Mercurial > repos > galaxyp > openms_spectramerger
diff SpectraMerger.xml @ 14:b20b1f195cf2 draft default tip
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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--- a/SpectraMerger.xml Thu Dec 01 19:03:02 2022 +0000 +++ b/SpectraMerger.xml Fri Jun 14 21:28:09 2024 +0000 @@ -1,8 +1,7 @@ -<?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> -<!--Proposed Tool Section: [Signal processing and preprocessing]--> +<!--Proposed Tool Section: [Spectrum processing: Misc / Helpers]--> <tool id="SpectraMerger" name="SpectraMerger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>Merges spectra (each MS level separately), increasing S/N ratios.</description> + <description>Merges spectra (each MS level separately), increasing S/N ratios</description> <macros> <token name="@EXECUTABLE@">SpectraMerger</token> <import>macros.xml</import> @@ -15,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call @@ -39,8 +38,8 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param argument="-in" type="data" format="mzml" optional="false" label="Input mzML file" help=" select mzml data sets(s)"/> - <param argument="-merging_method" type="select" optional="true" label="Method of merging which should be used" help=""> + <param argument="-in" type="data" format="mzml" label="Input mzML file" help=" select mzml data sets(s)"/> + <param argument="-merging_method" type="select" label="Method of merging which should be used" help=""> <option value="average_gaussian" selected="true">average_gaussian</option> <option value="average_tophat">average_tophat</option> <option value="precursor_method">precursor_method</option> @@ -48,61 +47,64 @@ <expand macro="list_string_san" name="merging_method"/> </param> <section name="algorithm" title="Algorithm section for merging spectra" help="" expanded="false"> - <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"/> - <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=""> + <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"/> + <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=""> <option value="Da">Da</option> <option value="ppm" selected="true">ppm</option> <expand macro="list_string_san" name="mz_binning_width_unit"/> </param> - <param name="sort_blocks" argument="-algorithm:sort_blocks" type="select" optional="true" label="Sort blocks by <?> before merging them (useful for precursor order)" help=""> + <param name="sort_blocks" argument="-algorithm:sort_blocks" type="select" label="Sort blocks by <?> before merging them (useful for precursor order)" help=""> <option value="RT_ascending" selected="true">RT_ascending</option> <option value="RT_descending">RT_descending</option> <expand macro="list_string_san" name="sort_blocks"/> </param> <section name="average_gaussian" title="" help="" expanded="false"> - <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=""> + <param name="spectrum_type" argument="-algorithm:average_gaussian:spectrum_type" type="select" label="Spectrum type of the MS level to be averaged" help=""> <option value="profile">profile</option> <option value="centroid">centroid</option> <option value="automatic" selected="true">automatic</option> <expand macro="list_string_san" name="spectrum_type"/> </param> - <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"/> - <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=""/> - <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"/> + <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"/> + <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=""/> + <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"/> + <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>2) spectra of precursor masses within the tolerance are averaged"/> + <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"/> </section> <section name="average_tophat" title="" help="" expanded="false"> - <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=""> + <param name="spectrum_type" argument="-algorithm:average_tophat:spectrum_type" type="select" label="Spectrum type of the MS level to be averaged" help=""> <option value="profile">profile</option> <option value="centroid">centroid</option> <option value="automatic" selected="true">automatic</option> <expand macro="list_string_san" name="spectrum_type"/> </param> - <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"/> - <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"/> - <param name="rt_unit" argument="-algorithm:average_tophat:rt_unit" type="select" optional="true" label="Unit for RT range" help=""> + <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"/> + <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"/> + <param name="rt_unit" argument="-algorithm:average_tophat:rt_unit" type="select" label="Unit for RT range" help=""> <option value="scans" selected="true">scans</option> <option value="seconds">seconds</option> <expand macro="list_string_san" name="rt_unit"/> </param> </section> <section name="block_method" title="" help="" expanded="false"> - <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)"> + <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)"> <expand macro="list_integer_valsan" name="ms_levels"> <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(_)]) ]]></validator> </expand> </param> - <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=""/> - <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=""/> + <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=""/> + <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=""/> </section> <section name="precursor_method" title="" help="" expanded="false"> - <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=""/> - <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=""/> + <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=""/> + <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"/> + <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=""/> </section> </section> <expand macro="adv_opts_macro"> <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> <expand macro="list_string_san" name="test"/> </param> </expand> @@ -116,15 +118,22 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output--> - <param name="adv_opts|test" value="true"/> - <param name="in" ftype="mzml" value="NovorAdapter_in.mzML"/> - <output name="out" ftype="mzml" value="SpectraMerger_1.mzML" compare="sim_size"/> - </test> -</tests> + <tests> + <test expect_num_outputs="1"> + <!-- just chosen an arbitrary input and autgenerated output--> + <param name="adv_opts|test" value="true"/> + <param name="in" ftype="mzml" value="NovorAdapter_in.mzML"/> + <section name="algorithm"> + <section name="average_gaussian"> + <param name="ms_level" value="2"/> + </section> + </section> + <output name="out" ftype="mzml" value="SpectraMerger_1.mzML" compare="sim_size"/> + </test> + </tests> <help><![CDATA[Merges spectra (each MS level separately), increasing S/N ratios. -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraMerger.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpectraMerger.html]]></help> <expand macro="references"/> </tool>