Mercurial > repos > galaxyp > openms_rnpxlsearch

comparison RNPxlSearch.xml @ 4:3822d4b3c74d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author galaxyp
date Mon, 12 Feb 2018 13:12:23 -0500
parents c6911370f25e
children 2e5df305c372
comparison
equal deleted inserted replaced
3:14a0112f0705 4:3822d4b3c74d
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="RNPxlSearch" name="RNPxlSearch" version="2.2.0"> 4 <tool id="RNPxlSearch" name="RNPxlSearch" version="2.3.0">
5 <description>Annotate RNA to peptide crosslinks in MS/MS spectra.</description> 5 <description>Annotate RNA to peptide crosslinks in MS/MS spectra.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">RNPxlSearch</token> 7 <token name="@EXECUTABLE@">RNPxlSearch</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
38 #if $param_precursor_min_charge: 38 #if $param_precursor_min_charge:
39 -precursor:min_charge $param_precursor_min_charge 39 -precursor:min_charge $param_precursor_min_charge
40 #end if 40 #end if
41 #if $param_precursor_max_charge: 41 #if $param_precursor_max_charge:
42 -precursor:max_charge $param_precursor_max_charge 42 -precursor:max_charge $param_precursor_max_charge
43 #end if
44
45 #if $rep_param_precursor_isotopes:
46 -precursor:isotopes
47 #for token in $rep_param_precursor_isotopes:
48 #if " " in str(token):
49 "$token.param_precursor_isotopes"
50 #else
51 $token.param_precursor_isotopes
52 #end if
53 #end for
43 #end if 54 #end if
44 #if $param_fragment_mass_tolerance: 55 #if $param_fragment_mass_tolerance:
45 -fragment:mass_tolerance $param_fragment_mass_tolerance 56 -fragment:mass_tolerance $param_fragment_mass_tolerance
46 #end if 57 #end if
47 #if $param_fragment_mass_tolerance_unit: 58 #if $param_fragment_mass_tolerance_unit:
187 <option value="ppm" selected="true">ppm</option> 198 <option value="ppm" selected="true">ppm</option>
188 <option value="Da">Da</option> 199 <option value="Da">Da</option>
189 </param> 200 </param>
190 <param name="param_precursor_min_charge" type="integer" value="2" label="Minimum precursor charge to be considered" help="(-min_charge) "/> 201 <param name="param_precursor_min_charge" type="integer" value="2" label="Minimum precursor charge to be considered" help="(-min_charge) "/>
191 <param name="param_precursor_max_charge" type="integer" value="5" label="Maximum precursor charge to be considered" help="(-max_charge) "/> 202 <param name="param_precursor_max_charge" type="integer" value="5" label="Maximum precursor charge to be considered" help="(-max_charge) "/>
203 <repeat name="rep_param_precursor_isotopes" min="0" max="1" title="param_precursor_isotopes">
204 <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)">
205 <sanitizer>
206 <valid initial="string.printable">
207 <remove value="'"/>
208 <remove value="&quot;"/>
209 </valid>
210 </sanitizer>
211 </param>
212 </repeat>
192 <param name="param_fragment_mass_tolerance" type="float" value="10.0" label="Fragment mass tolerance (+/- around fragment m/z)" help="(-mass_tolerance) "/> 213 <param name="param_fragment_mass_tolerance" type="float" value="10.0" label="Fragment mass tolerance (+/- around fragment m/z)" help="(-mass_tolerance) "/>
193 <param name="param_fragment_mass_tolerance_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of fragment m" help="(-mass_tolerance_unit) "> 214 <param name="param_fragment_mass_tolerance_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of fragment m" help="(-mass_tolerance_unit) ">
194 <option value="ppm" selected="true">ppm</option> 215 <option value="ppm" selected="true">ppm</option>
195 <option value="Da">Da</option> 216 <option value="Da">Da</option>
196 </param> 217 </param>
197 <repeat name="rep_param_modifications_fixed" min="0" max="1" title="param_modifications_fixed"> 218 <repeat name="rep_param_modifications_fixed" min="0" title="param_modifications_fixed">
198 <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)'"> 219 <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)'">
199 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 220 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
200 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 221 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
201 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 222 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
202 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option> 223 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
2725 <option value="sulfo+amino (Y)">sulfo+amino (Y)</option> 2746 <option value="sulfo+amino (Y)">sulfo+amino (Y)</option>
2726 <option value="thioacylPA (K)">thioacylPA (K)</option> 2747 <option value="thioacylPA (K)">thioacylPA (K)</option>
2727 <option value="trifluoro (L)">trifluoro (L)</option> 2748 <option value="trifluoro (L)">trifluoro (L)</option>
2728 </param> 2749 </param>
2729 </repeat> 2750 </repeat>
2730 <repeat name="rep_param_modifications_variable" min="0" max="1" title="param_modifications_variable"> 2751 <repeat name="rep_param_modifications_variable" min="0" title="param_modifications_variable">
2731 <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)'"> 2752 <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)'">
2732 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 2753 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
2733 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 2754 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
2734 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 2755 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
2735 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option> 2756 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
5261 </param> 5282 </param>
5262 </repeat> 5283 </repeat>
5263 <param name="param_modifications_variable_max_per_peptide" type="integer" value="2" label="Maximum number of residues carrying a variable modification per candidate peptide" help="(-variable_max_per_peptide) "/> 5284 <param name="param_modifications_variable_max_per_peptide" type="integer" value="2" label="Maximum number of residues carrying a variable modification per candidate peptide" help="(-variable_max_per_peptide) "/>
5264 <param name="param_peptide_missed_cleavages" type="integer" value="1" label="Number of missed cleavages" help="(-missed_cleavages) "/> 5285 <param name="param_peptide_missed_cleavages" type="integer" value="1" label="Number of missed cleavages" help="(-missed_cleavages) "/>
5265 <param name="param_peptide_enzyme" type="select" optional="False" value="Trypsin" label="The enzyme used for peptide digestion" help="(-enzyme) "> 5286 <param name="param_peptide_enzyme" type="select" optional="False" value="Trypsin" label="The enzyme used for peptide digestion" help="(-enzyme) ">
5287 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
5288 <option value="Chymotrypsin">Chymotrypsin</option>
5289 <option value="Asp-N/B">Asp-N/B</option>
5290 <option value="Lys-N">Lys-N</option>
5291 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
5292 <option value="Asp-N_ambic">Asp-N_ambic</option>
5293 <option value="Lys-C">Lys-C</option>
5294 <option value="CNBr">CNBr</option>
5266 <option value="Trypsin" selected="true">Trypsin</option> 5295 <option value="Trypsin" selected="true">Trypsin</option>
5267 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
5268 <option value="TrypChymo">TrypChymo</option>
5269 <option value="V8-DE">V8-DE</option>
5270 <option value="Lys-C">Lys-C</option>
5271 <option value="V8-E">V8-E</option>
5272 <option value="no cleavage">no cleavage</option> 5296 <option value="no cleavage">no cleavage</option>
5273 <option value="CNBr">CNBr</option> 5297 <option value="Arg-C/P">Arg-C/P</option>
5274 <option value="leukocyte elastase">leukocyte elastase</option> 5298 <option value="leukocyte elastase">leukocyte elastase</option>
5275 <option value="unspecific cleavage">unspecific cleavage</option>
5276 <option value="Lys-C/P">Lys-C/P</option>
5277 <option value="PepsinA">PepsinA</option>
5278 <option value="proline endopeptidase">proline endopeptidase</option>
5279 <option value="Formic_acid">Formic_acid</option>
5280 <option value="Asp-N">Asp-N</option>
5281 <option value="Asp-N_ambic">Asp-N_ambic</option>
5282 <option value="Trypsin/P">Trypsin/P</option>
5283 <option value="Chymotrypsin">Chymotrypsin</option>
5284 <option value="2-iodobenzoate">2-iodobenzoate</option> 5299 <option value="2-iodobenzoate">2-iodobenzoate</option>
5285 <option value="Arg-C">Arg-C</option> 5300 <option value="Arg-C">Arg-C</option>
5301 <option value="PepsinA">PepsinA</option>
5302 <option value="TrypChymo">TrypChymo</option>
5303 <option value="Trypsin/P">Trypsin/P</option>
5304 <option value="V8-DE">V8-DE</option>
5305 <option value="unspecific cleavage">unspecific cleavage</option>
5306 <option value="proline endopeptidase">proline endopeptidase</option>
5307 <option value="Asp-N">Asp-N</option>
5308 <option value="Formic_acid">Formic_acid</option>
5309 <option value="V8-E">V8-E</option>
5310 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
5311 <option value="Lys-C/P">Lys-C/P</option>
5286 </param> 5312 </param>
5287 <param name="param_RNPxl_length" type="integer" value="2" label="Oligonucleotide maximum length" help="(-length) 0 = disable search for RNA variants"/> 5313 <param name="param_RNPxl_length" type="integer" value="2" label="Oligonucleotide maximum length" help="(-length) 0 = disable search for RNA variants"/>
5288 <param name="param_RNPxl_sequence" type="text" size="30" label="Sequence to restrict the generation of oligonucleotide chains" help="(-sequence) (disabled for empty sequence)"> 5314 <param name="param_RNPxl_sequence" type="text" size="30" label="Sequence to restrict the generation of oligonucleotide chains" help="(-sequence) (disabled for empty sequence)">
5289 <sanitizer> 5315 <sanitizer>
5290 <valid initial="string.printable"> 5316 <valid initial="string.printable">
5360 <data name="param_out_tsv" format="tabular"/> 5386 <data name="param_out_tsv" format="tabular"/>
5361 </outputs> 5387 </outputs>
5362 <help>Annotate RNA to peptide crosslinks in MS/MS spectra. 5388 <help>Annotate RNA to peptide crosslinks in MS/MS spectra.
5363 5389
5364 5390
5365 For more information, visit http://ftp.mi.fu-berlin.de/pub/OpenMS/develop-documentation/html/classRNPxlSearch.html</help> 5391 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RNPxlSearch.html</help>
5366 </tool> 5392 </tool>