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comparison SpectraMerger.xml @ 13:4333c513b7a1 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:03:02 +0000
parents e08b7d2880f4
children b20b1f195cf2
comparison
equal deleted inserted replaced
12:85738bba683a 13:4333c513b7a1
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="SpectraMerger" name="SpectraMerger" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="SpectraMerger" name="SpectraMerger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Merges spectra (each MS level separately), increasing S/N ratios.</description> 5 <description>Merges spectra (each MS level separately), increasing S/N ratios.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">SpectraMerger</token> 7 <token name="@EXECUTABLE@">SpectraMerger</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 mzML file" help=" select mzml data sets(s)"/> 42 <param argument="-in" type="data" format="mzml" optional="false" label="Input mzML file" help=" select mzml data sets(s)"/>
45 <param name="merging_method" argument="-merging_method" display="radio" type="select" optional="false" label="Method of merging which should be used" help=""> 43 <param argument="-merging_method" type="select" optional="true" label="Method of merging which should be used" help="">
46 <option value="average_gaussian" selected="true">average_gaussian</option> 44 <option value="average_gaussian" selected="true">average_gaussian</option>
47 <option value="average_tophat">average_tophat</option> 45 <option value="average_tophat">average_tophat</option>
48 <option value="precursor_method">precursor_method</option> 46 <option value="precursor_method">precursor_method</option>
49 <option value="block_method">block_method</option> 47 <option value="block_method">block_method</option>
50 <expand macro="list_string_san"/> 48 <expand macro="list_string_san" name="merging_method"/>
51 </param> 49 </param>
52 <section name="algorithm" title="Algorithm section for merging spectra" help="" expanded="false"> 50 <section name="algorithm" title="Algorithm section for merging spectra" help="" expanded="false">
53 <param name="mz_binning_width" argument="-algorithm:mz_binning_width" type="float" optional="true" min="0.0" value="5.0" label="minimum m/z distance for two data points (profile data) or peaks (centroided data) to be considered distinct" help="Closer data points or peaks will be merged"/> 51 <param name="mz_binning_width" argument="-algorithm:mz_binning_width" type="float" optional="true" min="0.0" value="5.0" label="minimum m/z distance for two data points (profile data) or peaks (centroided data) to be considered distinct" help="Closer data points or peaks will be merged"/>
54 <param name="mz_binning_width_unit" argument="-algorithm:mz_binning_width_unit" display="radio" type="select" optional="false" label="Unit in which the distance between two data points or peaks is given" help=""> 52 <param name="mz_binning_width_unit" argument="-algorithm:mz_binning_width_unit" type="select" optional="true" label="Unit in which the distance between two data points or peaks is given" help="">
55 <option value="Da">Da</option> 53 <option value="Da">Da</option>
56 <option value="ppm" selected="true">ppm</option> 54 <option value="ppm" selected="true">ppm</option>
57 <expand macro="list_string_san"/> 55 <expand macro="list_string_san" name="mz_binning_width_unit"/>
58 </param> 56 </param>
59 <param name="sort_blocks" argument="-algorithm:sort_blocks" display="radio" type="select" optional="false" label="Sort blocks by &lt;?&gt; before merging them (useful for precursor order)" help=""> 57 <param name="sort_blocks" argument="-algorithm:sort_blocks" type="select" optional="true" label="Sort blocks by &lt;?&gt; before merging them (useful for precursor order)" help="">
60 <option value="RT_ascending" selected="true">RT_ascending</option> 58 <option value="RT_ascending" selected="true">RT_ascending</option>
61 <option value=" RT_descending"> RT_descending</option> 59 <option value="RT_descending">RT_descending</option>
62 <expand macro="list_string_san"/> 60 <expand macro="list_string_san" name="sort_blocks"/>
63 </param> 61 </param>
64 <section name="average_gaussian" title="" help="" expanded="false"> 62 <section name="average_gaussian" title="" help="" expanded="false">
65 <param name="spectrum_type" argument="-algorithm:average_gaussian:spectrum_type" display="radio" type="select" optional="false" label="Spectrum type of the MS level to be averaged" help=""> 63 <param name="spectrum_type" argument="-algorithm:average_gaussian:spectrum_type" type="select" optional="true" label="Spectrum type of the MS level to be averaged" help="">
66 <option value="profile">profile</option> 64 <option value="profile">profile</option>
67 <option value="centroid">centroid</option> 65 <option value="centroid">centroid</option>
68 <option value="automatic" selected="true">automatic</option> 66 <option value="automatic" selected="true">automatic</option>
69 <expand macro="list_string_san"/> 67 <expand macro="list_string_san" name="spectrum_type"/>
70 </param> 68 </param>
71 <param name="ms_level" argument="-algorithm:average_gaussian:ms_level" type="integer" optional="true" min="1" value="1" label="Average spectra of this level" help="All other spectra remain unchanged"/> 69 <param name="ms_level" argument="-algorithm:average_gaussian:ms_level" type="integer" optional="true" min="1" value="1" label="Average spectra of this level" help="All other spectra remain unchanged"/>
72 <param name="rt_FWHM" argument="-algorithm:average_gaussian:rt_FWHM" type="float" optional="true" min="0.0" max="100000000000.0" value="5.0" label="FWHM of Gauss curve in seconds to be averaged ove" help=""/> 70 <param name="rt_FWHM" argument="-algorithm:average_gaussian:rt_FWHM" type="float" optional="true" min="0.0" max="100000000000.0" value="5.0" label="FWHM of Gauss curve in seconds to be averaged ove" help=""/>
73 <param name="cutoff" argument="-algorithm:average_gaussian:cutoff" type="float" optional="true" min="0.0" max="1.0" value="0.01" label="Intensity cutoff for Gaussian" help="The Gaussian RT profile decreases from 1 at its apex to 0 at infinity. Spectra for which the intensity of the Gaussian drops below the cutoff do not contribute to the average"/> 71 <param name="cutoff" argument="-algorithm:average_gaussian:cutoff" type="float" optional="true" min="0.0" max="1.0" value="0.01" label="Intensity cutoff for Gaussian" help="The Gaussian RT profile decreases from 1 at its apex to 0 at infinity. Spectra for which the intensity of the Gaussian drops below the cutoff do not contribute to the average"/>
74 </section> 72 </section>
75 <section name="average_tophat" title="" help="" expanded="false"> 73 <section name="average_tophat" title="" help="" expanded="false">
76 <param name="spectrum_type" argument="-algorithm:average_tophat:spectrum_type" display="radio" type="select" optional="false" label="Spectrum type of the MS level to be averaged" help=""> 74 <param name="spectrum_type" argument="-algorithm:average_tophat:spectrum_type" type="select" optional="true" label="Spectrum type of the MS level to be averaged" help="">
77 <option value="profile">profile</option> 75 <option value="profile">profile</option>
78 <option value="centroid">centroid</option> 76 <option value="centroid">centroid</option>
79 <option value="automatic" selected="true">automatic</option> 77 <option value="automatic" selected="true">automatic</option>
80 <expand macro="list_string_san"/> 78 <expand macro="list_string_san" name="spectrum_type"/>
81 </param> 79 </param>
82 <param name="ms_level" argument="-algorithm:average_tophat:ms_level" type="integer" optional="true" min="1" value="1" label="Average spectra of this level" help="All other spectra remain unchanged"/> 80 <param name="ms_level" argument="-algorithm:average_tophat:ms_level" type="integer" optional="true" min="1" value="1" label="Average spectra of this level" help="All other spectra remain unchanged"/>
83 <param name="rt_range" argument="-algorithm:average_tophat:rt_range" type="float" optional="true" min="0.0" max="100000000000.0" value="5.0" label="RT range to be averaged ove" help="i.e. +/-(RT range)/2 from each spectrum"/> 81 <param name="rt_range" argument="-algorithm:average_tophat:rt_range" type="float" optional="true" min="0.0" max="100000000000.0" value="5.0" label="RT range to be averaged ove" help="i.e. +/-(RT range)/2 from each spectrum"/>
84 <param name="rt_unit" argument="-algorithm:average_tophat:rt_unit" display="radio" type="select" optional="false" label="Unit for RT range" help=""> 82 <param name="rt_unit" argument="-algorithm:average_tophat:rt_unit" type="select" optional="true" label="Unit for RT range" help="">
85 <option value="scans" selected="true">scans</option> 83 <option value="scans" selected="true">scans</option>
86 <option value="seconds">seconds</option> 84 <option value="seconds">seconds</option>
87 <expand macro="list_string_san"/> 85 <expand macro="list_string_san" name="rt_unit"/>
88 </param> 86 </param>
89 </section> 87 </section>
90 <section name="block_method" title="" help="" expanded="false"> 88 <section name="block_method" title="" help="" expanded="false">
91 <param name="ms_levels" argument="-algorithm:block_method:ms_levels" type="text" optional="true" value="1" label="Merge spectra of this level" help="All spectra with other MS levels remain untouched (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 89 <param name="ms_levels" argument="-algorithm:block_method:ms_levels" type="text" optional="true" value="1" label="Merge spectra of this level" help="All spectra with other MS levels remain untouched (space separated list, in order to allow for spaces in list items surround them by single quotes)">
92 <expand macro="list_integer_valsan"> 90 <expand macro="list_integer_valsan" name="ms_levels">
93 <validator type="expression" message="a space separated list of integer values in the range 1: is required"><![CDATA[len(value.split(' ')) == len([_ for _ in value.split(' ') if 1 <= int(_)]) 91 <validator type="expression" message="a space separated list of integer values in the range 1: is required"><![CDATA[len(value.split(' ')) == len([_ for _ in value.split(' ') if 1 <= int(_)])
94 ]]></validator> 92 ]]></validator>
95 </expand> 93 </expand>
96 </param> 94 </param>
97 <param name="rt_block_size" argument="-algorithm:block_method:rt_block_size" type="integer" optional="true" min="1" value="5" label="Maximum number of scans to be summed up" help=""/> 95 <param name="rt_block_size" argument="-algorithm:block_method:rt_block_size" type="integer" optional="true" min="1" value="5" label="Maximum number of scans to be summed up" help=""/>
101 <param name="mz_tolerance" argument="-algorithm:precursor_method:mz_tolerance" type="float" optional="true" min="0.0" value="0.0001" label="Max m/z distance of the precursor entries of two spectra to be merged in [Da]" help=""/> 99 <param name="mz_tolerance" argument="-algorithm:precursor_method:mz_tolerance" type="float" optional="true" min="0.0" value="0.0001" label="Max m/z distance of the precursor entries of two spectra to be merged in [Da]" help=""/>
102 <param name="rt_tolerance" argument="-algorithm:precursor_method:rt_tolerance" type="float" optional="true" min="0.0" value="5.0" label="Max RT distance of the precursor entries of two spectra to be merged in [s]" help=""/> 100 <param name="rt_tolerance" argument="-algorithm:precursor_method:rt_tolerance" type="float" optional="true" min="0.0" value="5.0" label="Max RT distance of the precursor entries of two spectra to be merged in [s]" help=""/>
103 </section> 101 </section>
104 </section> 102 </section>
105 <expand macro="adv_opts_macro"> 103 <expand macro="adv_opts_macro">
106 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 104 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
107 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 105 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
108 <expand macro="list_string_san"/> 106 <expand macro="list_string_san" name="test"/>
109 </param> 107 </param>
110 </expand> 108 </expand>
111 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 109 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
112 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 110 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
113 </param> 111 </param>
116 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 114 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
117 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 115 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
118 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 116 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
119 </data> 117 </data>
120 </outputs> 118 </outputs>
121 <tests> 119 <tests><test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output-->
122 <expand macro="autotest_SpectraMerger"/> 120 <param name="adv_opts|test" value="true"/>
123 <expand macro="manutest_SpectraMerger"/> 121 <param name="in" ftype="mzml" value="NovorAdapter_in.mzML"/>
124 </tests> 122 <output name="out" ftype="mzml" value="SpectraMerger_1.mzML" compare="sim_size"/>
123 </test>
124 </tests>
125 <help><![CDATA[Merges spectra (each MS level separately), increasing S/N ratios. 125 <help><![CDATA[Merges spectra (each MS level separately), increasing S/N ratios.
126 126
127 127
128 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_SpectraMerger.html]]></help> 128 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraMerger.html]]></help>
129 <expand macro="references"/> 129 <expand macro="references"/>
130 </tool> 130 </tool>