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comparison SimpleSearchEngine.xml @ 13:da78f97a6dda 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 19:17:17 +0000
parents 1b56031ac321
children a1724438d580
comparison
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12:4ef2f946290d 13:da78f97a6dda
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: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="SimpleSearchEngine" name="SimpleSearchEngine" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="SimpleSearchEngine" name="SimpleSearchEngine" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Annotates MS/MS spectra using SimpleSearchEngine.</description> 5 <description>Annotates MS/MS spectra using SimpleSearchEngine.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">SimpleSearchEngine</token> 7 <token name="@EXECUTABLE@">SimpleSearchEngine</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@
43 <configfiles> 41 <configfiles>
44 <inputs name="args_json" data_style="paths"/> 42 <inputs name="args_json" data_style="paths"/>
45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
46 </configfiles> 44 </configfiles>
47 <inputs> 45 <inputs>
48 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> 46 <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
49 <param name="database" argument="-database" type="data" format="fasta" optional="false" label="input file" help=" select fasta data sets(s)"/> 47 <param argument="-database" type="data" format="fasta" optional="false" label="input file" help=" select fasta data sets(s)"/>
50 <section name="Search" title="" help="" expanded="false"> 48 <section name="Search" title="" help="" expanded="false">
51 <param name="enzyme" argument="-Search:enzyme" type="select" optional="false" label="The enzyme used for peptide digestion" help=""> 49 <param name="enzyme" argument="-Search:enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help="">
52 <option value="Trypsin" selected="true">Trypsin</option> 50 <option value="Trypsin" selected="true">Trypsin</option>
53 <option value="Lys-C/P">Lys-C/P</option> 51 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
54 <option value="PepsinA">PepsinA</option>
55 <option value="TrypChymo">TrypChymo</option>
56 <option value="Trypsin/P">Trypsin/P</option>
57 <option value="no cleavage">no cleavage</option>
58 <option value="unspecific cleavage">unspecific cleavage</option>
59 <option value="Arg-C/P">Arg-C/P</option>
60 <option value="V8-DE">V8-DE</option>
61 <option value="V8-E">V8-E</option>
62 <option value="leukocyte elastase">leukocyte elastase</option>
63 <option value="proline endopeptidase">proline endopeptidase</option>
64 <option value="Arg-C">Arg-C</option>
65 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
66 <option value="CNBr">CNBr</option>
67 <option value="Formic_acid">Formic_acid</option>
68 <option value="Lys-C">Lys-C</option>
69 <option value="Lys-N">Lys-N</option>
70 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> 52 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
71 <option value="Glu-C+P">Glu-C+P</option> 53 <option value="Glu-C+P">Glu-C+P</option>
72 <option value="PepsinA + P">PepsinA + P</option> 54 <option value="PepsinA + P">PepsinA + P</option>
73 <option value="cyanogen-bromide">cyanogen-bromide</option> 55 <option value="cyanogen-bromide">cyanogen-bromide</option>
74 <option value="Clostripain/P">Clostripain/P</option> 56 <option value="Clostripain/P">Clostripain/P</option>
75 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> 57 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
58 <option value="CNBr">CNBr</option>
59 <option value="Formic_acid">Formic_acid</option>
60 <option value="Lys-C">Lys-C</option>
61 <option value="Arg-C/P">Arg-C/P</option>
62 <option value="Asp-N">Asp-N</option>
63 <option value="Asp-N/B">Asp-N/B</option>
64 <option value="PepsinA">PepsinA</option>
65 <option value="TrypChymo">TrypChymo</option>
66 <option value="Trypsin/P">Trypsin/P</option>
67 <option value="V8-DE">V8-DE</option>
68 <option value="V8-E">V8-E</option>
69 <option value="leukocyte elastase">leukocyte elastase</option>
70 <option value="proline endopeptidase">proline endopeptidase</option>
71 <option value="no cleavage">no cleavage</option>
72 <option value="unspecific cleavage">unspecific cleavage</option>
76 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> 73 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
77 <option value="Alpha-lytic protease">Alpha-lytic protease</option> 74 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
78 <option value="2-iodobenzoate">2-iodobenzoate</option> 75 <option value="2-iodobenzoate">2-iodobenzoate</option>
79 <option value="iodosobenzoate">iodosobenzoate</option> 76 <option value="iodosobenzoate">iodosobenzoate</option>
80 <option value="staphylococcal protease/D">staphylococcal protease/D</option> 77 <option value="Arg-C">Arg-C</option>
81 <option value="Asp-N">Asp-N</option> 78 <option value="Lys-N">Lys-N</option>
82 <option value="Asp-N/B">Asp-N/B</option> 79 <option value="Lys-C/P">Lys-C/P</option>
83 <option value="Asp-N_ambic">Asp-N_ambic</option> 80 <option value="Asp-N_ambic">Asp-N_ambic</option>
84 <option value="Chymotrypsin">Chymotrypsin</option> 81 <option value="Chymotrypsin">Chymotrypsin</option>
85 <expand macro="list_string_san"/> 82 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
83 <expand macro="list_string_san" name="enzyme"/>
86 </param> 84 </param>
87 <param name="decoys" argument="-Search:decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Should decoys be generated?" help=""/> 85 <param name="decoys" argument="-Search:decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Should decoys be generated?" help=""/>
88 <section name="precursor" title="Precursor (Parent Ion) Options" help="" expanded="false"> 86 <section name="precursor" title="Precursor (Parent Ion) Options" help="" expanded="false">
89 <param name="mass_tolerance" argument="-Search:precursor:mass_tolerance" type="float" optional="true" value="10.0" label="Width of precursor mass tolerance window" help=""/> 87 <param name="mass_tolerance" argument="-Search:precursor:mass_tolerance" type="float" optional="true" value="10.0" label="+/- tolerance for precursor mass" help=""/>
90 <param name="mass_tolerance_unit" argument="-Search:precursor:mass_tolerance_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help=""> 88 <param name="mass_tolerance_unit" argument="-Search:precursor:mass_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
91 <option value="ppm" selected="true">ppm</option> 89 <option value="ppm" selected="true">ppm</option>
92 <option value="Da">Da</option> 90 <option value="Da">Da</option>
93 <expand macro="list_string_san"/> 91 <expand macro="list_string_san" name="mass_tolerance_unit"/>
94 </param> 92 </param>
95 <param name="min_charge" argument="-Search:precursor:min_charge" type="integer" optional="true" value="2" label="Minimum precursor charge to be considered" help=""/> 93 <param name="min_charge" argument="-Search:precursor:min_charge" type="integer" optional="true" value="2" label="Minimum precursor charge to be considered" help=""/>
96 <param name="max_charge" argument="-Search:precursor:max_charge" type="integer" optional="true" value="5" label="Maximum precursor charge to be considered" help=""/> 94 <param name="max_charge" argument="-Search:precursor:max_charge" type="integer" optional="true" value="5" label="Maximum precursor charge to be considered" help=""/>
97 <param name="isotopes" argument="-Search:precursor:isotopes" type="text" optional="true" value="0 1" label="Corrects for mono-isotopic peak misassignments" help="(E.g.: 1 = prec. may be misassigned to first isotopic peak) (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 95 <param name="isotopes" argument="-Search:precursor:isotopes" type="text" optional="true" value="0 1" label="Corrects for mono-isotopic peak misassignments" help="(E.g.: 1 = prec. may be misassigned to first isotopic peak) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
98 <expand macro="list_integer_valsan"/> 96 <expand macro="list_integer_valsan" name="isotopes"/>
99 </param> 97 </param>
100 </section> 98 </section>
101 <section name="fragment" title="Fragments (Product Ion) Options" help="" expanded="false"> 99 <section name="fragment" title="Fragments (Product Ion) Options" help="" expanded="false">
102 <param name="mass_tolerance" argument="-Search:fragment:mass_tolerance" type="float" optional="true" value="10.0" label="Fragment mass tolerance" help=""/> 100 <param name="mass_tolerance" argument="-Search:fragment:mass_tolerance" type="float" optional="true" value="10.0" label="Fragment mass tolerance" help=""/>
103 <param name="mass_tolerance_unit" argument="-Search:fragment:mass_tolerance_unit" display="radio" type="select" optional="false" label="Unit of fragment m" help=""> 101 <param name="mass_tolerance_unit" argument="-Search:fragment:mass_tolerance_unit" type="select" optional="true" label="Unit of fragment m" help="">
104 <option value="ppm" selected="true">ppm</option> 102 <option value="ppm" selected="true">ppm</option>
105 <option value="Da">Da</option> 103 <option value="Da">Da</option>
106 <expand macro="list_string_san"/> 104 <expand macro="list_string_san" name="mass_tolerance_unit"/>
107 </param> 105 </param>
108 </section> 106 </section>
109 <section name="modifications" title="Modifications Options" help="" expanded="false"> 107 <section name="modifications" title="Modifications Options" help="" expanded="false">
110 <param name="fixed" argument="-Search:modifications:fixed" multiple="true" type="select" optional="true" label="Fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'"> 108 <param name="fixed" argument="-Search:modifications:fixed" multiple="true" type="select" optional="true" label="Fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'">
111 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 109 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
1474 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option> 1472 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
1475 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 1473 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
1476 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 1474 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
1477 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 1475 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
1478 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 1476 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
1479 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1480 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 1477 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1481 <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> 1478 <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>
1482 <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> 1479 <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>
1483 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 1480 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
1484 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 1481 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
3034 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option> 3031 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
3035 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option> 3032 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
3036 <option value="ZGB (K)">ZGB (K)</option> 3033 <option value="ZGB (K)">ZGB (K)</option>
3037 <option value="ZGB (N-term)">ZGB (N-term)</option> 3034 <option value="ZGB (N-term)">ZGB (N-term)</option>
3038 <option value="ZQG (K)">ZQG (K)</option> 3035 <option value="ZQG (K)">ZQG (K)</option>
3039 <expand macro="list_string_san"/> 3036 <expand macro="list_string_san" name="fixed"/>
3040 </param> 3037 </param>
3041 <param name="variable" argument="-Search:modifications:variable" multiple="true" type="select" optional="true" label="Variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Oxidation (M)'"> 3038 <param name="variable" argument="-Search:modifications:variable" multiple="true" type="select" optional="true" label="Variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Oxidation (M)'">
3042 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 3039 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
3043 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 3040 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
3044 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 3041 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
4405 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option> 4402 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
4406 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 4403 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
4407 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 4404 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
4408 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 4405 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
4409 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 4406 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
4410 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
4411 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 4407 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
4412 <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> 4408 <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>
4413 <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> 4409 <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>
4414 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 4410 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
4415 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 4411 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
5965 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option> 5961 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
5966 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option> 5962 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
5967 <option value="ZGB (K)">ZGB (K)</option> 5963 <option value="ZGB (K)">ZGB (K)</option>
5968 <option value="ZGB (N-term)">ZGB (N-term)</option> 5964 <option value="ZGB (N-term)">ZGB (N-term)</option>
5969 <option value="ZQG (K)">ZQG (K)</option> 5965 <option value="ZQG (K)">ZQG (K)</option>
5970 <expand macro="list_string_san"/> 5966 <expand macro="list_string_san" name="variable"/>
5971 </param> 5967 </param>
5972 <param name="variable_max_per_peptide" argument="-Search:modifications:variable_max_per_peptide" type="integer" optional="true" value="2" label="Maximum number of residues carrying a variable modification per candidate peptide" help=""/> 5968 <param name="variable_max_per_peptide" argument="-Search:modifications:variable_max_per_peptide" type="integer" optional="true" value="2" label="Maximum number of residues carrying a variable modification per candidate peptide" help=""/>
5973 </section> 5969 </section>
5974 <section name="annotate" title="Annotation Options" help="" expanded="false"> 5970 <section name="annotate" title="Annotation Options" help="" expanded="false">
5975 <param name="PSM" argument="-Search:annotate:PSM" multiple="true" type="select" optional="true" label="Annotations added to each PSM" help=""> 5971 <param name="PSM" argument="-Search:annotate:PSM" multiple="true" type="select" optional="true" label="Annotations added to each PSM" help="">
5976 <option value="">default (nothing chosen)</option> 5972 <option value="ALL" selected="true">ALL</option>
5977 <option value="fragment_mz_error_median_ppm">fragment_mz_error_median_ppm</option> 5973 <option value="fragment_mz_error_median_ppm">fragment_mz_error_median_ppm</option>
5978 <option value="precursor_mz_error_ppm">precursor_mz_error_ppm</option> 5974 <option value="precursor_mz_error_ppm">precursor_mz_error_ppm</option>
5979 <expand macro="list_string_san"/> 5975 <option value="matched_prefix_ions_fraction">matched_prefix_ions_fraction</option>
5976 <option value="matched_suffix_ions_fraction">matched_suffix_ions_fraction</option>
5977 <expand macro="list_string_san" name="PSM"/>
5980 </param> 5978 </param>
5981 </section> 5979 </section>
5982 <section name="peptide" title="Peptide Options" help="" expanded="false"> 5980 <section name="peptide" title="Peptide Options" help="" expanded="false">
5983 <param name="min_size" argument="-Search:peptide:min_size" type="integer" optional="true" value="7" label="Minimum size a peptide must have after digestion to be considered in the search" help=""/> 5981 <param name="min_size" argument="-Search:peptide:min_size" type="integer" optional="true" value="7" label="Minimum size a peptide must have after digestion to be considered in the search" help=""/>
5984 <param name="max_size" argument="-Search:peptide:max_size" type="integer" optional="true" value="40" label="Maximum size a peptide must have after digestion to be considered in the search (0 = disabled)" help=""/> 5982 <param name="max_size" argument="-Search:peptide:max_size" type="integer" optional="true" value="40" label="Maximum size a peptide must have after digestion to be considered in the search (0 = disabled)" help=""/>
5985 <param name="missed_cleavages" argument="-Search:peptide:missed_cleavages" type="integer" optional="true" value="1" label="Number of missed cleavages" help=""/> 5983 <param name="missed_cleavages" argument="-Search:peptide:missed_cleavages" type="integer" optional="true" value="1" label="Number of missed cleavages" help=""/>
5986 <param name="motif" argument="-Search:peptide:motif" type="text" optional="true" value="" label="If set, only peptides that contain this motif (provided as RegEx) will be considered" help=""> 5984 <param name="motif" argument="-Search:peptide:motif" type="text" optional="true" value="" label="If set, only peptides that contain this motif (provided as RegEx) will be considered" help="">
5987 <expand macro="list_string_san"/> 5985 <expand macro="list_string_san" name="motif"/>
5988 </param> 5986 </param>
5989 </section> 5987 </section>
5990 <section name="report" title="Reporting Options" help="" expanded="false"> 5988 <section name="report" title="Reporting Options" help="" expanded="false">
5991 <param name="top_hits" argument="-Search:report:top_hits" type="integer" optional="true" value="1" label="Maximum number of top scoring hits per spectrum that are reported" help=""/> 5989 <param name="top_hits" argument="-Search:report:top_hits" type="integer" optional="true" value="1" label="Maximum number of top scoring hits per spectrum that are reported" help=""/>
5992 </section> 5990 </section>
5993 </section> 5991 </section>
5994 <expand macro="adv_opts_macro"> 5992 <expand macro="adv_opts_macro">
5995 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 5993 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
5996 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 5994 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
5997 <expand macro="list_string_san"/> 5995 <expand macro="list_string_san" name="test"/>
5998 </param> 5996 </param>
5999 </expand> 5997 </expand>
6000 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 5998 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
6001 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 5999 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
6002 </param> 6000 </param>
6005 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 6003 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
6006 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 6004 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
6007 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 6005 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
6008 </data> 6006 </data>
6009 </outputs> 6007 </outputs>
6010 <tests> 6008 <tests><!-- UTILS_SimpleSearchEngine_1 -->
6011 <expand macro="autotest_SimpleSearchEngine"/> 6009 <test expect_num_outputs="2">
6012 <expand macro="manutest_SimpleSearchEngine"/> 6010 <section name="adv_opts">
6011 <param name="force" value="false"/>
6012 <param name="test" value="true"/>
6013 </section>
6014 <param name="in" value="SimpleSearchEngine_1.mzML"/>
6015 <param name="database" value="SimpleSearchEngine_1.fasta"/>
6016 <output name="out" file="SimpleSearchEngine_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6017 <section name="Search">
6018 <param name="enzyme" value="Trypsin"/>
6019 <param name="decoys" value="false"/>
6020 <section name="precursor">
6021 <param name="mass_tolerance" value="5.0"/>
6022 <param name="mass_tolerance_unit" value="ppm"/>
6023 <param name="min_charge" value="2"/>
6024 <param name="max_charge" value="5"/>
6025 <param name="isotopes" value="0 1"/>
6026 </section>
6027 <section name="fragment">
6028 <param name="mass_tolerance" value="0.3"/>
6029 <param name="mass_tolerance_unit" value="Da"/>
6030 </section>
6031 <section name="modifications">
6032 <param name="fixed"/>
6033 <param name="variable" value="Oxidation (M)"/>
6034 <param name="variable_max_per_peptide" value="2"/>
6035 </section>
6036 <section name="annotate">
6037 <param name="PSM" value="ALL"/>
6038 </section>
6039 <section name="peptide">
6040 <param name="min_size" value="7"/>
6041 <param name="max_size" value="40"/>
6042 <param name="missed_cleavages" value="1"/>
6043 <param name="motif" value=""/>
6044 </section>
6045 <section name="report">
6046 <param name="top_hits" value="1"/>
6047 </section>
6048 </section>
6049 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6050 <output name="ctd_out" ftype="xml">
6051 <assert_contents>
6052 <is_valid_xml/>
6053 </assert_contents>
6054 </output>
6055 </test>
6056 <!-- UTILS_SimpleSearchEngine_2 -->
6057 <test expect_num_outputs="2">
6058 <section name="adv_opts">
6059 <param name="force" value="false"/>
6060 <param name="test" value="true"/>
6061 </section>
6062 <param name="in" value="SimpleSearchEngine_1.mzML"/>
6063 <param name="database" value="SimpleSearchEngine_1.fasta"/>
6064 <output name="out" file="SimpleSearchEngine_2_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6065 <section name="Search">
6066 <param name="enzyme" value="Trypsin"/>
6067 <param name="decoys" value="false"/>
6068 <section name="precursor">
6069 <param name="mass_tolerance" value="10.0"/>
6070 <param name="mass_tolerance_unit" value="ppm"/>
6071 <param name="min_charge" value="2"/>
6072 <param name="max_charge" value="5"/>
6073 <param name="isotopes" value="0 1"/>
6074 </section>
6075 <section name="fragment">
6076 <param name="mass_tolerance" value="10.0"/>
6077 <param name="mass_tolerance_unit" value="ppm"/>
6078 </section>
6079 <section name="modifications">
6080 <param name="fixed" value="Carbamidomethyl (C)"/>
6081 <param name="variable" value="Oxidation (M)"/>
6082 <param name="variable_max_per_peptide" value="2"/>
6083 </section>
6084 <section name="annotate">
6085 <param name="PSM" value="ALL"/>
6086 </section>
6087 <section name="peptide">
6088 <param name="min_size" value="7"/>
6089 <param name="max_size" value="40"/>
6090 <param name="missed_cleavages" value="1"/>
6091 <param name="motif" value=""/>
6092 </section>
6093 <section name="report">
6094 <param name="top_hits" value="1"/>
6095 </section>
6096 </section>
6097 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6098 <output name="ctd_out" ftype="xml">
6099 <assert_contents>
6100 <is_valid_xml/>
6101 </assert_contents>
6102 </output>
6103 </test>
6013 </tests> 6104 </tests>
6014 <help><![CDATA[Annotates MS/MS spectra using SimpleSearchEngine. 6105 <help><![CDATA[Annotates MS/MS spectra using SimpleSearchEngine.
6015 6106
6016 6107
6017 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_SimpleSearchEngine.html]]></help> 6108 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SimpleSearchEngine.html]]></help>
6018 <expand macro="references"/> 6109 <expand macro="references"/>
6019 </tool> 6110 </tool>