Mercurial > repos > galaxyp > openms_cometadapter
diff CometAdapter.xml @ 8:e75929491905 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 19:11:13 +0000 |
| parents | a4ada39679ae |
| children |
line wrap: on
line diff
--- a/CometAdapter.xml Fri Nov 06 20:30:48 2020 +0000 +++ b/CometAdapter.xml Thu Dec 01 19:11:13 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="CometAdapter" name="CometAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="CometAdapter" name="CometAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Annotates MS/MS spectra using Comet.</description> <macros> <token name="@EXECUTABLE@">CometAdapter</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -66,72 +64,73 @@ <configfile name="hardcoded_json"><![CDATA[{"comet_executable": "comet", "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="database" argument="-database" type="data" format="fasta" optional="false" label="FASTA file" help=" select fasta data sets(s)"/> - <param name="default_params_file" argument="-default_params_file" type="data" format="txt" optional="true" label="Default Comet params file" help="All parameters of this take precedence. A template file can be generated using 'comet.exe -p' select txt data sets(s)"/> - <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor monoisotopic mass tolerance (Comet parameter: peptide_mass_tolerance)" help="See also precursor_error_units to set the unit"/> - <param name="precursor_error_units" argument="-precursor_error_units" display="radio" type="select" optional="false" label="Unit of precursor monoisotopic mass tolerance for parameter precursor_mass_tolerance (Comet parameter: peptide_mass_units)" help=""> + <param argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/> + <param argument="-database" type="data" format="fasta" optional="false" label="FASTA file" help=" select fasta data sets(s)"/> + <param argument="-default_params_file" type="data" format="txt" optional="true" label="Default Comet params file" help="All parameters of this take precedence. A template file can be generated using 'comet.exe -p' select txt data sets(s)"/> + <param argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor monoisotopic mass tolerance (Comet parameter: peptide_mass_tolerance)" help="See also precursor_error_units to set the unit"/> + <param argument="-precursor_error_units" type="select" optional="true" label="Unit of precursor monoisotopic mass tolerance for parameter precursor_mass_tolerance (Comet parameter: peptide_mass_units)" help=""> <option value="amu">amu</option> <option value="ppm" selected="true">ppm</option> <option value="Da">Da</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="precursor_error_units"/> </param> - <param name="isotope_error" argument="-isotope_error" type="select" optional="false" label="This parameter controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement" help="Use -8/-4/0/4/8 only for SILAC"> + <param argument="-isotope_error" type="select" optional="true" label="This parameter controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement" help="Use -8/-4/0/4/8 only for SILAC"> <option value="off" selected="true">off</option> <option value="0/1">0/1</option> <option value="0/1/2">0/1/2</option> <option value="0/1/2/3">0/1/2/3</option> <option value="-8/-4/0/4/8">-8/-4/0/4/8</option> - <expand macro="list_string_san"/> + <option value="-1/0/1/2/3">-1/0/1/2/3</option> + <expand macro="list_string_san" name="isotope_error"/> </param> - <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" min="0.0001" value="0.01" label="This is half the bin size, which is used to segment the MS/MS spectrum" help="Thus, the value should be a bit higher than for other search engines, since the bin might not be centered around the peak apex (see 'fragment_bin_offset').CAUTION: Low tolerances have heavy impact on RAM usage (since Comet uses a lot of bins in this case). Consider using use_sparse_matrix and/or spectrum_batch_size"/> - <param name="fragment_error_units" argument="-fragment_error_units" display="radio" type="select" optional="false" label="Fragment monoisotopic mass error units" help=""> + <param argument="-fragment_mass_tolerance" type="float" optional="true" min="0.0001" value="0.01" label="This is half the bin size, which is used to segment the MS/MS spectrum" help="Thus, the value should be a bit higher than for other search engines, since the bin might not be centered around the peak apex (see 'fragment_bin_offset').CAUTION: Low tolerances have heavy impact on RAM usage (since Comet uses a lot of bins in this case). Consider using use_sparse_matrix and/or spectrum_batch_size"/> + <param argument="-fragment_error_units" type="select" optional="true" label="Fragment monoisotopic mass error units" help=""> <option value="Da" selected="true">Da</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="fragment_error_units"/> </param> - <param name="fragment_bin_offset" argument="-fragment_bin_offset" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Offset of fragment bins" help="Recommended by Comet: low-res: 0.4, high-res: 0.0"/> - <param name="instrument" argument="-instrument" display="radio" type="select" optional="false" label="Comets theoretical_fragment_ions parameter: theoretical fragment ion peak representation, high-res: sum of intensities plus flanking bins, ion trap (low-res) ms/ms: sum of intensities of central M bin only" help=""> + <param argument="-fragment_bin_offset" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Offset of fragment bins" help="Recommended by Comet: low-res: 0.4, high-res: 0.0"/> + <param argument="-instrument" type="select" optional="true" label="Comets theoretical_fragment_ions parameter: theoretical fragment ion peak representation, high-res: sum of intensities plus flanking bins, ion trap (low-res) ms/ms: sum of intensities of central M bin only" help=""> <option value="low_res">low_res</option> <option value="high_res" selected="true">high_res</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="instrument"/> </param> - <param name="enzyme" argument="-enzyme" type="select" optional="false" label="The enzyme used for peptide digestion" help=""> - <option value="Arg-C">Arg-C</option> - <option value="Asp-N">Asp-N</option> - <option value="Trypsin" selected="true">Trypsin</option> - <option value="unspecific cleavage">unspecific cleavage</option> - <option value="Chymotrypsin">Chymotrypsin</option> + <param argument="-enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help=""> <option value="CNBr">CNBr</option> <option value="Lys-C">Lys-C</option> + <option value="Trypsin" selected="true">Trypsin</option> + <option value="Arg-C">Arg-C</option> + <option value="Chymotrypsin">Chymotrypsin</option> + <option value="Asp-N">Asp-N</option> + <option value="unspecific cleavage">unspecific cleavage</option> <option value="Lys-N">Lys-N</option> <option value="PepsinA">PepsinA</option> <option value="Trypsin/P">Trypsin/P</option> <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="enzyme"/> </param> - <param name="num_enzyme_termini" argument="-num_enzyme_termini" display="radio" type="select" optional="false" label="Specify the termini where the cleavage rule has to match" help=""> + <param argument="-num_enzyme_termini" type="select" optional="true" label="Specify the termini where the cleavage rule has to match" help=""> <option value="semi">semi</option> <option value="fully" selected="true">fully</option> <option value="C-term unspecific">C-term unspecific</option> <option value="N-term unspecific">N-term unspecific</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="num_enzyme_termini"/> </param> - <param name="missed_cleavages" argument="-missed_cleavages" type="integer" optional="true" min="0" max="5" value="1" label="Number of possible cleavage sites missed by the enzyme" help="It has no effect if enzyme is unspecific cleavage"/> - <param name="min_peptide_length" argument="-min_peptide_length" type="integer" optional="true" min="5" max="63" value="5" label="Minimum peptide length to conside" help=""/> - <param name="max_peptide_length" argument="-max_peptide_length" type="integer" optional="true" min="5" max="63" value="63" label="Maximum peptide length to conside" help=""/> - <param name="num_hits" argument="-num_hits" type="integer" optional="true" value="1" label="Number of peptide hits in output file" help=""/> - <param name="precursor_charge" argument="-precursor_charge" type="text" optional="true" value="0:0" label="Precursor charge range to search (if spectrum is not annotated with a charge or if override_charge!=keep any known): 0:[num] == search all charges, 2:6 == from +2 to +6, 3:3 == +3" help=""> - <expand macro="list_string_san"/> + <param argument="-missed_cleavages" type="integer" optional="true" min="0" max="5" value="1" label="Number of possible cleavage sites missed by the enzyme" help="It has no effect if enzyme is unspecific cleavage"/> + <param argument="-min_peptide_length" type="integer" optional="true" min="5" max="63" value="5" label="Minimum peptide length to conside" help=""/> + <param argument="-max_peptide_length" type="integer" optional="true" min="5" max="63" value="63" label="Maximum peptide length to conside" help=""/> + <param argument="-num_hits" type="integer" optional="true" value="1" label="Number of peptide hits in output file" help=""/> + <param argument="-precursor_charge" type="text" optional="true" value="0:0" label="Precursor charge range to search (if spectrum is not annotated with a charge or if override_charge!=keep any known): 0:[num] == search all charges, 2:6 == from +2 to +6, 3:3 == +3" help=""> + <expand macro="list_string_san" name="precursor_charge"/> </param> - <param name="override_charge" argument="-override_charge" display="radio" type="select" optional="false" label="_keep any known_: keep any precursor charge state (from input), _ignore known_: ignore known precursor charge state and use precursor_charge parameter, _ignore outside range_: ignore precursor charges outside precursor_charge range, _keep known search unknown_: keep any known precursor charge state" help="For unknown charge states, search as singly charged if there is no signal above the precursor m/z or use the precursor_charge range"> + <param argument="-override_charge" type="select" optional="true" label="_keep any known_: keep any precursor charge state (from input), _ignore known_: ignore known precursor charge state and use precursor_charge parameter, _ignore outside range_: ignore precursor charges outside precursor_charge range, _keep known search unknown_: keep any known precursor charge state" help="For unknown charge states, search as singly charged if there is no signal above the precursor m/z or use the precursor_charge range"> <option value="keep any known">keep any known</option> <option value="ignore known">ignore known</option> <option value="ignore outside range">ignore outside range</option> <option value="keep known search unknown" selected="true">keep known search unknown</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="override_charge"/> </param> - <param name="ms_level" argument="-ms_level" type="integer" optional="true" min="2" max="3" value="2" label="MS level to analyze, valid are levels 2 (default) or 3" help=""/> - <param name="activation_method" argument="-activation_method" type="select" optional="false" label="If not ALL, only searches spectra of the given method" help=""> + <param argument="-ms_level" type="integer" optional="true" min="2" max="3" value="2" label="MS level to analyze, valid are levels 2 (default) or 3" help=""/> + <param argument="-activation_method" type="select" optional="true" label="If not ALL, only searches spectra of the given method" help=""> <option value="ALL" selected="true">ALL</option> <option value="CID">CID</option> <option value="ECD">ECD</option> @@ -139,11 +138,11 @@ <option value="PQD">PQD</option> <option value="HCD">HCD</option> <option value="IRMPD">IRMPD</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="activation_method"/> </param> - <param name="max_fragment_charge" argument="-max_fragment_charge" type="integer" optional="true" min="1" max="5" value="3" label="Set maximum fragment charge state to analyze as long as still lower than precursor charge - 1" help="(Allowed max 5)"/> - <param name="clip_nterm_methionine" argument="-clip_nterm_methionine" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true, also considers the peptide sequence w/o N-term methionine separately and applies appropriate N-term mods to it" help=""/> - <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="-max_fragment_charge" type="integer" optional="true" min="1" max="5" value="3" label="Set maximum fragment charge state to analyze as long as still lower than precursor charge - 1" help="(Allowed max 5)"/> + <param argument="-clip_nterm_methionine" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true, also considers the peptide sequence w/o N-term methionine separately and applies appropriate N-term mods to it" help=""/> + <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> @@ -1513,7 +1512,6 @@ <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> @@ -3072,9 +3070,9 @@ <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> @@ -4444,7 +4442,6 @@ <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> @@ -6003,60 +6000,134 @@ <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 argument="-binary_modifications" type="text" optional="true" value="" label="List of modification group indices" help="Indices correspond to the binary modification index used by comet to group individually searched lists of variable modifications.. Note: if set, both variable_modifications and binary_modifications need to have the same number of entries as the N-th entry corresponds to the N-th variable_modification.. if left empty (default), all entries are internally set to 0 generating all permutations of modified and unmodified residues.. For a detailed explanation please see the parameter description in the Comet help (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <expand macro="list_integer_valsan" name="binary_modifications"/> </param> - <param name="binary_modifications" argument="-binary_modifications" type="text" optional="true" value="" label="List of modification group indices" help="Indices correspond to the binary modification index used by comet to group individually searched lists of variable modifications.. Note: if set, both variable_modifications and binary_modifications need to have the same number of entries as the N-th entry corresponds to the N-th variable_modification.. if left empty (default), all entries are internally set to 0 generating all permutations of modified and unmodified residues.. For a detailed explanation please see the parameter description in the Comet help (space separated list, in order to allow for spaces in list items surround them by single quotes)"> - <expand macro="list_integer_valsan"/> - </param> + <param argument="-reindex" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Recalculate peptide to protein association using OpenMS" help="Annotates target-decoy information"/> + <section name="PeptideIndexing" title="" help="" expanded="false"> + <param name="decoy_string" argument="-PeptideIndexing:decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)"> + <expand macro="list_string_san" name="decoy_string"/> + </param> + <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" optional="true" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)"> + <option value="prefix" selected="true">prefix</option> + <option value="suffix">suffix</option> + <expand macro="list_string_san" name="decoy_string_position"/> + </param> + <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" optional="true" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help=""> + <option value="error">error</option> + <option value="warn" selected="true">warn</option> + <option value="silent">silent</option> + <expand macro="list_string_san" name="missing_decoy_action"/> + </param> + <param name="write_protein_sequence" argument="-PeptideIndexing:write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/> + <param name="write_protein_description" argument="-PeptideIndexing:write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/> + <param name="keep_unreferenced_proteins" argument="-PeptideIndexing:keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/> + <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" optional="true" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help=""> + <option value="error" selected="true">error</option> + <option value="warn">warn</option> + <option value="remove">remove</option> + <expand macro="list_string_san" name="unmatched_action"/> + </param> + <param name="aaa_max" argument="-PeptideIndexing:aaa_max" type="integer" optional="true" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are 'B', 'J', 'Z' and 'X'"/> + <param name="mismatches_max" argument="-PeptideIndexing:mismatches_max" type="integer" optional="true" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/> + <param name="IL_equivalent" argument="-PeptideIndexing:IL_equivalent" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="Also occurrences of 'J' will be treated as 'I' thus avoiding ambiguous matching"/> + <section name="enzyme" title="" help="" expanded="false"> + <param name="name" argument="-PeptideIndexing:enzyme:name" type="select" optional="true" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input"> + <option value="auto" selected="true">auto</option> + <option value="Trypsin">Trypsin</option> + <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> + <option value="Glu-C+P">Glu-C+P</option> + <option value="PepsinA + P">PepsinA + P</option> + <option value="cyanogen-bromide">cyanogen-bromide</option> + <option value="Clostripain/P">Clostripain/P</option> + <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> + <option value="no cleavage">no cleavage</option> + <option value="proline endopeptidase">proline endopeptidase</option> + <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> + <option value="Alpha-lytic protease">Alpha-lytic protease</option> + <option value="2-iodobenzoate">2-iodobenzoate</option> + <option value="iodosobenzoate">iodosobenzoate</option> + <option value="staphylococcal protease/D">staphylococcal protease/D</option> + <option value="Trypsin/P">Trypsin/P</option> + <option value="V8-DE">V8-DE</option> + <option value="V8-E">V8-E</option> + <option value="leukocyte elastase">leukocyte elastase</option> + <option value="PepsinA">PepsinA</option> + <option value="TrypChymo">TrypChymo</option> + <option value="Asp-N">Asp-N</option> + <option value="unspecific cleavage">unspecific cleavage</option> + <option value="Asp-N/B">Asp-N/B</option> + <option value="Asp-N_ambic">Asp-N_ambic</option> + <option value="Chymotrypsin">Chymotrypsin</option> + <option value="Chymotrypsin/P">Chymotrypsin/P</option> + <option value="CNBr">CNBr</option> + <option value="Arg-C/P">Arg-C/P</option> + <option value="Lys-N">Lys-N</option> + <option value="Lys-C/P">Lys-C/P</option> + <option value="Formic_acid">Formic_acid</option> + <option value="Lys-C">Lys-C</option> + <option value="Arg-C">Arg-C</option> + <expand macro="list_string_san" name="name"/> + </param> + <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" optional="true" label="Specificity of the enzyme" help="Default: deduce from input.. 'full': both internal cleavage sites must match.. 'semi': one of two internal cleavage sites must match.. 'none': allow all peptide hits no matter their context (enzyme is irrelevant)"> + <option value="auto" selected="true">auto</option> + <option value="full">full</option> + <option value="semi">semi</option> + <option value="none">none</option> + <expand macro="list_string_san" name="specificity"/> + </param> + </section> + </section> <expand macro="adv_opts_macro"> - <param name="use_A_ions" argument="-use_A_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use A ions for PSM" help=""/> - <param name="use_B_ions" argument="-use_B_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="use B ions for PSM" help=""/> - <param name="use_C_ions" argument="-use_C_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use C ions for PSM" help=""/> - <param name="use_X_ions" argument="-use_X_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use X ions for PSM" help=""/> - <param name="use_Y_ions" argument="-use_Y_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="use Y ions for PSM" help=""/> - <param name="use_Z_ions" argument="-use_Z_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use Z ions for PSM" help=""/> - <param name="use_NL_ions" argument="-use_NL_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use neutral loss (NH3, H2O) ions from b/y for PSM" help=""/> - <param name="second_enzyme" argument="-second_enzyme" type="select" optional="true" label="Additional enzyme used for peptide digestion" help=""> - <option value="">default (nothing chosen)</option> - <option value="Arg-C">Arg-C</option> - <option value="Asp-N">Asp-N</option> - <option value="Trypsin">Trypsin</option> - <option value="unspecific cleavage">unspecific cleavage</option> - <option value="Chymotrypsin">Chymotrypsin</option> + <param argument="-use_A_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use A ions for PSM" help=""/> + <param argument="-use_B_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="use B ions for PSM" help=""/> + <param argument="-use_C_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use C ions for PSM" help=""/> + <param argument="-use_X_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use X ions for PSM" help=""/> + <param argument="-use_Y_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="use Y ions for PSM" help=""/> + <param argument="-use_Z_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use Z ions for PSM" help=""/> + <param argument="-use_NL_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use neutral loss (NH3, H2O) ions from b/y for PSM" help=""/> + <param argument="-second_enzyme" type="select" optional="true" label="Additional enzyme used for peptide digestion" help=""> <option value="CNBr">CNBr</option> <option value="Lys-C">Lys-C</option> + <option value="Trypsin">Trypsin</option> + <option value="Arg-C">Arg-C</option> + <option value="Chymotrypsin">Chymotrypsin</option> + <option value="Asp-N">Asp-N</option> + <option value="unspecific cleavage">unspecific cleavage</option> <option value="Lys-N">Lys-N</option> <option value="PepsinA">PepsinA</option> <option value="Trypsin/P">Trypsin/P</option> <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="second_enzyme"/> </param> - <param name="digest_mass_range" argument="-digest_mass_range" type="text" optional="true" value="600:5000" label="MH+ peptide mass range to analyze" help=""> - <expand macro="list_string_san"/> + <param argument="-digest_mass_range" type="text" optional="true" value="600:5000" label="MH+ peptide mass range to analyze" help=""> + <expand macro="list_string_san" name="digest_mass_range"/> </param> - <param name="max_precursor_charge" argument="-max_precursor_charge" type="integer" optional="true" min="1" max="9" value="5" label="set maximum precursor charge state to analyze (allowed max 9)" help=""/> - <param name="spectrum_batch_size" argument="-spectrum_batch_size" type="integer" optional="true" min="0" value="20000" label="max" help="number of spectra to search at a time; use 0 to search the entire scan range in one batch"/> - <param name="mass_offsets" argument="-mass_offsets" type="text" optional="true" value="0.0" label="One or more mass offsets to search (values subtracted from deconvoluted precursor mass)" help="Has to include 0.0 if you want the default mass to be searched (space separated list, in order to allow for spaces in list items surround them by single quotes)"> - <expand macro="list_float_valsan"/> + <param argument="-max_precursor_charge" type="integer" optional="true" min="1" max="9" value="5" label="set maximum precursor charge state to analyze (allowed max 9)" help=""/> + <param argument="-spectrum_batch_size" type="integer" optional="true" min="0" value="20000" label="max" help="number of spectra to search at a time; use 0 to search the entire scan range in one batch"/> + <param argument="-mass_offsets" type="text" optional="true" value="0.0" label="One or more mass offsets to search (values subtracted from deconvoluted precursor mass)" help="Has to include 0.0 if you want the default mass to be searched (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <expand macro="list_float_valsan" name="mass_offsets"/> </param> - <param name="minimum_peaks" argument="-minimum_peaks" type="integer" optional="true" value="10" label="Required minimum number of peaks in spectrum to search (default 10)" help=""/> - <param name="minimum_intensity" argument="-minimum_intensity" type="float" optional="true" min="0.0" value="0.0" label="Minimum intensity value to read in" help=""/> - <param name="remove_precursor_peak" argument="-remove_precursor_peak" display="radio" type="select" optional="false" label="no = no removal, yes = remove all peaks around precursor m/z, charge_reduced = remove all charge reduced precursor peaks (for ETD/ECD)" help="phosphate_loss = remove the HPO3 (-80) and H3PO4 (-98) precursor phosphate neutral loss peaks. See also remove_precursor_tolerance"> + <param argument="-minimum_peaks" type="integer" optional="true" value="10" label="Required minimum number of peaks in spectrum to search (default 10)" help=""/> + <param argument="-minimum_intensity" type="float" optional="true" min="0.0" value="0.0" label="Minimum intensity value to read in" help=""/> + <param argument="-remove_precursor_peak" type="select" optional="true" label="no = no removal, yes = remove all peaks around precursor m/z, charge_reduced = remove all charge reduced precursor peaks (for ETD/ECD)" help="phosphate_loss = remove the HPO3 (-80) and H3PO4 (-98) precursor phosphate neutral loss peaks. See also remove_precursor_tolerance"> <option value="no" selected="true">no</option> <option value="yes">yes</option> <option value="charge_reduced">charge_reduced</option> <option value="phosphate_loss">phosphate_loss</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="remove_precursor_peak"/> </param> - <param name="remove_precursor_tolerance" argument="-remove_precursor_tolerance" type="float" optional="true" value="1.5" label="one-sided tolerance for precursor removal in Thompson" help=""/> - <param name="clear_mz_range" argument="-clear_mz_range" type="text" optional="true" value="0:0" label="for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range, if not 0:0" help=""> - <expand macro="list_string_san"/> + <param argument="-remove_precursor_tolerance" type="float" optional="true" value="1.5" label="one-sided tolerance for precursor removal in Thompson" help=""/> + <param argument="-clear_mz_range" type="text" optional="true" value="0:0" label="for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range, if not 0:0" help=""> + <expand macro="list_string_san" name="clear_mz_range"/> </param> - <param name="max_variable_mods_in_peptide" argument="-max_variable_mods_in_peptide" type="integer" optional="true" value="5" label="Set a maximum number of variable modifications per peptide" help=""/> - <param name="require_variable_mod" argument="-require_variable_mod" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, requires at least one variable modification per peptide" help=""/> - <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="-max_variable_mods_in_peptide" type="integer" optional="true" value="5" label="Set a maximum number of variable modifications per peptide" help=""/> + <param argument="-require_variable_mod" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, requires at least one variable modification per peptide" help=""/> + <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"> @@ -6073,13 +6144,309 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_CometAdapter"/> - <expand macro="manutest_CometAdapter"/> + <tests><!-- TOPP_CometAdapter_1 --> + <test expect_num_outputs="3"> + <section name="adv_opts"> + <param name="use_A_ions" value="false"/> + <param name="use_B_ions" value="true"/> + <param name="use_C_ions" value="false"/> + <param name="use_X_ions" value="false"/> + <param name="use_Y_ions" value="true"/> + <param name="use_Z_ions" value="false"/> + <param name="use_NL_ions" value="false"/> + <param name="second_enzyme"/> + <param name="digest_mass_range" value="600:5000"/> + <param name="max_precursor_charge" value="5"/> + <param name="spectrum_batch_size" value="1000"/> + <param name="mass_offsets" value="0.0"/> + <param name="minimum_peaks" value="10"/> + <param name="minimum_intensity" value="0.0"/> + <param name="remove_precursor_peak" value="no"/> + <param name="remove_precursor_tolerance" value="1.5"/> + <param name="clear_mz_range" value="0:0"/> + <param name="max_variable_mods_in_peptide" value="5"/> + <param name="require_variable_mod" value="false"/> + <param name="force" value="true"/> + <param name="test" value="true"/> + </section> + <param name="in" value="spectra_comet.mzML"/> + <output name="out" file="CometAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <param name="database" value="proteins.fasta"/> + <output name="pin_out" file="CometAdapter_1_out2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> + <param name="precursor_mass_tolerance" value="3.0"/> + <param name="precursor_error_units" value="ppm"/> + <param name="isotope_error" value="off"/> + <param name="fragment_mass_tolerance" value="0.50025"/> + <param name="fragment_error_units" value="Da"/> + <param name="fragment_bin_offset" value="0.25"/> + <param name="instrument" value="high_res"/> + <param name="enzyme" value="Trypsin"/> + <param name="num_enzyme_termini" value="fully"/> + <param name="missed_cleavages" value="1"/> + <param name="min_peptide_length" value="5"/> + <param name="max_peptide_length" value="63"/> + <param name="num_hits" value="5"/> + <param name="precursor_charge" value="0:0"/> + <param name="override_charge" value="keep any known"/> + <param name="ms_level" value="2"/> + <param name="activation_method" value="ALL"/> + <param name="max_fragment_charge" value="3"/> + <param name="clip_nterm_methionine" value="false"/> + <param name="fixed_modifications"/> + <param name="variable_modifications"/> + <param name="binary_modifications" value=""/> + <param name="reindex" value="true"/> + <section name="PeptideIndexing"> + <param name="decoy_string" value=""/> + <param name="decoy_string_position" value="prefix"/> + <param name="missing_decoy_action" value="warn"/> + <param name="write_protein_sequence" value="false"/> + <param name="write_protein_description" value="false"/> + <param name="keep_unreferenced_proteins" value="false"/> + <param name="unmatched_action" value="error"/> + <param name="aaa_max" value="3"/> + <param name="mismatches_max" value="0"/> + <param name="IL_equivalent" value="false"/> + <section name="enzyme"> + <param name="name" value="auto"/> + <param name="specificity" value="auto"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_CometAdapter_2 --> + <test expect_num_outputs="3"> + <section name="adv_opts"> + <param name="use_A_ions" value="false"/> + <param name="use_B_ions" value="true"/> + <param name="use_C_ions" value="false"/> + <param name="use_X_ions" value="false"/> + <param name="use_Y_ions" value="true"/> + <param name="use_Z_ions" value="false"/> + <param name="use_NL_ions" value="false"/> + <param name="second_enzyme"/> + <param name="digest_mass_range" value="600:5000"/> + <param name="max_precursor_charge" value="5"/> + <param name="spectrum_batch_size" value="1000"/> + <param name="mass_offsets" value="0.0"/> + <param name="minimum_peaks" value="10"/> + <param name="minimum_intensity" value="0.0"/> + <param name="remove_precursor_peak" value="no"/> + <param name="remove_precursor_tolerance" value="1.5"/> + <param name="clear_mz_range" value="0:0"/> + <param name="max_variable_mods_in_peptide" value="5"/> + <param name="require_variable_mod" value="false"/> + <param name="force" value="true"/> + <param name="test" value="true"/> + </section> + <param name="in" value="CometAdapter_2_prepared.mzML"/> + <output name="out" file="CometAdapter_2_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <param name="database" value="CometAdapter_2_in.fasta"/> + <output name="pin_out" file="CometAdapter_2_out2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> + <param name="precursor_mass_tolerance" value="3.0"/> + <param name="precursor_error_units" value="Da"/> + <param name="isotope_error" value="off"/> + <param name="fragment_mass_tolerance" value="0.50025"/> + <param name="fragment_error_units" value="Da"/> + <param name="fragment_bin_offset" value="0.25"/> + <param name="instrument" value="high_res"/> + <param name="enzyme" value="Trypsin"/> + <param name="num_enzyme_termini" value="fully"/> + <param name="missed_cleavages" value="1"/> + <param name="min_peptide_length" value="5"/> + <param name="max_peptide_length" value="63"/> + <param name="num_hits" value="5"/> + <param name="precursor_charge" value="0:0"/> + <param name="override_charge" value="keep any known"/> + <param name="ms_level" value="2"/> + <param name="activation_method" value="ALL"/> + <param name="max_fragment_charge" value="3"/> + <param name="clip_nterm_methionine" value="false"/> + <param name="fixed_modifications"/> + <param name="variable_modifications"/> + <param name="binary_modifications" value=""/> + <param name="reindex" value="true"/> + <section name="PeptideIndexing"> + <param name="decoy_string" value=""/> + <param name="decoy_string_position" value="prefix"/> + <param name="missing_decoy_action" value="warn"/> + <param name="write_protein_sequence" value="false"/> + <param name="write_protein_description" value="false"/> + <param name="keep_unreferenced_proteins" value="false"/> + <param name="unmatched_action" value="error"/> + <param name="aaa_max" value="3"/> + <param name="mismatches_max" value="0"/> + <param name="IL_equivalent" value="false"/> + <section name="enzyme"> + <param name="name" value="auto"/> + <param name="specificity" value="auto"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_CometAdapter_3 --> + <test expect_num_outputs="3"> + <section name="adv_opts"> + <param name="use_A_ions" value="false"/> + <param name="use_B_ions" value="true"/> + <param name="use_C_ions" value="false"/> + <param name="use_X_ions" value="false"/> + <param name="use_Y_ions" value="true"/> + <param name="use_Z_ions" value="false"/> + <param name="use_NL_ions" value="false"/> + <param name="second_enzyme"/> + <param name="digest_mass_range" value="600:5000"/> + <param name="max_precursor_charge" value="5"/> + <param name="spectrum_batch_size" value="20000"/> + <param name="mass_offsets" value="0.0"/> + <param name="minimum_peaks" value="10"/> + <param name="minimum_intensity" value="0.0"/> + <param name="remove_precursor_peak" value="no"/> + <param name="remove_precursor_tolerance" value="1.5"/> + <param name="clear_mz_range" value="0:0"/> + <param name="max_variable_mods_in_peptide" value="3"/> + <param name="require_variable_mod" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="CometAdapter_3.mzML"/> + <output name="out" file="CometAdapter_3_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <param name="database" value="CometAdapter_3.fasta"/> + <output name="pin_out" file="CometAdapter_3_out2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> + <param name="precursor_mass_tolerance" value="5.0"/> + <param name="precursor_error_units" value="ppm"/> + <param name="isotope_error" value="off"/> + <param name="fragment_mass_tolerance" value="0.01"/> + <param name="fragment_error_units" value="Da"/> + <param name="fragment_bin_offset" value="0.0"/> + <param name="instrument" value="high_res"/> + <param name="enzyme" value="Trypsin"/> + <param name="num_enzyme_termini" value="fully"/> + <param name="missed_cleavages" value="3"/> + <param name="min_peptide_length" value="5"/> + <param name="max_peptide_length" value="63"/> + <param name="num_hits" value="5"/> + <param name="precursor_charge" value="0:0"/> + <param name="override_charge" value="keep known search unknown"/> + <param name="ms_level" value="2"/> + <param name="activation_method" value="ALL"/> + <param name="max_fragment_charge" value="3"/> + <param name="clip_nterm_methionine" value="false"/> + <param name="fixed_modifications" value="Carbamidomethyl (C)"/> + <param name="variable_modifications" value="Acetyl (Protein N-term),Carbamidomethyl (N-term),Phospho (S),Phospho (T),Phospho (Y)"/> + <param name="binary_modifications" value=""/> + <param name="reindex" value="true"/> + <section name="PeptideIndexing"> + <param name="decoy_string" value=""/> + <param name="decoy_string_position" value="prefix"/> + <param name="missing_decoy_action" value="warn"/> + <param name="write_protein_sequence" value="false"/> + <param name="write_protein_description" value="false"/> + <param name="keep_unreferenced_proteins" value="false"/> + <param name="unmatched_action" value="error"/> + <param name="aaa_max" value="3"/> + <param name="mismatches_max" value="0"/> + <param name="IL_equivalent" value="false"/> + <section name="enzyme"> + <param name="name" value="auto"/> + <param name="specificity" value="auto"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_CometAdapter_4 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="use_A_ions" value="false"/> + <param name="use_B_ions" value="true"/> + <param name="use_C_ions" value="false"/> + <param name="use_X_ions" value="false"/> + <param name="use_Y_ions" value="true"/> + <param name="use_Z_ions" value="false"/> + <param name="use_NL_ions" value="false"/> + <param name="second_enzyme"/> + <param name="digest_mass_range" value="600:1200"/> + <param name="max_precursor_charge" value="5"/> + <param name="spectrum_batch_size" value="20000"/> + <param name="mass_offsets" value="0.0"/> + <param name="minimum_peaks" value="10"/> + <param name="minimum_intensity" value="0.0"/> + <param name="remove_precursor_peak" value="no"/> + <param name="remove_precursor_tolerance" value="1.5"/> + <param name="clear_mz_range" value="0:0"/> + <param name="max_variable_mods_in_peptide" value="3"/> + <param name="require_variable_mod" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="examples/FRACTIONS/BSA1_F1.mzML"/> + <output name="out" file="CometAdapter_4_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <param name="database" value="examples/TOPPAS/data/BSA_Identification/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta"/> + <param name="precursor_mass_tolerance" value="5.0"/> + <param name="precursor_error_units" value="ppm"/> + <param name="isotope_error" value="off"/> + <param name="fragment_mass_tolerance" value="0.01"/> + <param name="fragment_error_units" value="Da"/> + <param name="fragment_bin_offset" value="0.0"/> + <param name="instrument" value="high_res"/> + <param name="enzyme" value="Trypsin"/> + <param name="num_enzyme_termini" value="fully"/> + <param name="missed_cleavages" value="3"/> + <param name="min_peptide_length" value="5"/> + <param name="max_peptide_length" value="63"/> + <param name="num_hits" value="5"/> + <param name="precursor_charge" value="0:0"/> + <param name="override_charge" value="keep known search unknown"/> + <param name="ms_level" value="2"/> + <param name="activation_method" value="ALL"/> + <param name="max_fragment_charge" value="3"/> + <param name="clip_nterm_methionine" value="false"/> + <param name="fixed_modifications" value="Carbamidomethyl (C)"/> + <param name="variable_modifications" value="Met-loss (Protein N-term M)"/> + <param name="binary_modifications" value=""/> + <param name="reindex" value="true"/> + <section name="PeptideIndexing"> + <param name="decoy_string" value=""/> + <param name="decoy_string_position" value="prefix"/> + <param name="missing_decoy_action" value="warn"/> + <param name="write_protein_sequence" value="false"/> + <param name="write_protein_description" value="false"/> + <param name="keep_unreferenced_proteins" value="false"/> + <param name="unmatched_action" value="error"/> + <param name="aaa_max" value="3"/> + <param name="mismatches_max" value="0"/> + <param name="IL_equivalent" value="false"/> + <section name="enzyme"> + <param name="name" value="auto"/> + <param name="specificity" value="auto"/> + </section> + </section> + <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 Comet. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_CometAdapter.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_CometAdapter.html]]></help> <expand macro="references"/> </tool>