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comparison NoiseFilterGaussian.xml @ 14:464f7877215b draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:37:30 +0000
parents 47982606f542
children
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13:47982606f542 14:464f7877215b
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>