Mercurial > repos > galaxyp > openms_noisefiltersgolay
comparison NoiseFilterSGolay.xml @ 13:cf86c9091cb3 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 19:05:55 +0000 |
parents | 1312f9119f74 |
children | 35468667de97 |
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12:677d716a1bff | 13:cf86c9091cb3 |
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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="NoiseFilterSGolay" name="NoiseFilterSGolay" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> | 4 <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> | 5 <description>Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">NoiseFilterSGolay</token> | 7 <token name="@EXECUTABLE@">NoiseFilterSGolay</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="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"/> | 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"/> |
47 <param name="polynomial_order" argument="-algorithm:polynomial_order" type="integer" optional="true" value="4" label="Order or the polynomial that is fitted" help=""/> | 45 <param name="polynomial_order" argument="-algorithm:polynomial_order" type="integer" optional="true" value="4" label="Order or the polynomial that is fitted" help=""/> |
48 </section> | 46 </section> |
49 <expand macro="adv_opts_macro"> | 47 <expand macro="adv_opts_macro"> |
50 <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=""> | 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=""> |
51 <option value="inmemory" selected="true">inmemory</option> | 49 <option value="inmemory" selected="true">inmemory</option> |
52 <option value="lowmemory">lowmemory</option> | 50 <option value="lowmemory">lowmemory</option> |
53 <expand macro="list_string_san"/> | 51 <expand macro="list_string_san" name="processOption"/> |
54 </param> | 52 </param> |
55 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 53 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
56 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 54 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
57 <expand macro="list_string_san"/> | 55 <expand macro="list_string_san" name="test"/> |
58 </param> | 56 </param> |
59 </expand> | 57 </expand> |
60 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 58 <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> | 59 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
62 </param> | 60 </param> |
65 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> | 63 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> |
66 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 64 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
67 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 65 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
68 </data> | 66 </data> |
69 </outputs> | 67 </outputs> |
70 <tests> | 68 <tests><!-- TOPP_NoiseFilterSGolay_1 --> |
71 <expand macro="autotest_NoiseFilterSGolay"/> | 69 <test expect_num_outputs="2"> |
72 <expand macro="manutest_NoiseFilterSGolay"/> | 70 <section name="adv_opts"> |
71 <param name="processOption" value="inmemory"/> | |
72 <param name="force" value="false"/> | |
73 <param name="test" value="true"/> | |
74 </section> | |
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"/> | |
77 <section name="algorithm"> | |
78 <param name="frame_length" value="9"/> | |
79 <param name="polynomial_order" value="4"/> | |
80 </section> | |
81 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
82 <output name="ctd_out" ftype="xml"> | |
83 <assert_contents> | |
84 <is_valid_xml/> | |
85 </assert_contents> | |
86 </output> | |
87 </test> | |
88 <!-- TOPP_NoiseFilterSGolay_2 --> | |
89 <test expect_num_outputs="2"> | |
90 <section name="adv_opts"> | |
91 <param name="processOption" value="inmemory"/> | |
92 <param name="force" value="false"/> | |
93 <param name="test" value="true"/> | |
94 </section> | |
95 <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"/> | |
97 <section name="algorithm"> | |
98 <param name="frame_length" value="11"/> | |
99 <param name="polynomial_order" value="4"/> | |
100 </section> | |
101 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
102 <output name="ctd_out" ftype="xml"> | |
103 <assert_contents> | |
104 <is_valid_xml/> | |
105 </assert_contents> | |
106 </output> | |
107 </test> | |
108 <!-- TOPP_NoiseFilterSGolay_3 --> | |
109 <test expect_num_outputs="2"> | |
110 <section name="adv_opts"> | |
111 <param name="processOption" value="lowmemory"/> | |
112 <param name="force" value="false"/> | |
113 <param name="test" value="true"/> | |
114 </section> | |
115 <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"/> | |
117 <section name="algorithm"> | |
118 <param name="frame_length" value="9"/> | |
119 <param name="polynomial_order" value="4"/> | |
120 </section> | |
121 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
122 <output name="ctd_out" ftype="xml"> | |
123 <assert_contents> | |
124 <is_valid_xml/> | |
125 </assert_contents> | |
126 </output> | |
127 </test> | |
128 <!-- TOPP_NoiseFilterSGolay_4 --> | |
129 <test expect_num_outputs="2"> | |
130 <section name="adv_opts"> | |
131 <param name="processOption" value="lowmemory"/> | |
132 <param name="force" value="false"/> | |
133 <param name="test" value="true"/> | |
134 </section> | |
135 <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"/> | |
137 <section name="algorithm"> | |
138 <param name="frame_length" value="11"/> | |
139 <param name="polynomial_order" value="4"/> | |
140 </section> | |
141 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
142 <output name="ctd_out" ftype="xml"> | |
143 <assert_contents> | |
144 <is_valid_xml/> | |
145 </assert_contents> | |
146 </output> | |
147 </test> | |
73 </tests> | 148 </tests> |
74 <help><![CDATA[Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data. | 149 <help><![CDATA[Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data. |
75 | 150 |
76 | 151 |
77 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_NoiseFilterSGolay.html]]></help> | 152 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_NoiseFilterSGolay.html]]></help> |
78 <expand macro="references"/> | 153 <expand macro="references"/> |
79 </tool> | 154 </tool> |