Mercurial > repos > galaxyp > openms_xtandemadapter
diff XTandemAdapter.xml @ 14:5c2a97a234d6 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:15:43 +0000 |
| parents | 1add9bacdccd |
| children | 567de7cb1766 |
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--- a/XTandemAdapter.xml Fri Nov 06 19:58:54 2020 +0000 +++ b/XTandemAdapter.xml Thu Dec 01 19:15:43 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="XTandemAdapter" name="XTandemAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="XTandemAdapter" name="XTandemAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Annotates MS/MS spectra using X! Tandem.</description> <macros> <token name="@EXECUTABLE@">XTandemAdapter</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -72,25 +70,25 @@ <configfile name="hardcoded_json"><![CDATA[{"xtandem_executable": "xtandem", "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 containing MS2 spectra" help=" select mzml data sets(s)"/> - <param name="database" argument="-database" type="data" format="fasta" optional="false" label="FASTA file or pro file" help="Non-existing relative file-names are looked up via'OpenMS.ini:id_db_dir' select fasta data sets(s)"/> - <param name="default_config_file" argument="-default_config_file" type="data" format="xml" optional="true" label="Default X" help="Tandem configuration file. All parameters of this adapter take precedence over the file - use it for parameters not available here. A template file can be found at 'OpenMS/share/CHEMISTRY/XTandem_default_input.xml' select xml data sets(s)"/> - <param name="ignore_adapter_param" argument="-ignore_adapter_param" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this to use the configuration given in 'default_config_file' exclusively, ignoring other parameters (apart from 'in', 'out', 'database', 'xtandem_executable') set via this adapte" help=""/> - <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor mass tolerance" help=""/> - <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" value="0.3" label="Fragment mass erro" help=""/> - <param name="precursor_error_units" argument="-precursor_error_units" display="radio" type="select" optional="false" label="Parent monoisotopic mass error units" help=""> + <param argument="-in" type="data" format="mzml" optional="false" label="Input file containing MS2 spectra" help=" select mzml data sets(s)"/> + <param argument="-database" type="data" format="fasta" optional="false" label="FASTA file or pro file" help="Non-existing relative file-names are looked up via'OpenMS.ini:id_db_dir' select fasta data sets(s)"/> + <param argument="-default_config_file" type="data" format="xml" optional="true" label="Default X" help="Tandem configuration file. All parameters of this adapter take precedence over the file - use it for parameters not available here. A template file can be found at 'OpenMS/share/CHEMISTRY/XTandem_default_config.xml' select xml data sets(s)"/> + <param argument="-ignore_adapter_param" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this to use the configuration given in 'default_config_file' exclusively, ignoring other parameters (apart from 'in', 'out', 'database', 'xtandem_executable') set via this adapte" help=""/> + <param argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor mass tolerance" help=""/> + <param argument="-fragment_mass_tolerance" type="float" optional="true" value="0.3" label="Fragment mass erro" help=""/> + <param argument="-precursor_error_units" type="select" optional="true" label="Parent monoisotopic mass error units" help=""> <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="fragment_error_units" argument="-fragment_error_units" display="radio" type="select" optional="false" label="Fragment monoisotopic mass error units" help=""> + <param argument="-fragment_error_units" type="select" optional="true" label="Fragment monoisotopic mass error units" help=""> <option value="ppm">ppm</option> <option value="Da" selected="true">Da</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="fragment_error_units"/> </param> - <param name="max_precursor_charge" argument="-max_precursor_charge" type="integer" optional="true" min="0" value="4" label="Maximum precursor charge ('0' to use X" help="Tandem default)"/> - <param name="no_isotope_error" argument="-no_isotope_error" type="boolean" truevalue="true" falsevalue="false" checked="false" label="By default, misassignment to the first and second isotopic 13C peak are also considered" help="Set this flag to disable"/> - <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_precursor_charge" type="integer" optional="true" min="0" value="4" label="Maximum precursor charge ('0' to use X" help="Tandem default)"/> + <param argument="-no_isotope_error" type="boolean" truevalue="true" falsevalue="false" checked="false" label="By default, misassignment to the first and second isotopic 13C peak are also considered" help="Set this flag to disable"/> + <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> @@ -1460,7 +1458,6 @@ <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> @@ -3019,9 +3016,9 @@ <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> @@ -4391,7 +4388,6 @@ <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> @@ -5950,48 +5946,123 @@ <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="minimum_fragment_mz" argument="-minimum_fragment_mz" type="float" optional="true" value="150.0" label="Minimum fragment m/z" help=""/> - <param name="enzyme" argument="-enzyme" type="select" optional="false" label="The enzyme used for peptide digestion" help=""> + <param argument="-minimum_fragment_mz" type="float" optional="true" value="150.0" label="Minimum fragment m/z" help=""/> + <param argument="-enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help=""> + <option value="Chymotrypsin/P">Chymotrypsin/P</option> + <option value="CNBr">CNBr</option> + <option value="Formic_acid">Formic_acid</option> + <option value="Trypsin" selected="true">Trypsin</option> + <option value="unspecific cleavage">unspecific cleavage</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="Trypsin" selected="true">Trypsin</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="Alpha-lytic protease">Alpha-lytic protease</option> - <option value="2-iodobenzoate">2-iodobenzoate</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="Asp-N/B">Asp-N/B</option> + <option value="Asp-N_ambic">Asp-N_ambic</option> + <option value="Chymotrypsin">Chymotrypsin</option> + <option value="Arg-C/P">Arg-C/P</option> + <option value="Arg-C">Arg-C</option> <option value="V8-E">V8-E</option> - <option value="Formic_acid">Formic_acid</option> - <option value="Lys-C">Lys-C</option> - <option value="Chymotrypsin">Chymotrypsin</option> - <option value="Chymotrypsin/P">Chymotrypsin/P</option> - <option value="CNBr">CNBr</option> <option value="leukocyte elastase">leukocyte elastase</option> <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> - <option value="Arg-C">Arg-C</option> - <option value="unspecific cleavage">unspecific cleavage</option> - <option value="Arg-C/P">Arg-C/P</option> - <expand macro="list_string_san"/> + <option value="Alpha-lytic protease">Alpha-lytic protease</option> + <option value="2-iodobenzoate">2-iodobenzoate</option> + <option value="Asp-N">Asp-N</option> + <expand macro="list_string_san" name="enzyme"/> </param> - <param name="missed_cleavages" argument="-missed_cleavages" type="integer" optional="true" value="1" label="Number of possible cleavage sites missed by the enzyme" help=""/> - <param name="semi_cleavage" argument="-semi_cleavage" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require only peptide end to have a valid cleavage site, not both" help=""/> - <param name="output_results" argument="-output_results" display="radio" type="select" optional="false" label="Which hits should be reported" help="All, valid ones (passing the E-Value threshold), or stochastic (failing the threshold)"> + <param argument="-missed_cleavages" type="integer" optional="true" value="1" label="Number of possible cleavage sites missed by the enzyme" help=""/> + <param argument="-semi_cleavage" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require only peptide end to have a valid cleavage site, not both" help=""/> + <param argument="-output_results" type="select" optional="true" label="Which hits should be reported" help="All, valid ones (passing the E-Value threshold), or stochastic (failing the threshold)"> <option value="all" selected="true">all</option> <option value="valid">valid</option> <option value="stochastic">stochastic</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="output_results"/> </param> - <param name="max_valid_expect" argument="-max_valid_expect" type="float" optional="true" value="0.1" label="Maximal E-Value of a hit to be reported (only evaluated if 'output_result' is 'valid' or 'stochastic')" help=""/> + <param argument="-max_valid_expect" type="float" optional="true" value="0.1" label="Maximal E-Value of a hit to be reported (only evaluated if 'output_result' is 'valid' or 'stochastic')" help=""/> + <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="Chymotrypsin/P">Chymotrypsin/P</option> + <option value="CNBr">CNBr</option> + <option value="Formic_acid">Formic_acid</option> + <option value="Trypsin">Trypsin</option> + <option value="Lys-C/P">Lys-C/P</option> + <option value="PepsinA">PepsinA</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="Lys-C">Lys-C</option> + <option value="Lys-N">Lys-N</option> + <option value="Arg-C">Arg-C</option> + <option value="leukocyte elastase">leukocyte elastase</option> + <option value="proline endopeptidase">proline endopeptidase</option> + <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> + <option value="V8-DE">V8-DE</option> + <option value="V8-E">V8-E</option> + <option value="Arg-C/P">Arg-C/P</option> + <option value="Asp-N">Asp-N</option> + <option value="TrypChymo">TrypChymo</option> + <option value="Trypsin/P">Trypsin/P</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="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> + <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="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="-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"> @@ -6014,13 +6085,157 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_XTandemAdapter"/> - <expand macro="manutest_XTandemAdapter"/> + <tests><!-- TOPP_XTandemAdapter_1 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="spectra.mzML"/> + <output name="out" file="XTandemAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <param name="database" value="proteins.fasta"/> + <param name="default_config_file" value="CHEMISTRY/XTandem_default_config.xml"/> + <param name="ignore_adapter_param" value="false"/> + <param name="precursor_mass_tolerance" value="5.0"/> + <param name="fragment_mass_tolerance" value="0.3"/> + <param name="precursor_error_units" value="ppm"/> + <param name="fragment_error_units" value="Da"/> + <param name="max_precursor_charge" value="0"/> + <param name="no_isotope_error" value="false"/> + <param name="fixed_modifications"/> + <param name="variable_modifications" value="Oxidation (M)"/> + <param name="minimum_fragment_mz" value="150.0"/> + <param name="enzyme" value="Trypsin"/> + <param name="missed_cleavages" value="1"/> + <param name="semi_cleavage" value="false"/> + <param name="output_results" value="all"/> + <param name="max_valid_expect" value="0.1"/> + <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"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_XTandemAdapter_2 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="spectra.mzML"/> + <output name="out" file="XTandemAdapter_2_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <param name="database" value="proteins.fasta"/> + <param name="default_config_file" value="CHEMISTRY/XTandem_default_config.xml"/> + <param name="ignore_adapter_param" value="false"/> + <param name="precursor_mass_tolerance" value="5.0"/> + <param name="fragment_mass_tolerance" value="0.3"/> + <param name="precursor_error_units" value="ppm"/> + <param name="fragment_error_units" value="Da"/> + <param name="max_precursor_charge" value="0"/> + <param name="no_isotope_error" value="false"/> + <param name="fixed_modifications"/> + <param name="variable_modifications" value="Oxidation (M)"/> + <param name="minimum_fragment_mz" value="150.0"/> + <param name="enzyme" value="Trypsin"/> + <param name="missed_cleavages" value="1"/> + <param name="semi_cleavage" value="false"/> + <param name="output_results" value="valid"/> + <param name="max_valid_expect" value="1e-14"/> + <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"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_XTandemAdapter_3 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="spectra.mzML"/> + <output name="out" file="XTandemAdapter_3_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <param name="database" value="proteinslong.fasta"/> + <param name="default_config_file" value="CHEMISTRY/XTandem_default_config.xml"/> + <param name="ignore_adapter_param" value="false"/> + <param name="precursor_mass_tolerance" value="5.0"/> + <param name="fragment_mass_tolerance" value="0.3"/> + <param name="precursor_error_units" value="ppm"/> + <param name="fragment_error_units" value="Da"/> + <param name="max_precursor_charge" value="0"/> + <param name="no_isotope_error" value="false"/> + <param name="fixed_modifications"/> + <param name="variable_modifications" value="Oxidation (M)"/> + <param name="minimum_fragment_mz" value="150.0"/> + <param name="enzyme" value="Trypsin"/> + <param name="missed_cleavages" value="1"/> + <param name="semi_cleavage" value="false"/> + <param name="output_results" value="all"/> + <param name="max_valid_expect" value="0.1"/> + <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"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Annotates MS/MS spectra using X! Tandem. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_XTandemAdapter.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_XTandemAdapter.html]]></help> <expand macro="references"/> </tool>