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comparison SpectraMerger.xml @ 14:b20b1f195cf2 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 21:28:09 +0000
parents 4333c513b7a1
children
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13:4333c513b7a1 14:b20b1f195cf2
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: Misc / Helpers]-->
4 <tool id="SpectraMerger" name="SpectraMerger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <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> 4 <description>Merges spectra (each MS level separately), increasing S/N ratios</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">SpectraMerger</token> 6 <token name="@EXECUTABLE@">SpectraMerger</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 mzML file" help=" select mzml data sets(s)"/> 41 <param argument="-in" type="data" format="mzml" label="Input mzML file" help=" select mzml data sets(s)"/>
43 <param argument="-merging_method" type="select" optional="true" label="Method of merging which should be used" help=""> 42 <param argument="-merging_method" type="select" label="Method of merging which should be used" help="">
44 <option value="average_gaussian" selected="true">average_gaussian</option> 43 <option value="average_gaussian" selected="true">average_gaussian</option>
45 <option value="average_tophat">average_tophat</option> 44 <option value="average_tophat">average_tophat</option>
46 <option value="precursor_method">precursor_method</option> 45 <option value="precursor_method">precursor_method</option>
47 <option value="block_method">block_method</option> 46 <option value="block_method">block_method</option>
48 <expand macro="list_string_san" name="merging_method"/> 47 <expand macro="list_string_san" name="merging_method"/>
49 </param> 48 </param>
50 <section name="algorithm" title="Algorithm section for merging spectra" help="" expanded="false"> 49 <section name="algorithm" title="Algorithm section for merging spectra" help="" expanded="false">
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"/> 50 <param name="mz_binning_width" argument="-algorithm:mz_binning_width" type="float" 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"/>
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=""> 51 <param name="mz_binning_width_unit" argument="-algorithm:mz_binning_width_unit" type="select" label="Unit in which the distance between two data points or peaks is given" help="">
53 <option value="Da">Da</option> 52 <option value="Da">Da</option>
54 <option value="ppm" selected="true">ppm</option> 53 <option value="ppm" selected="true">ppm</option>
55 <expand macro="list_string_san" name="mz_binning_width_unit"/> 54 <expand macro="list_string_san" name="mz_binning_width_unit"/>
56 </param> 55 </param>
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=""> 56 <param name="sort_blocks" argument="-algorithm:sort_blocks" type="select" label="Sort blocks by &lt;?&gt; before merging them (useful for precursor order)" help="">
58 <option value="RT_ascending" selected="true">RT_ascending</option> 57 <option value="RT_ascending" selected="true">RT_ascending</option>
59 <option value="RT_descending">RT_descending</option> 58 <option value="RT_descending">RT_descending</option>
60 <expand macro="list_string_san" name="sort_blocks"/> 59 <expand macro="list_string_san" name="sort_blocks"/>
61 </param> 60 </param>
62 <section name="average_gaussian" title="" help="" expanded="false"> 61 <section name="average_gaussian" title="" help="" expanded="false">
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=""> 62 <param name="spectrum_type" argument="-algorithm:average_gaussian:spectrum_type" type="select" label="Spectrum type of the MS level to be averaged" help="">
64 <option value="profile">profile</option> 63 <option value="profile">profile</option>
65 <option value="centroid">centroid</option> 64 <option value="centroid">centroid</option>
66 <option value="automatic" selected="true">automatic</option> 65 <option value="automatic" selected="true">automatic</option>
67 <expand macro="list_string_san" name="spectrum_type"/> 66 <expand macro="list_string_san" name="spectrum_type"/>
68 </param> 67 </param>
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"/> 68 <param name="ms_level" argument="-algorithm:average_gaussian:ms_level" type="integer" min="0" value="1" label="If set to be 0, each MS level will be merged from 1 to max" help="Otherwise, average spectra of this level. All other spectra remain unchanged"/>
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=""/> 69 <param name="rt_FWHM" argument="-algorithm:average_gaussian:rt_FWHM" type="float" min="0.0" max="100000000000.0" value="5.0" label="FWHM of Gauss curve in seconds to be averaged ove" help=""/>
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"/> 70 <param name="cutoff" argument="-algorithm:average_gaussian:cutoff" type="float" 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="precursor_mass_tol" argument="-algorithm:average_gaussian:precursor_mass_tol" type="float" min="0.0" value="0.0" label="PPM mass tolerance for precursor mass" help="If set, MSn (n&gt;2) spectra of precursor masses within the tolerance are averaged"/>
72 <param name="precursor_max_charge" argument="-algorithm:average_gaussian:precursor_max_charge" type="integer" min="1" value="1" label="Possible maximum precursor ion charge" help="Effective only when average_gaussian:precursor_mass_tol option is active"/>
72 </section> 73 </section>
73 <section name="average_tophat" title="" help="" expanded="false"> 74 <section name="average_tophat" title="" help="" expanded="false">
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=""> 75 <param name="spectrum_type" argument="-algorithm:average_tophat:spectrum_type" type="select" label="Spectrum type of the MS level to be averaged" help="">
75 <option value="profile">profile</option> 76 <option value="profile">profile</option>
76 <option value="centroid">centroid</option> 77 <option value="centroid">centroid</option>
77 <option value="automatic" selected="true">automatic</option> 78 <option value="automatic" selected="true">automatic</option>
78 <expand macro="list_string_san" name="spectrum_type"/> 79 <expand macro="list_string_san" name="spectrum_type"/>
79 </param> 80 </param>
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"/> 81 <param name="ms_level" argument="-algorithm:average_tophat:ms_level" type="integer" min="0" value="1" label="If set to be 0, each MS level will be merged from 1 to max" help="Otherwise, average spectra of this level. All other spectra remain unchanged"/>
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"/> 82 <param name="rt_range" argument="-algorithm:average_tophat:rt_range" type="float" 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"/>
82 <param name="rt_unit" argument="-algorithm:average_tophat:rt_unit" type="select" optional="true" label="Unit for RT range" help=""> 83 <param name="rt_unit" argument="-algorithm:average_tophat:rt_unit" type="select" label="Unit for RT range" help="">
83 <option value="scans" selected="true">scans</option> 84 <option value="scans" selected="true">scans</option>
84 <option value="seconds">seconds</option> 85 <option value="seconds">seconds</option>
85 <expand macro="list_string_san" name="rt_unit"/> 86 <expand macro="list_string_san" name="rt_unit"/>
86 </param> 87 </param>
87 </section> 88 </section>
88 <section name="block_method" title="" help="" expanded="false"> 89 <section name="block_method" title="" help="" expanded="false">
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)"> 90 <param name="ms_levels" argument="-algorithm:block_method:ms_levels" type="text" 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)">
90 <expand macro="list_integer_valsan" name="ms_levels"> 91 <expand macro="list_integer_valsan" name="ms_levels">
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(_)]) 92 <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(_)])
92 ]]></validator> 93 ]]></validator>
93 </expand> 94 </expand>
94 </param> 95 </param>
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=""/> 96 <param name="rt_block_size" argument="-algorithm:block_method:rt_block_size" type="integer" min="1" value="5" label="Maximum number of scans to be summed up" help=""/>
96 <param name="rt_max_length" argument="-algorithm:block_method:rt_max_length" type="float" optional="true" min="0.0" max="100000000000.0" value="0.0" label="Maximum RT size of the block in seconds (0.0 = no size restriction)" help=""/> 97 <param name="rt_max_length" argument="-algorithm:block_method:rt_max_length" type="float" min="0.0" max="100000000000.0" value="0.0" label="Maximum RT size of the block in seconds (0.0 = no size restriction)" help=""/>
97 </section> 98 </section>
98 <section name="precursor_method" title="" help="" expanded="false"> 99 <section name="precursor_method" title="" help="" expanded="false">
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=""/> 100 <param name="mz_tolerance" argument="-algorithm:precursor_method:mz_tolerance" type="float" min="0.0" value="0.0001" label="Max m/z distance of the precursor entries of two spectra to be merged in [Da]" 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=""/> 101 <param name="mass_tolerance" argument="-algorithm:precursor_method:mass_tolerance" type="float" min="0.0" value="0.0" label="Max mass distance of the precursor entries of two spectra to be merged in [Da]" help="Active when set to a positive value"/>
102 <param name="rt_tolerance" argument="-algorithm:precursor_method:rt_tolerance" type="float" min="0.0" value="5.0" label="Max RT distance of the precursor entries of two spectra to be merged in [s]" help=""/>
101 </section> 103 </section>
102 </section> 104 </section>
103 <expand macro="adv_opts_macro"> 105 <expand macro="adv_opts_macro">
104 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 106 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
105 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 107 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
106 <expand macro="list_string_san" name="test"/> 108 <expand macro="list_string_san" name="test"/>
107 </param> 109 </param>
108 </expand> 110 </expand>
109 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 111 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
110 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 112 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
114 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 116 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
115 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 117 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
116 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 118 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
117 </data> 119 </data>
118 </outputs> 120 </outputs>
119 <tests><test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output--> 121 <tests>
120 <param name="adv_opts|test" value="true"/> 122 <test expect_num_outputs="1">
121 <param name="in" ftype="mzml" value="NovorAdapter_in.mzML"/> 123 <!-- just chosen an arbitrary input and autgenerated output-->
122 <output name="out" ftype="mzml" value="SpectraMerger_1.mzML" compare="sim_size"/> 124 <param name="adv_opts|test" value="true"/>
123 </test> 125 <param name="in" ftype="mzml" value="NovorAdapter_in.mzML"/>
124 </tests> 126 <section name="algorithm">
127 <section name="average_gaussian">
128 <param name="ms_level" value="2"/>
129 </section>
130 </section>
131 <output name="out" ftype="mzml" value="SpectraMerger_1.mzML" compare="sim_size"/>
132 </test>
133 </tests>
125 <help><![CDATA[Merges spectra (each MS level separately), increasing S/N ratios. 134 <help><![CDATA[Merges spectra (each MS level separately), increasing S/N ratios.
126 135
127 136
128 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraMerger.html]]></help> 137 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpectraMerger.html]]></help>
129 <expand macro="references"/> 138 <expand macro="references"/>
130 </tool> 139 </tool>