Mercurial > repos > galaxyp > openms_simplesearchengine

comparison SimpleSearchEngine.xml @ 5:242ba7640825 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author galaxyp
date Mon, 12 Feb 2018 12:54:18 -0500
parents 6ae859b4f243
children 3cec90deb64b
comparison
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4:a62e8d76a463 5:242ba7640825
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 CTD2Galaxy.--> 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="2.2.0"> 4 <tool id="SimpleSearchEngine" name="SimpleSearchEngine" version="2.3.0">
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 </macros> 9 </macros>
37 #if " " in str($param_precursor_mass_tolerance_unit): 37 #if " " in str($param_precursor_mass_tolerance_unit):
38 "$param_precursor_mass_tolerance_unit" 38 "$param_precursor_mass_tolerance_unit"
39 #else 39 #else
40 $param_precursor_mass_tolerance_unit 40 $param_precursor_mass_tolerance_unit
41 #end if 41 #end if
42 #end if
43
44 #if $rep_param_precursor_isotopes:
45 -precursor:isotopes
46 #for token in $rep_param_precursor_isotopes:
47 #if " " in str(token):
48 "$token.param_precursor_isotopes"
49 #else
50 $token.param_precursor_isotopes
51 #end if
52 #end for
42 #end if 53 #end if
43 #if $param_fragment_mass_tolerance: 54 #if $param_fragment_mass_tolerance:
44 -fragment:mass_tolerance $param_fragment_mass_tolerance 55 -fragment:mass_tolerance $param_fragment_mass_tolerance
45 #end if 56 #end if
46 #if $param_fragment_mass_tolerance_unit: 57 #if $param_fragment_mass_tolerance_unit:
102 </command> 113 </command>
103 <inputs> 114 <inputs>
104 <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/> 115 <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/>
105 <param name="param_database" type="data" format="fasta" optional="False" label="input file" help="(-database) "/> 116 <param name="param_database" type="data" format="fasta" optional="False" label="input file" help="(-database) "/>
106 <param name="param_enzyme" type="select" optional="False" value="Trypsin" label="The enzyme used for peptide digestion" help="(-enzyme) "> 117 <param name="param_enzyme" type="select" optional="False" value="Trypsin" label="The enzyme used for peptide digestion" help="(-enzyme) ">
118 <option value="leukocyte elastase">leukocyte elastase</option>
119 <option value="Arg-C/P">Arg-C/P</option>
120 <option value="V8-E">V8-E</option>
121 <option value="2-iodobenzoate">2-iodobenzoate</option>
122 <option value="Asp-N/B">Asp-N/B</option>
123 <option value="PepsinA">PepsinA</option>
124 <option value="Trypsin" selected="true">Trypsin</option>
125 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
126 <option value="no cleavage">no cleavage</option>
127 <option value="Arg-C">Arg-C</option>
128 <option value="CNBr">CNBr</option>
129 <option value="V8-DE">V8-DE</option>
130 <option value="Chymotrypsin">Chymotrypsin</option>
131 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
132 <option value="Lys-C/P">Lys-C/P</option>
107 <option value="unspecific cleavage">unspecific cleavage</option> 133 <option value="unspecific cleavage">unspecific cleavage</option>
108 <option value="Trypsin" selected="true">Trypsin</option> 134 <option value="Asp-N">Asp-N</option>
109 <option value="leukocyte elastase">leukocyte elastase</option> 135 <option value="Trypsin/P">Trypsin/P</option>
110 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> 136 <option value="Lys-N">Lys-N</option>
137 <option value="TrypChymo">TrypChymo</option>
138 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
111 <option value="Asp-N_ambic">Asp-N_ambic</option> 139 <option value="Asp-N_ambic">Asp-N_ambic</option>
112 <option value="2-iodobenzoate">2-iodobenzoate</option> 140 <option value="proline endopeptidase">proline endopeptidase</option>
113 <option value="PepsinA">PepsinA</option>
114 <option value="CNBr">CNBr</option>
115 <option value="Chymotrypsin">Chymotrypsin</option>
116 <option value="Arg-C">Arg-C</option>
117 <option value="Formic_acid">Formic_acid</option> 141 <option value="Formic_acid">Formic_acid</option>
118 <option value="Asp-N">Asp-N</option>
119 <option value="Lys-C">Lys-C</option> 142 <option value="Lys-C">Lys-C</option>
120 <option value="TrypChymo">TrypChymo</option>
121 <option value="V8-DE">V8-DE</option>
122 <option value="no cleavage">no cleavage</option>
123 <option value="V8-E">V8-E</option>
124 <option value="proline endopeptidase">proline endopeptidase</option>
125 <option value="Trypsin/P">Trypsin/P</option>
126 <option value="Lys-C/P">Lys-C/P</option>
127 </param> 143 </param>
128 <param name="param_precursor_mass_tolerance" type="float" value="10.0" label="Width of precursor mass tolerance window" help="(-mass_tolerance) "/> 144 <param name="param_precursor_mass_tolerance" type="float" value="10.0" label="Width of precursor mass tolerance window" help="(-mass_tolerance) "/>
129 <param name="param_precursor_mass_tolerance_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of precursor mass tolerance" help="(-mass_tolerance_unit) "> 145 <param name="param_precursor_mass_tolerance_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of precursor mass tolerance" help="(-mass_tolerance_unit) ">
130 <option value="ppm" selected="true">ppm</option> 146 <option value="ppm" selected="true">ppm</option>
131 <option value="Da">Da</option> 147 <option value="Da">Da</option>
132 </param> 148 </param>
149 <repeat name="rep_param_precursor_isotopes" min="0" max="1" title="param_precursor_isotopes">
150 <param name="param_precursor_isotopes" type="text" size="30" value="0 1" label="Corrects for mono-isotopic peak misassignments" help="(-isotopes) (E.g.: 1 = prec. may be misassigned to first isotopic peak)">
151 <sanitizer>
152 <valid initial="string.printable">
153 <remove value="'"/>
154 <remove value="&quot;"/>
155 </valid>
156 </sanitizer>
157 </param>
158 </repeat>
133 <param name="param_fragment_mass_tolerance" type="float" value="10.0" label="Fragment mass tolerance" help="(-mass_tolerance) "/> 159 <param name="param_fragment_mass_tolerance" type="float" value="10.0" label="Fragment mass tolerance" help="(-mass_tolerance) "/>
134 <param name="param_fragment_mass_tolerance_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of fragment m" help="(-mass_tolerance_unit) "> 160 <param name="param_fragment_mass_tolerance_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of fragment m" help="(-mass_tolerance_unit) ">
135 <option value="ppm" selected="true">ppm</option> 161 <option value="ppm" selected="true">ppm</option>
136 <option value="Da">Da</option> 162 <option value="Da">Da</option>
137 </param> 163 </param>
138 <repeat name="rep_param_modifications_fixed" min="0" max="1" title="param_modifications_fixed"> 164 <repeat name="rep_param_modifications_fixed" min="0" title="param_modifications_fixed">
139 <param name="param_modifications_fixed" type="select" optional="True" label="Fixed modifications, specified using UniMod (www.unimod.org) terms," help="(-fixed) e.g. 'Carbamidomethyl (C)'"> 165 <param name="param_modifications_fixed" type="select" optional="True" label="Fixed modifications, specified using UniMod (www.unimod.org) terms," help="(-fixed) e.g. 'Carbamidomethyl (C)'">
140 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 166 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
141 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 167 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
142 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 168 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
143 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option> 169 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
2666 <option value="sulfo+amino (Y)">sulfo+amino (Y)</option> 2692 <option value="sulfo+amino (Y)">sulfo+amino (Y)</option>
2667 <option value="thioacylPA (K)">thioacylPA (K)</option> 2693 <option value="thioacylPA (K)">thioacylPA (K)</option>
2668 <option value="trifluoro (L)">trifluoro (L)</option> 2694 <option value="trifluoro (L)">trifluoro (L)</option>
2669 </param> 2695 </param>
2670 </repeat> 2696 </repeat>
2671 <repeat name="rep_param_modifications_variable" min="0" max="1" title="param_modifications_variable"> 2697 <repeat name="rep_param_modifications_variable" min="0" title="param_modifications_variable">
2672 <param name="param_modifications_variable" type="select" optional="True" label="Variable modifications, specified using UniMod (www.unimod.org) terms," help="(-variable) e.g. 'Oxidation (M)'"> 2698 <param name="param_modifications_variable" type="select" optional="True" label="Variable modifications, specified using UniMod (www.unimod.org) terms," help="(-variable) e.g. 'Oxidation (M)'">
2673 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 2699 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
2674 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 2700 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
2675 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 2701 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
2676 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option> 2702 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
5216 <data name="param_out" format="idxml"/> 5242 <data name="param_out" format="idxml"/>
5217 </outputs> 5243 </outputs>
5218 <help>Annotates MS/MS spectra using SimpleSearchEngine. 5244 <help>Annotates MS/MS spectra using SimpleSearchEngine.
5219 5245
5220 5246
5221 For more information, visit http://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentation/html/classSimpleSearchEngine.html</help> 5247 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SimpleSearchEngine.html</help>
5222 </tool> 5248 </tool>