Mercurial > repos > galaxyp > openms_mssimulator

comparison MSSimulator.xml @ 12:582f4ea310c5 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 06:02:53 -0400
parents fcbdc271f48c
children 140b883daa61
comparison
equal deleted inserted replaced
11:b277ce57c4dc 12:582f4ea310c5
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="MSSimulator" name="MSSimulator" version="2.2.0"> 4 <tool id="MSSimulator" name="MSSimulator" version="2.3.0">
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>
10 <expand macro="references"/> 10 <expand macro="references"/>
11 <expand macro="stdio"/> 11 <expand macro="stdio"/>
12 <expand macro="requirements"/> 12 <expand macro="requirements"/>
13 <command>MSSimulator 13 <command detect_errors="aggressive"><![CDATA[MSSimulator
14 14
15 -in 15 -in
16 #for token in $param_in: 16 #for token in $param_in:
17 $token 17 $token
18 #end for 18 #end for
613 $token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex 613 $token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex
614 #end if 614 #end if
615 #end for 615 #end for
616 #end if 616 #end if
617 #end if 617 #end if
618 </command> 618 ]]></command>
619 <inputs> 619 <inputs>
620 <param name="param_in" type="data" format="fasta" multiple="true" optional="False" size="30" label="Input protein sequences" help="(-in) "> 620 <param name="param_in" type="data" format="fasta" multiple="true" optional="False" size="30" label="Input protein sequences" help="(-in) ">
621 <sanitizer> 621 <sanitizer>
622 <valid initial="string.printable"> 622 <valid initial="string.printable">
623 <remove value="'"/> 623 <remove value="'"/>
624 <remove value="&quot;"/> 624 <remove value="&quot;"/>
625 </valid> 625 </valid>
626 </sanitizer> 626 </sanitizer>
627 </param> 627 </param>
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) "> 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) ">
629 <option value="CNBr">CNBr</option>
630 <option value="Trypsin/P">Trypsin/P</option>
631 <option value="Lys-C">Lys-C</option>
632 <option value="Formic_acid">Formic_acid</option>
633 <option value="Arg-C/P">Arg-C/P</option>
634 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
629 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> 635 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
630 <option value="Trypsin/P">Trypsin/P</option> 636 <option value="proline endopeptidase">proline endopeptidase</option>
631 <option value="Formic_acid">Formic_acid</option> 637 <option value="Arg-C">Arg-C</option>
638 <option value="unspecific cleavage">unspecific cleavage</option>
639 <option value="Trypsin" selected="true">Trypsin</option>
632 <option value="TrypChymo">TrypChymo</option> 640 <option value="TrypChymo">TrypChymo</option>
641 <option value="V8-E">V8-E</option>
642 <option value="2-iodobenzoate">2-iodobenzoate</option>
643 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
644 <option value="no cleavage">no cleavage</option>
645 <option value="Asp-N_ambic">Asp-N_ambic</option>
646 <option value="PepsinA">PepsinA</option>
647 <option value="Chymotrypsin">Chymotrypsin</option>
633 <option value="V8-DE">V8-DE</option> 648 <option value="V8-DE">V8-DE</option>
634 <option value="CNBr">CNBr</option> 649 <option value="Asp-N/B">Asp-N/B</option>
635 <option value="Chymotrypsin">Chymotrypsin</option> 650 <option value="Lys-N">Lys-N</option>
651 <option value="Lys-C/P">Lys-C/P</option>
652 <option value="leukocyte elastase">leukocyte elastase</option>
636 <option value="Asp-N">Asp-N</option> 653 <option value="Asp-N">Asp-N</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>
645 <option value="no cleavage">no cleavage</option>
646 <option value="unspecific cleavage">unspecific cleavage</option>
647 <option value="V8-E">V8-E</option>
648 <option value="leukocyte elastase">leukocyte elastase</option>
649 </param> 654 </param>
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)"> 655 <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)">
651 <option value="trained">trained</option> 656 <option value="trained">trained</option>
652 <option value="naive" selected="true">naive</option> 657 <option value="naive" selected="true">naive</option>
653 </param> 658 </param>
1018 <data name="param_out_id" format="idxml"/> 1023 <data name="param_out_id" format="idxml"/>
1019 </outputs> 1024 </outputs>
1020 <help>A highly configurable simulator for mass spectrometry experiments. 1025 <help>A highly configurable simulator for mass spectrometry experiments.
1021 1026
1022 1027
1023 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MSSimulator.html</help> 1028 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_MSSimulator.html</help>
1024 </tool> 1029 </tool>