Mercurial > repos > galaxyp > openms_msgfplusadapter
diff MSGFPlusAdapter.xml @ 15:f5ec766d80cf 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 19:07:07 +0000 |
| parents | c18d8efa4474 |
| children |
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--- a/MSGFPlusAdapter.xml Mon Dec 14 16:57:17 2020 +0000 +++ b/MSGFPlusAdapter.xml Thu Dec 01 19:07:07 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="MSGFPlusAdapter" name="MSGFPlusAdapter" version="@TOOL_VERSION@+galaxy1" profile="20.05"> +<tool id="MSGFPlusAdapter" name="MSGFPlusAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>MS/MS database search using MS-GF+.</description> <macros> <token name="@EXECUTABLE@">MSGFPlusAdapter</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -72,32 +70,32 @@ <configfile name="hardcoded_json"><![CDATA[{"executable": "\$(msgf_plus -get_jar_path)", "java_executable": "java", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param name="in" argument="-in" type="data" format="mgf,ms2,mzml,mzxml" optional="false" label="Input file (MS-GF+ parameter '-s')" help=" select mgf,ms2,mzml,mzxml data sets(s)"/> - <param name="database" argument="-database" type="data" format="fasta" optional="false" label="Protein sequence database (FASTA file; MS-GF+ parameter '-d')" help="Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir' select fasta data sets(s)"/> - <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor monoisotopic mass tolerance (MS-GF+ parameter '-t')" help=""/> - <param name="precursor_error_units" argument="-precursor_error_units" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance (MS-GF+ parameter '-t')" help=""> + <param argument="-in" type="data" format="mgf,ms2,mzml,mzxml" optional="false" label="Input file (MS-GF+ parameter '-s')" help=" select mgf,ms2,mzml,mzxml data sets(s)"/> + <param argument="-database" type="data" format="fasta" optional="false" label="Protein sequence database (FASTA file; MS-GF+ parameter '-d')" help="Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir' select fasta data sets(s)"/> + <param argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor monoisotopic mass tolerance (MS-GF+ parameter '-t')" help=""/> + <param argument="-precursor_error_units" type="select" optional="true" label="Unit of precursor mass tolerance (MS-GF+ parameter '-t')" 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_error_units"/> </param> - <param name="isotope_error_range" argument="-isotope_error_range" type="text" optional="true" value="0,1" label="Range of allowed isotope peak errors (MS-GF+ parameter '-ti')" help="Takes into account the error introduced by choosing a non-monoisotopic peak for fragmentation. Combined with 'precursor_mass_tolerance'/'precursor_error_units', this determines the actual precursor mass tolerance. E.g. for experimental mass 'exp' and calculated mass 'calc', '-precursor_mass_tolerance 20 -precursor_error_units ppm -isotope_error_range -1,2' tests '|exp - calc - n * 1.00335 Da| < 20 ppm' for n = -1, 0, 1, 2"> - <expand macro="list_string_san"/> + <param argument="-isotope_error_range" type="text" optional="true" value="0,1" label="Range of allowed isotope peak errors (MS-GF+ parameter '-ti')" help="Takes into account the error introduced by choosing a non-monoisotopic peak for fragmentation. Combined with 'precursor_mass_tolerance'/'precursor_error_units', this determines the actual precursor mass tolerance. E.g. for experimental mass 'exp' and calculated mass 'calc', '-precursor_mass_tolerance 20 -precursor_error_units ppm -isotope_error_range -1,2' tests '|exp - calc - n * 1.00335 Da| < 20 ppm' for n = -1, 0, 1, 2"> + <expand macro="list_string_san" name="isotope_error_range"/> </param> - <param name="fragment_method" argument="-fragment_method" display="radio" type="select" optional="false" label="Fragmentation method ('from_spectrum' relies on spectrum meta data and uses CID as fallback option; MS-GF+ parameter '-m')" help=""> + <param argument="-fragment_method" type="select" optional="true" label="Fragmentation method ('from_spectrum' relies on spectrum meta data and uses CID as fallback option; MS-GF+ parameter '-m')" help=""> <option value="from_spectrum" selected="true">from_spectrum</option> <option value="CID">CID</option> <option value="ETD">ETD</option> <option value="HCD">HCD</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="fragment_method"/> </param> - <param name="instrument" argument="-instrument" display="radio" type="select" optional="false" label="Instrument that generated the data ('low_res'/'high_res' refer to LCQ and LTQ instruments; MS-GF+ parameter '-inst')" help=""> + <param argument="-instrument" type="select" optional="true" label="Instrument that generated the data ('low_res'/'high_res' refer to LCQ and LTQ instruments; MS-GF+ parameter '-inst')" help=""> <option value="low_res" selected="true">low_res</option> <option value="high_res">high_res</option> <option value="TOF">TOF</option> <option value="Q_Exactive">Q_Exactive</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="instrument"/> </param> - <param name="enzyme" argument="-enzyme" type="select" optional="false" label="Enzyme used for digestion, or type of cleavage" help="Note: MS-GF+ does not support blocking rules. (MS-GF+ parameter '-e')"> + <param argument="-enzyme" type="select" optional="true" label="Enzyme used for digestion, or type of cleavage" help="Note: MS-GF+ does not support blocking rules. (MS-GF+ parameter '-e')"> <option value="Alpha-lytic protease">Alpha-lytic protease</option> <option value="Arg-C/P">Arg-C/P</option> <option value="Asp-N/B">Asp-N/B</option> @@ -108,33 +106,33 @@ <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> <option value="no cleavage">no cleavage</option> <option value="unspecific cleavage">unspecific cleavage</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="enzyme"/> </param> - <param name="protocol" argument="-protocol" type="select" optional="false" label="Labeling or enrichment protocol used, if any (MS-GF+ parameter '-p')" help=""> + <param argument="-protocol" type="select" optional="true" label="Labeling or enrichment protocol used, if any (MS-GF+ parameter '-p')" help=""> <option value="automatic" selected="true">automatic</option> <option value="phospho">phospho</option> <option value="iTRAQ">iTRAQ</option> <option value="iTRAQ_phospho">iTRAQ_phospho</option> <option value="TMT">TMT</option> <option value="none">none</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="protocol"/> </param> - <param name="tryptic" argument="-tryptic" display="radio" type="select" optional="false" label="Level of cleavage specificity required (MS-GF+ parameter '-ntt')" help=""> + <param argument="-tryptic" type="select" optional="true" label="Level of cleavage specificity required (MS-GF+ parameter '-ntt')" help=""> <option value="non">non</option> <option value="semi">semi</option> <option value="fully" selected="true">fully</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="tryptic"/> </param> - <param name="min_precursor_charge" argument="-min_precursor_charge" type="integer" optional="true" min="1" value="2" label="Minimum precursor ion charge (only used for spectra without charge information; MS-GF+ parameter '-minCharge')" help=""/> - <param name="max_precursor_charge" argument="-max_precursor_charge" type="integer" optional="true" min="1" value="3" label="Maximum precursor ion charge (only used for spectra without charge information; MS-GF+ parameter '-maxCharge')" help=""/> - <param name="min_peptide_length" argument="-min_peptide_length" type="integer" optional="true" min="1" value="6" label="Minimum peptide length to consider (MS-GF+ parameter '-minLength')" help=""/> - <param name="max_peptide_length" argument="-max_peptide_length" type="integer" optional="true" min="1" value="40" label="Maximum peptide length to consider (MS-GF+ parameter '-maxLength')" help=""/> - <param name="matches_per_spec" argument="-matches_per_spec" type="integer" optional="true" min="1" value="1" label="Number of matches per spectrum to be reported (MS-GF+ parameter '-n')" help=""/> - <param name="add_features" argument="-add_features" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Output additional features (MS-GF+ parameter '-addFeatures')" help="This is required by Percolator and hence by default enabled"/> - <param name="max_mods" argument="-max_mods" type="integer" optional="true" min="0" value="2" label="Maximum number of modifications per peptide" help="If this value is large, the search may take very long"/> - <param name="max_missed_cleavages" argument="-max_missed_cleavages" type="integer" optional="true" min="-1" value="-1" label="Maximum number of missed cleavages allowed for a peptide to be considered for scoring" help="(default: -1 meaning unlimited)"/> - <param name="tasks" argument="-tasks" type="integer" optional="true" value="0" label="(Override the number of tasks to use on the threads; Default: (internally calculated based on inputs))" help="More tasks than threads will reduce the memory requirements of the search, but will be slower (how much depends on the inputs).. 1 <= tasks <= numThreads: will create one task per thread, which is the original behavior.. tasks = 0: use default calculation - minimum of: (threads*3) and (numSpectra/250).. tasks < 0: multiply number of threads by abs(tasks) to determine number of tasks (i.e., -2 means "2 * numThreads" tasks).. One task per thread will use the most memory, but will usually finish the fastest.. 2-3 tasks per thread will use comparably less memory, but may cause the search to take 1.5 to 2 times as long"/> - <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="-min_precursor_charge" type="integer" optional="true" min="1" value="2" label="Minimum precursor ion charge (only used for spectra without charge information; MS-GF+ parameter '-minCharge')" help=""/> + <param argument="-max_precursor_charge" type="integer" optional="true" min="1" value="3" label="Maximum precursor ion charge (only used for spectra without charge information; MS-GF+ parameter '-maxCharge')" help=""/> + <param argument="-min_peptide_length" type="integer" optional="true" min="1" value="6" label="Minimum peptide length to consider (MS-GF+ parameter '-minLength')" help=""/> + <param argument="-max_peptide_length" type="integer" optional="true" min="1" value="40" label="Maximum peptide length to consider (MS-GF+ parameter '-maxLength')" help=""/> + <param argument="-matches_per_spec" type="integer" optional="true" min="1" value="1" label="Number of matches per spectrum to be reported (MS-GF+ parameter '-n')" help=""/> + <param argument="-add_features" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Output additional features (MS-GF+ parameter '-addFeatures')" help="This is required by Percolator and hence by default enabled"/> + <param argument="-max_mods" type="integer" optional="true" min="0" value="2" label="Maximum number of modifications per peptide" help="If this value is large, the search may take very long"/> + <param argument="-max_missed_cleavages" type="integer" optional="true" min="-1" value="-1" label="Maximum number of missed cleavages allowed for a peptide to be considered for scoring" help="(default: -1 meaning unlimited)"/> + <param argument="-tasks" type="integer" optional="true" value="0" label="(Override the number of tasks to use on the threads; Default: (internally calculated based on inputs))" help="More tasks than threads will reduce the memory requirements of the search, but will be slower (how much depends on the inputs).. 1 <= tasks <= numThreads: will create one task per thread, which is the original behavior.. tasks = 0: use default calculation - minimum of: (threads*3) and (numSpectra/250).. tasks < 0: multiply number of threads by abs(tasks) to determine number of tasks (i.e., -2 means "2 * numThreads" tasks).. One task per thread will use the most memory, but will usually finish the fastest.. 2-3 tasks per thread will use comparably less memory, but may cause the search to take 1.5 to 2 times as long"/> + <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> @@ -1504,7 +1502,6 @@ <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> @@ -3063,9 +3060,9 @@ <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> @@ -4435,7 +4432,6 @@ <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> @@ -5994,15 +5990,90 @@ <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="conf" argument="-conf" type="data" format="txt" optional="true" label="Optional MSGF+ configuration file (passed as -conf <file> to MSGF+)" help="See documentation for examples. Parameters of the adapter take precedence. Use conf file only for settings not available here (for example, any fixed/var modifications, in the conf file will be ignored, since they are provided via -mod flag) select txt data sets(s)"/> + <param argument="-conf" type="data" format="txt" optional="true" label="Optional MSGF+ configuration file (passed as -conf <file> to MSGF+)" help="See documentation for examples. Parameters of the adapter take precedence. Use conf file only for settings not available here (for example, any fixed/var modifications, in the conf file will be ignored, since they are provided via -mod flag) select txt data sets(s)"/> + <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="CNBr">CNBr</option> + <option value="Formic_acid">Formic_acid</option> + <option value="PepsinA">PepsinA</option> + <option value="TrypChymo">TrypChymo</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="proline endopeptidase">proline endopeptidase</option> + <option value="glutamyl endopeptidase">glutamyl endopeptidase</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="unspecific cleavage">unspecific cleavage</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="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="Lys-C">Lys-C</option> + <option value="Lys-N">Lys-N</option> + <option value="Lys-C/P">Lys-C/P</option> + <option value="Arg-C/P">Arg-C/P</option> + <option value="Arg-C">Arg-C</option> + <option value="Asp-N">Asp-N</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> + <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="add_decoys" argument="-add_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Create decoy proteins (reversed sequences) and append them to the database for the search (MS-GF+ parameter '-tda')" help="This allows the calculation of FDRs, but should only be used if the database does not already contain decoys"/> - <param name="legacy_conversion" argument="-legacy_conversion" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the indirect conversion of MS-GF+ results to idXML via export to TSV" help="Try this only if the default conversion takes too long or uses too much memory"/> - <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="-add_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Create decoy proteins (reversed sequences) and append them to the database for the search (MS-GF+ parameter '-tda')" help="This allows the calculation of FDRs, but should only be used if the database does not already contain decoys"/> + <param argument="-legacy_conversion" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the indirect conversion of MS-GF+ results to idXML via export to TSV" help="Try this only if the default conversion takes too long or uses too much memory"/> + <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"> @@ -6025,13 +6096,65 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_MSGFPlusAdapter"/> - <expand macro="manutest_MSGFPlusAdapter"/> + <tests><!-- TOPP_MSGFPlusAdapter_1 --> + <test expect_num_outputs="3"> + <section name="adv_opts"> + <param name="add_decoys" value="false"/> + <param name="legacy_conversion" value="false"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="spectra.mzML"/> + <output name="out" file="MSGFPlusAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <output name="mzid_out" file="MSGFPlusAdapter_1_out2.tmp.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/> + <param name="database" value="proteins.fasta"/> + <param name="precursor_mass_tolerance" value="10.0"/> + <param name="precursor_error_units" value="ppm"/> + <param name="isotope_error_range" value="0,1"/> + <param name="fragment_method" value="from_spectrum"/> + <param name="instrument" value="high_res"/> + <param name="enzyme" value="Trypsin/P"/> + <param name="protocol" value="none"/> + <param name="tryptic" value="fully"/> + <param name="min_precursor_charge" value="1"/> + <param name="max_precursor_charge" value="3"/> + <param name="min_peptide_length" value="6"/> + <param name="max_peptide_length" value="40"/> + <param name="matches_per_spec" value="1"/> + <param name="add_features" value="false"/> + <param name="max_mods" value="2"/> + <param name="max_missed_cleavages" value="-1"/> + <param name="tasks" value="0"/> + <param name="fixed_modifications"/> + <param name="variable_modifications" value="Oxidation (M)"/> + <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,out_FLAG,mzid_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[MS/MS database search using MS-GF+. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_MSGFPlusAdapter.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MSGFPlusAdapter.html]]></help> <expand macro="references"/> </tool>