Mercurial > repos > galaxyp > openms_mssimulator

comparison MSSimulator.xml @ 3:fcbdc271f48c draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit daf6dfc513ede9b890125d9fff2c2657d834eea9
author galaxyp
date Fri, 14 Jul 2017 18:56:04 -0400
parents 0d788b696572
children 582f4ea310c5
comparison
equal deleted inserted replaced
2:b8103b8deae2 3:fcbdc271f48c
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 CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="MSSimulator" name="MSSimulator" version="2.1.0"> 4 <tool id="MSSimulator" name="MSSimulator" version="2.2.0">
5 <description>A highly configurable simulator for mass spectrometry experiments.</description> 5 <description>A highly configurable simulator for mass spectrometry experiments.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MSSimulator</token> 7 <token name="@EXECUTABLE@">MSSimulator</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
350 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses 350 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses
351 #end if 351 #end if
352 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_precursor_peaks: 352 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_precursor_peaks:
353 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks 353 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks
354 #end if 354 #end if
355 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_all_precursor_charges:
356 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_all_precursor_charges
357 #end if
355 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_abundant_immonium_ions: 358 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_abundant_immonium_ions:
356 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions 359 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions
357 #end if 360 #end if
358 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_first_prefix_ion: 361 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_first_prefix_ion:
359 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion 362 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion
621 <remove value="&quot;"/> 624 <remove value="&quot;"/>
622 </valid> 625 </valid>
623 </sanitizer> 626 </sanitizer>
624 </param> 627 </param>
625 <param name="param_algorithm_MSSim_Digestion_enzyme" type="select" optional="False" value="Trypsin" label="Enzyme to use for digestion (select 'no cleavage' to skip digestion)" help="(-enzyme) "> 628 <param name="param_algorithm_MSSim_Digestion_enzyme" type="select" optional="False" value="Trypsin" label="Enzyme to use for digestion (select 'no cleavage' to skip digestion)" help="(-enzyme) ">
626 <option value="leukocyte elastase">leukocyte elastase</option> 629 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
630 <option value="Trypsin/P">Trypsin/P</option>
631 <option value="Formic_acid">Formic_acid</option>
632 <option value="TrypChymo">TrypChymo</option>
633 <option value="V8-DE">V8-DE</option>
634 <option value="CNBr">CNBr</option>
635 <option value="Chymotrypsin">Chymotrypsin</option>
636 <option value="Asp-N">Asp-N</option>
627 <option value="Lys-C">Lys-C</option> 637 <option value="Lys-C">Lys-C</option>
638 <option value="PepsinA">PepsinA</option>
639 <option value="Lys-C/P">Lys-C/P</option>
640 <option value="Asp-N_ambic">Asp-N_ambic</option>
641 <option value="Arg-C">Arg-C</option>
642 <option value="proline endopeptidase">proline endopeptidase</option>
643 <option value="Trypsin" selected="true">Trypsin</option>
644 <option value="2-iodobenzoate">2-iodobenzoate</option>
628 <option value="no cleavage">no cleavage</option> 645 <option value="no cleavage">no cleavage</option>
629 <option value="unspecific cleavage">unspecific cleavage</option> 646 <option value="unspecific cleavage">unspecific cleavage</option>
630 <option value="Trypsin" selected="true">Trypsin</option>
631 <option value="Trypsin/P">Trypsin/P</option>
632 <option value="CNBr">CNBr</option>
633 <option value="Formic_acid">Formic_acid</option>
634 <option value="Lys-C/P">Lys-C/P</option>
635 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
636 <option value="2-iodobenzoate">2-iodobenzoate</option>
637 <option value="proline endopeptidase">proline endopeptidase</option>
638 <option value="Chymotrypsin">Chymotrypsin</option>
639 <option value="V8-E">V8-E</option> 647 <option value="V8-E">V8-E</option>
640 <option value="V8-DE">V8-DE</option> 648 <option value="leukocyte elastase">leukocyte elastase</option>
641 <option value="Asp-N_ambic">Asp-N_ambic</option>
642 <option value="TrypChymo">TrypChymo</option>
643 <option value="Arg-C">Arg-C</option>
644 <option value="Asp-N">Asp-N</option>
645 <option value="PepsinA">PepsinA</option>
646 </param> 649 </param>
647 <param name="param_algorithm_MSSim_Digestion_model" display="radio" type="select" optional="False" value="naive" label="The cleavage model to use for digestion" help="(-model) 'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u)"> 650 <param name="param_algorithm_MSSim_Digestion_model" display="radio" type="select" optional="False" value="naive" label="The cleavage model to use for digestion" help="(-model) 'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u)">
648 <option value="trained">trained</option> 651 <option value="trained">trained</option>
649 <option value="naive" selected="true">naive</option> 652 <option value="naive" selected="true">naive</option>
650 </param> 653 </param>
825 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_isotopes" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_isotopes" falsevalue="" checked="false" optional="True" label="If set to 1 isotope peaks of the product ion peaks are added" help="(-add_isotopes) "/> 828 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_isotopes" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_isotopes" falsevalue="" checked="false" optional="True" label="If set to 1 isotope peaks of the product ion peaks are added" help="(-add_isotopes) "/>
826 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_max_isotope" type="integer" value="2" label="Defines the maximal isotopic peak which is added, add_isotopes must be set to 1" help="(-max_isotope) "/> 829 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_max_isotope" type="integer" value="2" label="Defines the maximal isotopic peak which is added, add_isotopes must be set to 1" help="(-max_isotope) "/>
827 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_metainfo" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_metainfo" falsevalue="" checked="false" optional="True" label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" help="(-add_metainfo) "/> 830 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_metainfo" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_metainfo" falsevalue="" checked="false" optional="True" label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" help="(-add_metainfo) "/>
828 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_losses" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses" falsevalue="" checked="false" optional="True" label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" help="(-add_losses) "/> 831 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_losses" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses" falsevalue="" checked="false" optional="True" label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" help="(-add_losses) "/>
829 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_precursor_peaks" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks" falsevalue="" checked="false" optional="True" label="Adds peaks of the precursor to the spectrum, which happen to occur sometimes" help="(-add_precursor_peaks) "/> 832 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_precursor_peaks" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks" falsevalue="" checked="false" optional="True" label="Adds peaks of the precursor to the spectrum, which happen to occur sometimes" help="(-add_precursor_peaks) "/>
833 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_all_precursor_charges" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_all_precursor_charges" falsevalue="" checked="false" optional="True" label="Adds precursor peaks with all charges in the given range" help="(-add_all_precursor_charges) "/>
830 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_abundant_immonium_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions" falsevalue="" checked="false" optional="True" label="Add most abundant immonium ions" help="(-add_abundant_immonium_ions) "/> 834 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_abundant_immonium_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions" falsevalue="" checked="false" optional="True" label="Add most abundant immonium ions" help="(-add_abundant_immonium_ions) "/>
831 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_first_prefix_ion" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion" falsevalue="" checked="false" optional="True" label="If set to true e.g. b1 ions are added" help="(-add_first_prefix_ion) "/> 835 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_first_prefix_ion" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion" falsevalue="" checked="false" optional="True" label="If set to true e.g. b1 ions are added" help="(-add_first_prefix_ion) "/>
832 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions" display="radio" type="select" optional="False" value="true" label="Add peaks of y-ions to the spectrum" help="(-add_y_ions) "> 836 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions" display="radio" type="select" optional="False" value="true" label="Add peaks of y-ions to the spectrum" help="(-add_y_ions) ">
833 <option value="true" selected="true">true</option> 837 <option value="true" selected="true">true</option>
834 <option value="false">false</option> 838 <option value="false">false</option>