Mercurial > repos > galaxyp > openms_noisefiltersgolay
comparison NoiseFilterSGolay.xml @ 14:35468667de97 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 21:37:07 +0000 |
parents | cf86c9091cb3 |
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13:cf86c9091cb3 | 14:35468667de97 |
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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="NoiseFilterSGolay" name="NoiseFilterSGolay" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | 3 <tool id="NoiseFilterSGolay" name="NoiseFilterSGolay" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
5 <description>Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.</description> | 4 <description>Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data</description> |
6 <macros> | 5 <macros> |
7 <token name="@EXECUTABLE@">NoiseFilterSGolay</token> | 6 <token name="@EXECUTABLE@">NoiseFilterSGolay</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="frame_length" argument="-algorithm:frame_length" type="integer" optional="true" value="11" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/> | 43 <param name="frame_length" argument="-algorithm:frame_length" type="integer" value="11" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/> |
45 <param name="polynomial_order" argument="-algorithm:polynomial_order" type="integer" optional="true" value="4" label="Order or the polynomial that is fitted" help=""/> | 44 <param name="polynomial_order" argument="-algorithm:polynomial_order" type="integer" value="4" label="Order or the polynomial that is fitted" help=""/> |
46 </section> | 45 </section> |
47 <expand macro="adv_opts_macro"> | 46 <expand macro="adv_opts_macro"> |
48 <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=""> | 47 <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=""> |
49 <option value="inmemory" selected="true">inmemory</option> | 48 <option value="inmemory" selected="true">inmemory</option> |
50 <option value="lowmemory">lowmemory</option> | 49 <option value="lowmemory">lowmemory</option> |
51 <expand macro="list_string_san" name="processOption"/> | 50 <expand macro="list_string_san" name="processOption"/> |
52 </param> | 51 </param> |
53 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 52 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
54 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 53 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> |
55 <expand macro="list_string_san" name="test"/> | 54 <expand macro="list_string_san" name="test"/> |
56 </param> | 55 </param> |
57 </expand> | 56 </expand> |
58 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 57 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
59 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 58 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
63 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> | 62 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> |
64 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 63 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
65 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 64 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
66 </data> | 65 </data> |
67 </outputs> | 66 </outputs> |
68 <tests><!-- TOPP_NoiseFilterSGolay_1 --> | 67 <tests> |
68 <!-- TOPP_NoiseFilterSGolay_1 --> | |
69 <test expect_num_outputs="2"> | 69 <test expect_num_outputs="2"> |
70 <section name="adv_opts"> | 70 <section name="adv_opts"> |
71 <param name="processOption" value="inmemory"/> | 71 <param name="processOption" value="inmemory"/> |
72 <param name="force" value="false"/> | 72 <param name="force" value="false"/> |
73 <param name="test" value="true"/> | 73 <param name="test" value="true"/> |
74 </section> | 74 </section> |
75 <param name="in" value="NoiseFilterSGolay_1_input.mzML"/> | 75 <param name="in" value="NoiseFilterSGolay_1_input.mzML"/> |
76 <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> | 76 <output name="out" value="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
77 <section name="algorithm"> | 77 <section name="algorithm"> |
78 <param name="frame_length" value="9"/> | 78 <param name="frame_length" value="9"/> |
79 <param name="polynomial_order" value="4"/> | 79 <param name="polynomial_order" value="4"/> |
80 </section> | 80 </section> |
81 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | 81 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
82 <output name="ctd_out" ftype="xml"> | 82 <output name="ctd_out" ftype="xml"> |
83 <assert_contents> | 83 <assert_contents> |
84 <is_valid_xml/> | 84 <is_valid_xml/> |
85 </assert_contents> | 85 </assert_contents> |
86 </output> | 86 </output> |
87 <assert_stdout> | |
88 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> | |
89 </assert_stdout> | |
87 </test> | 90 </test> |
88 <!-- TOPP_NoiseFilterSGolay_2 --> | 91 <!-- TOPP_NoiseFilterSGolay_2 --> |
89 <test expect_num_outputs="2"> | 92 <test expect_num_outputs="2"> |
90 <section name="adv_opts"> | 93 <section name="adv_opts"> |
91 <param name="processOption" value="inmemory"/> | 94 <param name="processOption" value="inmemory"/> |
92 <param name="force" value="false"/> | 95 <param name="force" value="false"/> |
93 <param name="test" value="true"/> | 96 <param name="test" value="true"/> |
94 </section> | 97 </section> |
95 <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/> | 98 <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/> |
96 <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> | 99 <output name="out" value="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
97 <section name="algorithm"> | 100 <section name="algorithm"> |
98 <param name="frame_length" value="11"/> | 101 <param name="frame_length" value="11"/> |
99 <param name="polynomial_order" value="4"/> | 102 <param name="polynomial_order" value="4"/> |
100 </section> | 103 </section> |
101 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | 104 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
102 <output name="ctd_out" ftype="xml"> | 105 <output name="ctd_out" ftype="xml"> |
103 <assert_contents> | 106 <assert_contents> |
104 <is_valid_xml/> | 107 <is_valid_xml/> |
105 </assert_contents> | 108 </assert_contents> |
106 </output> | 109 </output> |
110 <assert_stdout> | |
111 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> | |
112 </assert_stdout> | |
107 </test> | 113 </test> |
108 <!-- TOPP_NoiseFilterSGolay_3 --> | 114 <!-- TOPP_NoiseFilterSGolay_3 --> |
109 <test expect_num_outputs="2"> | 115 <test expect_num_outputs="2"> |
110 <section name="adv_opts"> | 116 <section name="adv_opts"> |
111 <param name="processOption" value="lowmemory"/> | 117 <param name="processOption" value="lowmemory"/> |
112 <param name="force" value="false"/> | 118 <param name="force" value="false"/> |
113 <param name="test" value="true"/> | 119 <param name="test" value="true"/> |
114 </section> | 120 </section> |
115 <param name="in" value="NoiseFilterSGolay_1_input.mzML"/> | 121 <param name="in" value="NoiseFilterSGolay_1_input.mzML"/> |
116 <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> | 122 <output name="out" value="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
117 <section name="algorithm"> | 123 <section name="algorithm"> |
118 <param name="frame_length" value="9"/> | 124 <param name="frame_length" value="9"/> |
119 <param name="polynomial_order" value="4"/> | 125 <param name="polynomial_order" value="4"/> |
120 </section> | 126 </section> |
121 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | 127 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
122 <output name="ctd_out" ftype="xml"> | 128 <output name="ctd_out" ftype="xml"> |
123 <assert_contents> | 129 <assert_contents> |
124 <is_valid_xml/> | 130 <is_valid_xml/> |
125 </assert_contents> | 131 </assert_contents> |
126 </output> | 132 </output> |
133 <assert_stdout> | |
134 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> | |
135 </assert_stdout> | |
127 </test> | 136 </test> |
128 <!-- TOPP_NoiseFilterSGolay_4 --> | 137 <!-- TOPP_NoiseFilterSGolay_4 --> |
129 <test expect_num_outputs="2"> | 138 <test expect_num_outputs="2"> |
130 <section name="adv_opts"> | 139 <section name="adv_opts"> |
131 <param name="processOption" value="lowmemory"/> | 140 <param name="processOption" value="lowmemory"/> |
132 <param name="force" value="false"/> | 141 <param name="force" value="false"/> |
133 <param name="test" value="true"/> | 142 <param name="test" value="true"/> |
134 </section> | 143 </section> |
135 <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/> | 144 <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/> |
136 <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> | 145 <output name="out" value="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
137 <section name="algorithm"> | 146 <section name="algorithm"> |
138 <param name="frame_length" value="11"/> | 147 <param name="frame_length" value="11"/> |
139 <param name="polynomial_order" value="4"/> | 148 <param name="polynomial_order" value="4"/> |
140 </section> | 149 </section> |
141 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | 150 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
142 <output name="ctd_out" ftype="xml"> | 151 <output name="ctd_out" ftype="xml"> |
143 <assert_contents> | 152 <assert_contents> |
144 <is_valid_xml/> | 153 <is_valid_xml/> |
145 </assert_contents> | 154 </assert_contents> |
146 </output> | 155 </output> |
156 <assert_stdout> | |
157 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> | |
158 </assert_stdout> | |
147 </test> | 159 </test> |
148 </tests> | 160 </tests> |
149 <help><![CDATA[Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data. | 161 <help><![CDATA[Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data. |
150 | 162 |
151 | 163 |
152 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_NoiseFilterSGolay.html]]></help> | 164 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_NoiseFilterSGolay.html]]></help> |
153 <expand macro="references"/> | 165 <expand macro="references"/> |
154 </tool> | 166 </tool> |