Mercurial > repos > galaxyp > openms_simplesearchengine

comparison SimpleSearchEngine.xml @ 10:047d6bdf5c9f draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
author galaxyp
date Thu, 24 Sep 2020 12:23:18 +0000
parents e42e8b553f7d
children 1b56031ac321
comparison
equal deleted inserted replaced
9:e42e8b553f7d 10:047d6bdf5c9f
48 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> 48 <param name="in" 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)"/> 49 <param name="database" 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"> 50 <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=""> 51 <param name="enzyme" argument="-Search:enzyme" type="select" optional="false" label="The enzyme used for peptide digestion" help="">
52 <option value="Trypsin" selected="true">Trypsin</option> 52 <option value="Trypsin" selected="true">Trypsin</option>
53 <option value="leukocyte elastase">leukocyte elastase</option>
54 <option value="proline endopeptidase">proline endopeptidase</option>
55 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
56 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
57 <option value="2-iodobenzoate">2-iodobenzoate</option>
58 <option value="iodosobenzoate">iodosobenzoate</option>
59 <option value="Asp-N/B">Asp-N/B</option>
60 <option value="Asp-N_ambic">Asp-N_ambic</option>
61 <option value="Arg-C/P">Arg-C/P</option>
62 <option value="staphylococcal protease/D">staphylococcal protease/D</option> 53 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
63 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> 54 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
64 <option value="Glu-C+P">Glu-C+P</option> 55 <option value="Glu-C+P">Glu-C+P</option>
65 <option value="PepsinA + P">PepsinA + P</option> 56 <option value="PepsinA + P">PepsinA + P</option>
66 <option value="cyanogen-bromide">cyanogen-bromide</option> 57 <option value="cyanogen-bromide">cyanogen-bromide</option>
67 <option value="Clostripain/P">Clostripain/P</option> 58 <option value="Clostripain/P">Clostripain/P</option>
68 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> 59 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
69 <option value="no cleavage">no cleavage</option> 60 <option value="no cleavage">no cleavage</option>
70 <option value="unspecific cleavage">unspecific cleavage</option> 61 <option value="unspecific cleavage">unspecific cleavage</option>
62 <option value="Arg-C/P">Arg-C/P</option>
63 <option value="proline endopeptidase">proline endopeptidase</option>
64 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
65 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
66 <option value="2-iodobenzoate">2-iodobenzoate</option>
67 <option value="iodosobenzoate">iodosobenzoate</option>
68 <option value="Asp-N/B">Asp-N/B</option>
69 <option value="Asp-N_ambic">Asp-N_ambic</option>
71 <option value="Asp-N">Asp-N</option> 70 <option value="Asp-N">Asp-N</option>
72 <option value="Chymotrypsin">Chymotrypsin</option> 71 <option value="Chymotrypsin">Chymotrypsin</option>
73 <option value="Chymotrypsin/P">Chymotrypsin/P</option> 72 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
74 <option value="CNBr">CNBr</option> 73 <option value="CNBr">CNBr</option>
75 <option value="Formic_acid">Formic_acid</option> 74 <option value="Formic_acid">Formic_acid</option>
75 <option value="Lys-C">Lys-C</option>
76 <option value="Arg-C">Arg-C</option> 76 <option value="Arg-C">Arg-C</option>
77 <option value="TrypChymo">TrypChymo</option>
78 <option value="Trypsin/P">Trypsin/P</option> 77 <option value="Trypsin/P">Trypsin/P</option>
79 <option value="V8-DE">V8-DE</option> 78 <option value="V8-DE">V8-DE</option>
80 <option value="V8-E">V8-E</option> 79 <option value="V8-E">V8-E</option>
81 <option value="Lys-C">Lys-C</option> 80 <option value="leukocyte elastase">leukocyte elastase</option>
82 <option value="Lys-N">Lys-N</option> 81 <option value="Lys-N">Lys-N</option>
83 <option value="Lys-C/P">Lys-C/P</option> 82 <option value="Lys-C/P">Lys-C/P</option>
84 <option value="PepsinA">PepsinA</option> 83 <option value="PepsinA">PepsinA</option>
84 <option value="TrypChymo">TrypChymo</option>
85 <expand macro="list_string_san"/> 85 <expand macro="list_string_san"/>
86 </param> 86 </param>
87 <section name="precursor" title="Precursor (Parent Ion) Options" help="" expanded="false"> 87 <section name="precursor" title="Precursor (Parent Ion) Options" help="" expanded="false">
88 <param name="mass_tolerance" argument="-Search:precursor:mass_tolerance" type="float" optional="true" value="10.0" label="Width of precursor mass tolerance window" help=""/> 88 <param name="mass_tolerance" argument="-Search:precursor:mass_tolerance" type="float" optional="true" value="10.0" label="Width of precursor mass tolerance window" help=""/>
89 <param name="mass_tolerance_unit" argument="-Search:precursor:mass_tolerance_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help=""> 89 <param name="mass_tolerance_unit" argument="-Search:precursor:mass_tolerance_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
5371 <tests> 5371 <tests>
5372 <expand macro="autotest_SimpleSearchEngine"/> 5372 <expand macro="autotest_SimpleSearchEngine"/>
5373 <expand macro="manutest_SimpleSearchEngine"/> 5373 <expand macro="manutest_SimpleSearchEngine"/>
5374 </tests> 5374 </tests>
5375 <help><![CDATA[Annotates MS/MS spectra using SimpleSearchEngine. 5375 <help><![CDATA[Annotates MS/MS spectra using SimpleSearchEngine.
5376 5376 ]]></help>
5377
5378 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/TOPP_SimpleSearchEngine.html]]></help>
5379 <expand macro="references"/> 5377 <expand macro="references"/>
5380 </tool> 5378 </tool>