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comparison XTandemAdapter.xml @ 14:5c2a97a234d6 draft

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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
comparison
equal deleted inserted replaced
13:7f6a1f27553e 14:5c2a97a234d6
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Identification]--> 3 <!--Proposed Tool Section: [Identification]-->
4 <tool id="XTandemAdapter" name="XTandemAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="XTandemAdapter" name="XTandemAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Annotates MS/MS spectra using X! Tandem.</description> 5 <description>Annotates MS/MS spectra using X! Tandem.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">XTandemAdapter</token> 7 <token name="@EXECUTABLE@">XTandemAdapter</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
70 <configfiles> 68 <configfiles>
71 <inputs name="args_json" data_style="paths"/> 69 <inputs name="args_json" data_style="paths"/>
72 <configfile name="hardcoded_json"><![CDATA[{"xtandem_executable": "xtandem", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 70 <configfile name="hardcoded_json"><![CDATA[{"xtandem_executable": "xtandem", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
73 </configfiles> 71 </configfiles>
74 <inputs> 72 <inputs>
75 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file containing MS2 spectra" help=" select mzml data sets(s)"/> 73 <param argument="-in" type="data" format="mzml" optional="false" label="Input file containing MS2 spectra" help=" select mzml data sets(s)"/>
76 <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)"/> 74 <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)"/>
77 <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)"/> 75 <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)"/>
78 <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=""/> 76 <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=""/>
79 <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor mass tolerance" help=""/> 77 <param argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor mass tolerance" help=""/>
80 <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" value="0.3" label="Fragment mass erro" help=""/> 78 <param argument="-fragment_mass_tolerance" type="float" optional="true" value="0.3" label="Fragment mass erro" help=""/>
81 <param name="precursor_error_units" argument="-precursor_error_units" display="radio" type="select" optional="false" label="Parent monoisotopic mass error units" help=""> 79 <param argument="-precursor_error_units" type="select" optional="true" label="Parent monoisotopic mass error units" help="">
82 <option value="ppm" selected="true">ppm</option> 80 <option value="ppm" selected="true">ppm</option>
83 <option value="Da">Da</option> 81 <option value="Da">Da</option>
84 <expand macro="list_string_san"/> 82 <expand macro="list_string_san" name="precursor_error_units"/>
85 </param> 83 </param>
86 <param name="fragment_error_units" argument="-fragment_error_units" display="radio" type="select" optional="false" label="Fragment monoisotopic mass error units" help=""> 84 <param argument="-fragment_error_units" type="select" optional="true" label="Fragment monoisotopic mass error units" help="">
87 <option value="ppm">ppm</option> 85 <option value="ppm">ppm</option>
88 <option value="Da" selected="true">Da</option> 86 <option value="Da" selected="true">Da</option>
89 <expand macro="list_string_san"/> 87 <expand macro="list_string_san" name="fragment_error_units"/>
90 </param> 88 </param>
91 <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)"/> 89 <param argument="-max_precursor_charge" type="integer" optional="true" min="0" value="4" label="Maximum precursor charge ('0' to use X" help="Tandem default)"/>
92 <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"/> 90 <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"/>
93 <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)'"> 91 <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)'">
94 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 92 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
95 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 93 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
96 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 94 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
97 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 95 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
98 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 96 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
1457 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option> 1455 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
1458 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 1456 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
1459 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 1457 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
1460 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 1458 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
1461 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 1459 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
1462 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1463 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 1460 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1464 <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> 1461 <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>
1465 <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> 1462 <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>
1466 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 1463 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
1467 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 1464 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
3017 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option> 3014 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
3018 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option> 3015 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
3019 <option value="ZGB (K)">ZGB (K)</option> 3016 <option value="ZGB (K)">ZGB (K)</option>
3020 <option value="ZGB (N-term)">ZGB (N-term)</option> 3017 <option value="ZGB (N-term)">ZGB (N-term)</option>
3021 <option value="ZQG (K)">ZQG (K)</option> 3018 <option value="ZQG (K)">ZQG (K)</option>
3022 <expand macro="list_string_san"/> 3019 <expand macro="list_string_san" name="fixed_modifications"/>
3023 </param> 3020 </param>
3024 <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)'"> 3021 <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)'">
3025 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 3022 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
3026 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 3023 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
3027 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 3024 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
3028 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 3025 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
3029 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 3026 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
4388 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option> 4385 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
4389 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 4386 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
4390 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 4387 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
4391 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 4388 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
4392 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 4389 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
4393 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
4394 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 4390 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
4395 <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> 4391 <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>
4396 <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> 4392 <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>
4397 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 4393 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
4398 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 4394 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
5948 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option> 5944 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
5949 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option> 5945 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
5950 <option value="ZGB (K)">ZGB (K)</option> 5946 <option value="ZGB (K)">ZGB (K)</option>
5951 <option value="ZGB (N-term)">ZGB (N-term)</option> 5947 <option value="ZGB (N-term)">ZGB (N-term)</option>
5952 <option value="ZQG (K)">ZQG (K)</option> 5948 <option value="ZQG (K)">ZQG (K)</option>
5953 <expand macro="list_string_san"/> 5949 <expand macro="list_string_san" name="variable_modifications"/>
5954 </param> 5950 </param>
5955 <param name="minimum_fragment_mz" argument="-minimum_fragment_mz" type="float" optional="true" value="150.0" label="Minimum fragment m/z" help=""/> 5951 <param argument="-minimum_fragment_mz" type="float" optional="true" value="150.0" label="Minimum fragment m/z" help=""/>
5956 <param name="enzyme" argument="-enzyme" type="select" optional="false" label="The enzyme used for peptide digestion" help=""> 5952 <param argument="-enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help="">
5953 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
5954 <option value="CNBr">CNBr</option>
5955 <option value="Formic_acid">Formic_acid</option>
5956 <option value="Trypsin" selected="true">Trypsin</option>
5957 <option value="unspecific cleavage">unspecific cleavage</option>
5958 <option value="Lys-C">Lys-C</option>
5957 <option value="Lys-N">Lys-N</option> 5959 <option value="Lys-N">Lys-N</option>
5958 <option value="Lys-C/P">Lys-C/P</option> 5960 <option value="Lys-C/P">Lys-C/P</option>
5959 <option value="Trypsin" selected="true">Trypsin</option>
5960 <option value="Asp-N">Asp-N</option>
5961 <option value="Asp-N/B">Asp-N/B</option>
5962 <option value="Asp-N_ambic">Asp-N_ambic</option>
5963 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
5964 <option value="2-iodobenzoate">2-iodobenzoate</option>
5965 <option value="PepsinA">PepsinA</option> 5961 <option value="PepsinA">PepsinA</option>
5966 <option value="TrypChymo">TrypChymo</option> 5962 <option value="TrypChymo">TrypChymo</option>
5967 <option value="Trypsin/P">Trypsin/P</option> 5963 <option value="Trypsin/P">Trypsin/P</option>
5968 <option value="V8-DE">V8-DE</option> 5964 <option value="V8-DE">V8-DE</option>
5965 <option value="Asp-N/B">Asp-N/B</option>
5966 <option value="Asp-N_ambic">Asp-N_ambic</option>
5967 <option value="Chymotrypsin">Chymotrypsin</option>
5968 <option value="Arg-C/P">Arg-C/P</option>
5969 <option value="Arg-C">Arg-C</option>
5969 <option value="V8-E">V8-E</option> 5970 <option value="V8-E">V8-E</option>
5970 <option value="Formic_acid">Formic_acid</option>
5971 <option value="Lys-C">Lys-C</option>
5972 <option value="Chymotrypsin">Chymotrypsin</option>
5973 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
5974 <option value="CNBr">CNBr</option>
5975 <option value="leukocyte elastase">leukocyte elastase</option> 5971 <option value="leukocyte elastase">leukocyte elastase</option>
5976 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> 5972 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
5977 <option value="Arg-C">Arg-C</option> 5973 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
5978 <option value="unspecific cleavage">unspecific cleavage</option> 5974 <option value="2-iodobenzoate">2-iodobenzoate</option>
5979 <option value="Arg-C/P">Arg-C/P</option> 5975 <option value="Asp-N">Asp-N</option>
5980 <expand macro="list_string_san"/> 5976 <expand macro="list_string_san" name="enzyme"/>
5981 </param> 5977 </param>
5982 <param name="missed_cleavages" argument="-missed_cleavages" type="integer" optional="true" value="1" label="Number of possible cleavage sites missed by the enzyme" help=""/> 5978 <param argument="-missed_cleavages" type="integer" optional="true" value="1" label="Number of possible cleavage sites missed by the enzyme" help=""/>
5983 <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=""/> 5979 <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=""/>
5984 <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)"> 5980 <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)">
5985 <option value="all" selected="true">all</option> 5981 <option value="all" selected="true">all</option>
5986 <option value="valid">valid</option> 5982 <option value="valid">valid</option>
5987 <option value="stochastic">stochastic</option> 5983 <option value="stochastic">stochastic</option>
5988 <expand macro="list_string_san"/> 5984 <expand macro="list_string_san" name="output_results"/>
5989 </param> 5985 </param>
5990 <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=""/> 5986 <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=""/>
5987 <param argument="-reindex" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Recalculate peptide to protein association using OpenMS" help="Annotates target-decoy information"/>
5988 <section name="PeptideIndexing" title="" help="" expanded="false">
5989 <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)">
5990 <expand macro="list_string_san" name="decoy_string"/>
5991 </param>
5992 <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)">
5993 <option value="prefix" selected="true">prefix</option>
5994 <option value="suffix">suffix</option>
5995 <expand macro="list_string_san" name="decoy_string_position"/>
5996 </param>
5997 <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="">
5998 <option value="error">error</option>
5999 <option value="warn" selected="true">warn</option>
6000 <option value="silent">silent</option>
6001 <expand macro="list_string_san" name="missing_decoy_action"/>
6002 </param>
6003 <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=""/>
6004 <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=""/>
6005 <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=""/>
6006 <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="">
6007 <option value="error" selected="true">error</option>
6008 <option value="warn">warn</option>
6009 <option value="remove">remove</option>
6010 <expand macro="list_string_san" name="unmatched_action"/>
6011 </param>
6012 <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'"/>
6013 <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"/>
6014 <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"/>
6015 <section name="enzyme" title="" help="" expanded="false">
6016 <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">
6017 <option value="auto" selected="true">auto</option>
6018 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
6019 <option value="CNBr">CNBr</option>
6020 <option value="Formic_acid">Formic_acid</option>
6021 <option value="Trypsin">Trypsin</option>
6022 <option value="Lys-C/P">Lys-C/P</option>
6023 <option value="PepsinA">PepsinA</option>
6024 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
6025 <option value="2-iodobenzoate">2-iodobenzoate</option>
6026 <option value="iodosobenzoate">iodosobenzoate</option>
6027 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
6028 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
6029 <option value="Lys-C">Lys-C</option>
6030 <option value="Lys-N">Lys-N</option>
6031 <option value="Arg-C">Arg-C</option>
6032 <option value="leukocyte elastase">leukocyte elastase</option>
6033 <option value="proline endopeptidase">proline endopeptidase</option>
6034 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
6035 <option value="V8-DE">V8-DE</option>
6036 <option value="V8-E">V8-E</option>
6037 <option value="Arg-C/P">Arg-C/P</option>
6038 <option value="Asp-N">Asp-N</option>
6039 <option value="TrypChymo">TrypChymo</option>
6040 <option value="Trypsin/P">Trypsin/P</option>
6041 <option value="Glu-C+P">Glu-C+P</option>
6042 <option value="PepsinA + P">PepsinA + P</option>
6043 <option value="cyanogen-bromide">cyanogen-bromide</option>
6044 <option value="Clostripain/P">Clostripain/P</option>
6045 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
6046 <option value="no cleavage">no cleavage</option>
6047 <option value="unspecific cleavage">unspecific cleavage</option>
6048 <option value="Asp-N/B">Asp-N/B</option>
6049 <option value="Asp-N_ambic">Asp-N_ambic</option>
6050 <option value="Chymotrypsin">Chymotrypsin</option>
6051 <expand macro="list_string_san" name="name"/>
6052 </param>
6053 <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)">
6054 <option value="auto" selected="true">auto</option>
6055 <option value="full">full</option>
6056 <option value="semi">semi</option>
6057 <option value="none">none</option>
6058 <expand macro="list_string_san" name="specificity"/>
6059 </param>
6060 </section>
6061 </section>
5991 <expand macro="adv_opts_macro"> 6062 <expand macro="adv_opts_macro">
5992 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 6063 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
5993 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 6064 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
5994 <expand macro="list_string_san"/> 6065 <expand macro="list_string_san" name="test"/>
5995 </param> 6066 </param>
5996 </expand> 6067 </expand>
5997 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 6068 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
5998 <option value="out_FLAG">out (Output file containing search results)</option> 6069 <option value="out_FLAG">out (Output file containing search results)</option>
5999 <option value="xml_out_FLAG">xml_out (Raw output file directly from X)</option> 6070 <option value="xml_out_FLAG">xml_out (Raw output file directly from X)</option>
6012 </data> 6083 </data>
6013 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 6084 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
6014 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 6085 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
6015 </data> 6086 </data>
6016 </outputs> 6087 </outputs>
6017 <tests> 6088 <tests><!-- TOPP_XTandemAdapter_1 -->
6018 <expand macro="autotest_XTandemAdapter"/> 6089 <test expect_num_outputs="2">
6019 <expand macro="manutest_XTandemAdapter"/> 6090 <section name="adv_opts">
6091 <param name="force" value="false"/>
6092 <param name="test" value="true"/>
6093 </section>
6094 <param name="in" value="spectra.mzML"/>
6095 <output name="out" file="XTandemAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6096 <param name="database" value="proteins.fasta"/>
6097 <param name="default_config_file" value="CHEMISTRY/XTandem_default_config.xml"/>
6098 <param name="ignore_adapter_param" value="false"/>
6099 <param name="precursor_mass_tolerance" value="5.0"/>
6100 <param name="fragment_mass_tolerance" value="0.3"/>
6101 <param name="precursor_error_units" value="ppm"/>
6102 <param name="fragment_error_units" value="Da"/>
6103 <param name="max_precursor_charge" value="0"/>
6104 <param name="no_isotope_error" value="false"/>
6105 <param name="fixed_modifications"/>
6106 <param name="variable_modifications" value="Oxidation (M)"/>
6107 <param name="minimum_fragment_mz" value="150.0"/>
6108 <param name="enzyme" value="Trypsin"/>
6109 <param name="missed_cleavages" value="1"/>
6110 <param name="semi_cleavage" value="false"/>
6111 <param name="output_results" value="all"/>
6112 <param name="max_valid_expect" value="0.1"/>
6113 <param name="reindex" value="true"/>
6114 <section name="PeptideIndexing">
6115 <param name="decoy_string" value=""/>
6116 <param name="decoy_string_position" value="prefix"/>
6117 <param name="missing_decoy_action" value="warn"/>
6118 <param name="write_protein_sequence" value="false"/>
6119 <param name="write_protein_description" value="false"/>
6120 <param name="keep_unreferenced_proteins" value="false"/>
6121 <param name="unmatched_action" value="error"/>
6122 <param name="aaa_max" value="3"/>
6123 <param name="mismatches_max" value="0"/>
6124 <param name="IL_equivalent" value="false"/>
6125 <section name="enzyme">
6126 <param name="name" value="auto"/>
6127 <param name="specificity" value="auto"/>
6128 </section>
6129 </section>
6130 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
6131 <output name="ctd_out" ftype="xml">
6132 <assert_contents>
6133 <is_valid_xml/>
6134 </assert_contents>
6135 </output>
6136 </test>
6137 <!-- TOPP_XTandemAdapter_2 -->
6138 <test expect_num_outputs="2">
6139 <section name="adv_opts">
6140 <param name="force" value="false"/>
6141 <param name="test" value="true"/>
6142 </section>
6143 <param name="in" value="spectra.mzML"/>
6144 <output name="out" file="XTandemAdapter_2_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6145 <param name="database" value="proteins.fasta"/>
6146 <param name="default_config_file" value="CHEMISTRY/XTandem_default_config.xml"/>
6147 <param name="ignore_adapter_param" value="false"/>
6148 <param name="precursor_mass_tolerance" value="5.0"/>
6149 <param name="fragment_mass_tolerance" value="0.3"/>
6150 <param name="precursor_error_units" value="ppm"/>
6151 <param name="fragment_error_units" value="Da"/>
6152 <param name="max_precursor_charge" value="0"/>
6153 <param name="no_isotope_error" value="false"/>
6154 <param name="fixed_modifications"/>
6155 <param name="variable_modifications" value="Oxidation (M)"/>
6156 <param name="minimum_fragment_mz" value="150.0"/>
6157 <param name="enzyme" value="Trypsin"/>
6158 <param name="missed_cleavages" value="1"/>
6159 <param name="semi_cleavage" value="false"/>
6160 <param name="output_results" value="valid"/>
6161 <param name="max_valid_expect" value="1e-14"/>
6162 <param name="reindex" value="true"/>
6163 <section name="PeptideIndexing">
6164 <param name="decoy_string" value=""/>
6165 <param name="decoy_string_position" value="prefix"/>
6166 <param name="missing_decoy_action" value="warn"/>
6167 <param name="write_protein_sequence" value="false"/>
6168 <param name="write_protein_description" value="false"/>
6169 <param name="keep_unreferenced_proteins" value="false"/>
6170 <param name="unmatched_action" value="error"/>
6171 <param name="aaa_max" value="3"/>
6172 <param name="mismatches_max" value="0"/>
6173 <param name="IL_equivalent" value="false"/>
6174 <section name="enzyme">
6175 <param name="name" value="auto"/>
6176 <param name="specificity" value="auto"/>
6177 </section>
6178 </section>
6179 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
6180 <output name="ctd_out" ftype="xml">
6181 <assert_contents>
6182 <is_valid_xml/>
6183 </assert_contents>
6184 </output>
6185 </test>
6186 <!-- TOPP_XTandemAdapter_3 -->
6187 <test expect_num_outputs="2">
6188 <section name="adv_opts">
6189 <param name="force" value="false"/>
6190 <param name="test" value="true"/>
6191 </section>
6192 <param name="in" value="spectra.mzML"/>
6193 <output name="out" file="XTandemAdapter_3_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6194 <param name="database" value="proteinslong.fasta"/>
6195 <param name="default_config_file" value="CHEMISTRY/XTandem_default_config.xml"/>
6196 <param name="ignore_adapter_param" value="false"/>
6197 <param name="precursor_mass_tolerance" value="5.0"/>
6198 <param name="fragment_mass_tolerance" value="0.3"/>
6199 <param name="precursor_error_units" value="ppm"/>
6200 <param name="fragment_error_units" value="Da"/>
6201 <param name="max_precursor_charge" value="0"/>
6202 <param name="no_isotope_error" value="false"/>
6203 <param name="fixed_modifications"/>
6204 <param name="variable_modifications" value="Oxidation (M)"/>
6205 <param name="minimum_fragment_mz" value="150.0"/>
6206 <param name="enzyme" value="Trypsin"/>
6207 <param name="missed_cleavages" value="1"/>
6208 <param name="semi_cleavage" value="false"/>
6209 <param name="output_results" value="all"/>
6210 <param name="max_valid_expect" value="0.1"/>
6211 <param name="reindex" value="true"/>
6212 <section name="PeptideIndexing">
6213 <param name="decoy_string" value=""/>
6214 <param name="decoy_string_position" value="prefix"/>
6215 <param name="missing_decoy_action" value="warn"/>
6216 <param name="write_protein_sequence" value="false"/>
6217 <param name="write_protein_description" value="false"/>
6218 <param name="keep_unreferenced_proteins" value="false"/>
6219 <param name="unmatched_action" value="error"/>
6220 <param name="aaa_max" value="3"/>
6221 <param name="mismatches_max" value="0"/>
6222 <param name="IL_equivalent" value="false"/>
6223 <section name="enzyme">
6224 <param name="name" value="auto"/>
6225 <param name="specificity" value="auto"/>
6226 </section>
6227 </section>
6228 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
6229 <output name="ctd_out" ftype="xml">
6230 <assert_contents>
6231 <is_valid_xml/>
6232 </assert_contents>
6233 </output>
6234 </test>
6020 </tests> 6235 </tests>
6021 <help><![CDATA[Annotates MS/MS spectra using X! Tandem. 6236 <help><![CDATA[Annotates MS/MS spectra using X! Tandem.
6022 6237
6023 6238
6024 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_XTandemAdapter.html]]></help> 6239 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_XTandemAdapter.html]]></help>
6025 <expand macro="references"/> 6240 <expand macro="references"/>
6026 </tool> 6241 </tool>