Mercurial > repos > galaxyp > openms_myrimatchadapter
diff MyriMatchAdapter.xml @ 4:2253c491c157 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:00:03 +0000 |
| parents | 7b1dc8fbf6ab |
| children |
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--- a/MyriMatchAdapter.xml Fri Nov 06 20:16:34 2020 +0000 +++ b/MyriMatchAdapter.xml Thu Dec 01 19:00:03 2022 +0000 @@ -1,13 +1,11 @@ <?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: [Identification]--> -<tool id="MyriMatchAdapter" name="MyriMatchAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="MyriMatchAdapter" name="MyriMatchAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Annotates MS/MS spectra using MyriMatch.</description> <macros> <token name="@EXECUTABLE@">MyriMatchAdapter</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -45,22 +43,22 @@ <configfile name="hardcoded_json"><![CDATA[{"myrimatch_executable": "myrimatch", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/> - <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor monoisotopic mass tolerance" help=""/> - <param name="precursor_mass_tolerance_unit" argument="-precursor_mass_tolerance_unit" display="radio" type="select" optional="false" label="Unit to be used for precursor mass tolerance" help=""> + <param argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/> + <param argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor monoisotopic mass tolerance" help=""/> + <param argument="-precursor_mass_tolerance_unit" type="select" optional="true" label="Unit to be used for precursor mass tolerance" help=""> <option value="Da">Da</option> <option value="ppm" selected="true">ppm</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="precursor_mass_tolerance_unit"/> </param> - <param name="precursor_mass_tolerance_avg" argument="-precursor_mass_tolerance_avg" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is set, the average mass is used in the precursor mass tolerance" help=""/> - <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" value="0.3" label="Fragment mass error in Dalton" help=""/> - <param name="fragment_mass_tolerance_unit" argument="-fragment_mass_tolerance_unit" display="radio" type="select" optional="false" label="Unit to be used for fragment mass tolerance" help=""> + <param argument="-precursor_mass_tolerance_avg" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is set, the average mass is used in the precursor mass tolerance" help=""/> + <param argument="-fragment_mass_tolerance" type="float" optional="true" value="0.3" label="Fragment mass error in Dalton" help=""/> + <param argument="-fragment_mass_tolerance_unit" type="select" optional="true" label="Unit to be used for fragment mass tolerance" help=""> <option value="Da" selected="true">Da</option> <option value="ppm">ppm</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="fragment_mass_tolerance_unit"/> </param> - <param name="database" argument="-database" type="data" format="fasta" optional="false" label="FASTA protein database" help=" select fasta data sets(s)"/> - <param name="fixed_modifications" argument="-fixed_modifications" multiple="true" type="select" optional="true" label="Fixed modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'"> + <param argument="-database" type="data" format="fasta" optional="false" label="FASTA protein database" help=" select fasta data sets(s)"/> + <param argument="-fixed_modifications" multiple="true" type="select" optional="true" label="Fixed modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'"> <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> @@ -1430,7 +1428,6 @@ <option value="Glu->Pro (E)">Glu->Pro (E)</option> <option value="Glu->pyro-Glu (N-term E)">Glu->pyro-Glu (N-term E)</option> <option value="Glu->pyro-Glu+Methyl (N-term E)">Glu->pyro-Glu+Methyl (N-term E)</option> - <option value="Glu->pyro-Glu+Methyl (N-term E)">Glu->pyro-Glu+Methyl (N-term E)</option> <option value="Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)</option> <option value="Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option> <option value="Glu->Ser (E)">Glu->Ser (E)</option> @@ -2989,9 +2986,9 @@ <option value="ZGB (K)">ZGB (K)</option> <option value="ZGB (N-term)">ZGB (N-term)</option> <option value="ZQG (K)">ZQG (K)</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="fixed_modifications"/> </param> - <param name="variable_modifications" argument="-variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'"> + <param argument="-variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'"> <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> @@ -4361,7 +4358,6 @@ <option value="Glu->Pro (E)">Glu->Pro (E)</option> <option value="Glu->pyro-Glu (N-term E)">Glu->pyro-Glu (N-term E)</option> <option value="Glu->pyro-Glu+Methyl (N-term E)">Glu->pyro-Glu+Methyl (N-term E)</option> - <option value="Glu->pyro-Glu+Methyl (N-term E)">Glu->pyro-Glu+Methyl (N-term E)</option> <option value="Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)</option> <option value="Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option> <option value="Glu->Ser (E)">Glu->Ser (E)</option> @@ -5920,14 +5916,13 @@ <option value="ZGB (K)">ZGB (K)</option> <option value="ZGB (N-term)">ZGB (N-term)</option> <option value="ZQG (K)">ZQG (K)</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="variable_modifications"/> </param> - <param name="NumChargeStates" argument="-NumChargeStates" type="integer" optional="true" value="3" label="The number of charge states that MyriMatch will handle during all stages of the program" help=""/> - <param name="TicCutoffPercentage" argument="-TicCutoffPercentage" type="float" optional="true" value="0.98" label="Noise peaks are filtered out by sorting the original peaks in descending order of intensity, and then picking peaks from that list until the cumulative ion current of the picked peaks divided by the total ion current (TIC) is greater than or equal to this paramete" help=""/> - <param name="MaxDynamicMods" argument="-MaxDynamicMods" type="integer" optional="true" value="2" label="This parameter sets the maximum number of modified residues that may be in any candidate sequence" help=""/> - <param name="MaxResultRank" argument="-MaxResultRank" type="integer" optional="true" value="5" label="This parameter sets the maximum rank of peptide-spectrum-matches to report for each spectrum" help=""/> - <param name="CleavageRules" argument="-CleavageRules" type="select" optional="true" label="This parameter allows the user to control the way peptides are generated from the protein database" help="For more details, see http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MS&termId=MS:1001045&termName=cleavage%20agent%20name "> - <option value="">default (nothing chosen)</option> + <param argument="-NumChargeStates" type="integer" optional="true" value="3" label="The number of charge states that MyriMatch will handle during all stages of the program" help=""/> + <param argument="-TicCutoffPercentage" type="float" optional="true" value="0.98" label="Noise peaks are filtered out by sorting the original peaks in descending order of intensity, and then picking peaks from that list until the cumulative ion current of the picked peaks divided by the total ion current (TIC) is greater than or equal to this paramete" help=""/> + <param argument="-MaxDynamicMods" type="integer" optional="true" value="2" label="This parameter sets the maximum number of modified residues that may be in any candidate sequence" help=""/> + <param argument="-MaxResultRank" type="integer" optional="true" value="5" label="This parameter sets the maximum rank of peptide-spectrum-matches to report for each spectrum" help=""/> + <param argument="-CleavageRules" type="select" optional="true" label="This parameter allows the user to control the way peptides are generated from the protein database" help="For more details, see http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MS&termId=MS:1001045&termName=cleavage%20agent%20name "> <option value="Trypsin">Trypsin</option> <option value="Trypsin/P">Trypsin/P</option> <option value="Arg-C">Arg-C</option> @@ -5947,29 +5942,29 @@ <option value="no cleavage">no cleavage</option> <option value="proline endopeptidase">proline endopeptidase</option> <option value="unspecific cleavage">unspecific cleavage</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="CleavageRules"/> </param> - <param name="MinTerminiCleavages" argument="-MinTerminiCleavages" type="integer" optional="true" value="2" label="By default, when generating peptides from the protein database, a peptide must start and end at a valid cleavage site" help="Setting this parameter to 0 or 1 will reduce that requirement, so that neither terminus or only one terminus of the peptide must match one of the cleavage rules specified in the CleavageRules parameter. This parameter is useful to turn a tryptic digest into a semi-tryptic digest"/> - <param name="MaxMissedCleavages" argument="-MaxMissedCleavages" type="integer" optional="true" value="-1" label="By default, when generating peptides from the protein database, a peptide may contain any number of missed cleavages" help="A missed cleavage is a site within the peptide that matches one of the cleavage rules (refer to CleavageRules). Settings this parameter to some other number will stop generating peptides from a sequence if it contains more than the specified number of missed cleavages"/> + <param argument="-MinTerminiCleavages" type="integer" optional="true" value="2" label="By default, when generating peptides from the protein database, a peptide must start and end at a valid cleavage site" help="Setting this parameter to 0 or 1 will reduce that requirement, so that neither terminus or only one terminus of the peptide must match one of the cleavage rules specified in the CleavageRules parameter. This parameter is useful to turn a tryptic digest into a semi-tryptic digest"/> + <param argument="-MaxMissedCleavages" type="integer" optional="true" value="-1" label="By default, when generating peptides from the protein database, a peptide may contain any number of missed cleavages" help="A missed cleavage is a site within the peptide that matches one of the cleavage rules (refer to CleavageRules). Settings this parameter to some other number will stop generating peptides from a sequence if it contains more than the specified number of missed cleavages"/> <expand macro="adv_opts_macro"> - <param name="MinPeptideMass" argument="-MinPeptideMass" type="float" optional="true" value="0.0" label="When preprocessing the experimental spectra, any spectrum with a precursor mass that is less than the specified mass will be disqualified" help=""/> - <param name="MaxPeptideMass" argument="-MaxPeptideMass" type="float" optional="true" value="10000.0" label="When preprocessing the experimental spectra, any spectrum with a precursor mass that exceeds the specified mass will be disqualified" help=""/> - <param name="MinPeptideLength" argument="-MinPeptideLength" type="integer" optional="true" value="5" label="When digesting proteins, any peptide which does not meet or exceed the specified length will be disqualified" help=""/> - <param name="MaxPeptideLength" argument="-MaxPeptideLength" type="integer" optional="true" value="75" label="When digesting proteins, any peptide which exceeds this specified length will be disqualified" help=""/> - <param name="UseSmartPlusThreeModel" argument="-UseSmartPlusThreeModel" type="boolean" truevalue="true" falsevalue="false" checked="false" label="When this parameter is set, then for each peptide bond, an internal calculation is done to estimate the basicity of the b and y fragment sequence" help="The precursors protons are distributed to those ions based on that calculation, with the more basic sequence generally getting more of the protons"/> - <param name="NumIntensityClasses" argument="-NumIntensityClasses" type="integer" optional="true" value="3" label="Before scoring any candidates, experimental spectra have their peaks stratified into the number of intensity classes specified by this paramete" help=""/> - <param name="ClassSizeMultiplier" argument="-ClassSizeMultiplier" type="float" optional="true" value="2.0" label="When stratifying peaks into a specified, fixed number of intensity classes, this parameter controls the size of each class relative to the class above it (where the peaks are more intense)" help=""/> - <param name="MonoisotopeAdjustmentSet" argument="-MonoisotopeAdjustmentSet" type="text" optional="true" value="0" label="This parameter defines a set of isotopes (0 being the instrument-called monoisotope) to try as the monoisotopic precursor m/z" help="To disable this technique, set the value to '0'"> - <expand macro="list_string_san"/> + <param argument="-MinPeptideMass" type="float" optional="true" value="0.0" label="When preprocessing the experimental spectra, any spectrum with a precursor mass that is less than the specified mass will be disqualified" help=""/> + <param argument="-MaxPeptideMass" type="float" optional="true" value="10000.0" label="When preprocessing the experimental spectra, any spectrum with a precursor mass that exceeds the specified mass will be disqualified" help=""/> + <param argument="-MinPeptideLength" type="integer" optional="true" value="5" label="When digesting proteins, any peptide which does not meet or exceed the specified length will be disqualified" help=""/> + <param argument="-MaxPeptideLength" type="integer" optional="true" value="75" label="When digesting proteins, any peptide which exceeds this specified length will be disqualified" help=""/> + <param argument="-UseSmartPlusThreeModel" type="boolean" truevalue="true" falsevalue="false" checked="false" label="When this parameter is set, then for each peptide bond, an internal calculation is done to estimate the basicity of the b and y fragment sequence" help="The precursors protons are distributed to those ions based on that calculation, with the more basic sequence generally getting more of the protons"/> + <param argument="-NumIntensityClasses" type="integer" optional="true" value="3" label="Before scoring any candidates, experimental spectra have their peaks stratified into the number of intensity classes specified by this paramete" help=""/> + <param argument="-ClassSizeMultiplier" type="float" optional="true" value="2.0" label="When stratifying peaks into a specified, fixed number of intensity classes, this parameter controls the size of each class relative to the class above it (where the peaks are more intense)" help=""/> + <param argument="-MonoisotopeAdjustmentSet" type="text" optional="true" value="0" label="This parameter defines a set of isotopes (0 being the instrument-called monoisotope) to try as the monoisotopic precursor m/z" help="To disable this technique, set the value to '0'"> + <expand macro="list_string_san" name="MonoisotopeAdjustmentSet"/> </param> - <param name="SpectrumListFilters" argument="-SpectrumListFilters" type="text" optional="true" value="" label="Optional set of filters as described in the MyriMatch documentation" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> - <expand macro="list_string_val"/> - <expand macro="list_string_san"/> + <param argument="-SpectrumListFilters" type="text" optional="true" value="" label="Optional set of filters as described in the MyriMatch documentation" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <expand macro="list_string_val" name="SpectrumListFilters"/> + <expand macro="list_string_san" name="SpectrumListFilters"/> </param> - <param name="ignoreConfigErrors" argument="-ignoreConfigErrors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Ignore wrong parameter names or values" help="Use with maximum caution!"/> - <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> - <expand macro="list_string_san"/> + <param argument="-ignoreConfigErrors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Ignore wrong parameter names or values" help="Use with maximum caution!"/> + <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=""> + <expand macro="list_string_san" name="test"/> </param> </expand> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> @@ -5982,13 +5977,50 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_MyriMatchAdapter"/> - <expand macro="manutest_MyriMatchAdapter"/> + <tests><!-- TOPP_MyriMatchAdapter_1 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="MinPeptideMass" value="0.0"/> + <param name="MaxPeptideMass" value="10000.0"/> + <param name="MinPeptideLength" value="5"/> + <param name="MaxPeptideLength" value="75"/> + <param name="UseSmartPlusThreeModel" value="false"/> + <param name="NumIntensityClasses" value="3"/> + <param name="ClassSizeMultiplier" value="2.0"/> + <param name="MonoisotopeAdjustmentSet" value="[-1,2]"/> + <param name="SpectrumListFilters" value=""/> + <param name="ignoreConfigErrors" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="spectra.mzML"/> + <output name="out" file="MyriMatchAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <param name="precursor_mass_tolerance" value="5.0"/> + <param name="precursor_mass_tolerance_unit" value="ppm"/> + <param name="precursor_mass_tolerance_avg" value="false"/> + <param name="fragment_mass_tolerance" value="0.3"/> + <param name="fragment_mass_tolerance_unit" value="Da"/> + <param name="database" value="proteins.fasta"/> + <param name="fixed_modifications"/> + <param name="variable_modifications" value="Oxidation (M)"/> + <param name="NumChargeStates" value="3"/> + <param name="TicCutoffPercentage" value="0.98"/> + <param name="MaxDynamicMods" value="2"/> + <param name="MaxResultRank" value="5"/> + <param name="CleavageRules"/> + <param name="MinTerminiCleavages" value="2"/> + <param name="MaxMissedCleavages" value="-1"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Annotates MS/MS spectra using MyriMatch. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_MyriMatchAdapter.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MyriMatchAdapter.html]]></help> <expand macro="references"/> </tool>