <param name="write_log_messages" value="false"/> |
86 <output name="ctd_out" ftype="xml"> | 86 <output name="ctd_out" ftype="xml"> |
87 <assert_contents> | 87 <assert_contents> |
88 <is_valid_xml/> | 88 <is_valid_xml/> |
89 </assert_contents> | 89 </assert_contents> |
90 </output> | 90 </output> |
91 <assert_stdout> | |
92 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> | |
93 </assert_stdout> | |
91 </test> | 94 </test> |
92 <!-- TOPP_NoiseFilterGaussian_2 --> | 95 <!-- TOPP_NoiseFilterGaussian_2 --> |
93 <test expect_num_outputs="2"> | 96 <test expect_num_outputs="2"> |
94 <section name="adv_opts"> | 97 <section name="adv_opts"> |
95 <param name="processOption" value="inmemory"/> | 98 <param name="processOption" value="inmemory"/> |
96 <param name="force" value="false"/> | 99 <param name="force" value="false"/> |
97 <param name="test" value="true"/> | 100 <param name="test" value="true"/> |
98 </section> | 101 </section> |
99 <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/> | 102 <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"/> | 103 <output name="out" value="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
101 <section name="algorithm"> | 104 <section name="algorithm"> |
102 <param name="gaussian_width" value="50.0"/> | 105 <param name="gaussian_width" value="50.0"/> |
103 <param name="ppm_tolerance" value="10.0"/> | 106 <param name="ppm_tolerance" value="10.0"/> |
104 <param name="use_ppm_tolerance" value="false"/> | 107 <param name="use_ppm_tolerance" value="false"/> |
105 <param name="write_log_messages" value="false"/> | 108 <param name="write_log_messages" value="false"/> |
108 <output name="ctd_out" ftype="xml"> | 111 <output name="ctd_out" ftype="xml"> |
109 <assert_contents> | 112 <assert_contents> |
110 <is_valid_xml/> | 113 <is_valid_xml/> |
111 </assert_contents> | 114 </assert_contents> |
112 </output> | 115 </output> |
116 <assert_stdout> | |
117 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> | |
118 </assert_stdout> | |
113 </test> | 119 </test> |
114 <!-- TOPP_NoiseFilterGaussian_3 --> | 120 <!-- TOPP_NoiseFilterGaussian_3 --> |
115 <test expect_num_outputs="2"> | 121 <test expect_num_outputs="2"> |
116 <section name="adv_opts"> | 122 <section name="adv_opts"> |
117 <param name="processOption" value="lowmemory"/> | 123 <param name="processOption" value="lowmemory"/> |
118 <param name="force" value="false"/> | 124 <param name="force" value="false"/> |
119 <param name="test" value="true"/> | 125 <param name="test" value="true"/> |
120 </section> | 126 </section> |
121 <param name="in" value="NoiseFilterGaussian_1_input.mzML"/> | 127 <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"/> | 128 <output name="out" value="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
123 <section name="algorithm"> | 129 <section name="algorithm"> |
124 <param name="gaussian_width" value="1.0"/> | 130 <param name="gaussian_width" value="1.0"/> |
125 <param name="ppm_tolerance" value="10.0"/> | 131 <param name="ppm_tolerance" value="10.0"/> |
126 <param name="use_ppm_tolerance" value="false"/> | 132 <param name="use_ppm_tolerance" value="false"/> |
127 <param name="write_log_messages" value="false"/> | 133 <param name="write_log_messages" value="false"/> |
130 <output name="ctd_out" ftype="xml"> | 136 <output name="ctd_out" ftype="xml"> |
131 <assert_contents> | 137 <assert_contents> |
132 <is_valid_xml/> | 138 <is_valid_xml/> |
133 </assert_contents> | 139 </assert_contents> |
134 </output> | 140 </output> |
141 <assert_stdout> | |
142 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> | |
143 </assert_stdout> | |
135 </test> | 144 </test> |
136 <!-- TOPP_NoiseFilterGaussian_4 --> | 145 <!-- TOPP_NoiseFilterGaussian_4 --> |
137 <test expect_num_outputs="2"> | 146 <test expect_num_outputs="2"> |
138 <section name="adv_opts"> | 147 <section name="adv_opts"> |
139 <param name="processOption" value="lowmemory"/> | 148 <param name="processOption" value="lowmemory"/> |
140 <param name="force" value="false"/> | 149 <param name="force" value="false"/> |
141 <param name="test" value="true"/> | 150 <param name="test" value="true"/> |
142 </section> | 151 </section> |
143 <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/> | 152 <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"/> | 153 <output name="out" value="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
145 <section name="algorithm"> | 154 <section name="algorithm"> |
146 <param name="gaussian_width" value="50.0"/> | 155 <param name="gaussian_width" value="50.0"/> |
147 <param name="ppm_tolerance" value="10.0"/> | 156 <param name="ppm_tolerance" value="10.0"/> |
148 <param name="use_ppm_tolerance" value="false"/> | 157 <param name="use_ppm_tolerance" value="false"/> |
149 <param name="write_log_messages" value="false"/> | 158 <param name="write_log_messages" value="false"/> |
152 <output name="ctd_out" ftype="xml"> | 161 <output name="ctd_out" ftype="xml"> |
153 <assert_contents> | 162 <assert_contents> |
154 <is_valid_xml/> | 163 <is_valid_xml/> |
155 </assert_contents> | 164 </assert_contents> |
156 </output> | 165 </output> |
166 <assert_stdout> | |
167 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> | |
168 </assert_stdout> | |
157 </test> | 169 </test> |
158 </tests> | 170 </tests> |
159 <help><![CDATA[Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data). | 171 <help><![CDATA[Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data). |
160 | 172 |
161 | 173 |
162 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_NoiseFilterGaussian.html]]></help> | 174 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_NoiseFilterGaussian.html]]></help> |
163 <expand macro="references"/> | 175 <expand macro="references"/> |
164 </tool> | 176 </tool> |