openms_msgfplusadapter: MSGFPlusAdapter.xml comparison

comparison MSGFPlusAdapter.xml @ 15:f5ec766d80cf draft

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	810779f0cf49

comparison

equal deleted inserted replaced

-:c18d8efa4474
+:f5ec766d80cf
 <?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"/>
 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 <configfiles>
 <inputs name="args_json" data_style="paths"/>
 <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 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 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 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="-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| &lt; 20 ppm' for n = -1, 0, 1, 2">
+<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| &lt; 20 ppm' for n = -1, 0, 1, 2">
-<expand macro="list_string_san"/>
+<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>
 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
 <option value="Lys-C/P">Lys-C/P</option>
 <option value="Lys-N">Lys-N</option>
 <option value="Trypsin/P" selected="true">Trypsin/P</option>
 <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 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 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 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 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 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 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 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 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 &lt;= tasks &lt;= 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 &lt; 0: multiply number of threads by abs(tasks) to determine number of tasks (i.e., -2 means &quot;2 * numThreads&quot; 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="-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 &lt;= tasks &lt;= 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 &lt; 0: multiply number of threads by abs(tasks) to determine number of tasks (i.e., -2 means &quot;2 * numThreads&quot; 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="-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>
 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
-<option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
 <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>
 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
-<option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
 <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 &lt;file&gt; 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 &lt;file&gt; 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 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 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 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="">
+<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"/>
+<expand macro="list_string_san" name="test"/>
 </param>
 </expand>
 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
 <option value="out_FLAG">out (Output file)</option>
 <option value="mzid_out_FLAG">mzid_out (Alternative output file (MS-GF+ parameter '-o'))</option>
 </data>
 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
 </data>
 </outputs>
-<tests>
+<tests><!-- TOPP_MSGFPlusAdapter_1 -->
-<expand macro="autotest_MSGFPlusAdapter"/>
+<test expect_num_outputs="3">
-<expand macro="manutest_MSGFPlusAdapter"/>
+<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>

Mercurial > repos > galaxyp > openms_msgfplusadapter

comparison MSGFPlusAdapter.xml @ 15:f5ec766d80cf draft