Mercurial > repos > galaxyp > openms_digestor
view Digestor.xml @ 0:e661b6359f66 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author | galaxyp |
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date | Wed, 01 Mar 2017 12:34:47 -0500 |
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children | 62341892592a |
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<?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> <!--Proposed Tool Section: [Utilities]--> <tool id="Digestor" name="Digestor" version="2.1.0"> <description>Digests a protein database in-silico.</description> <macros> <token name="@EXECUTABLE@">Digestor</token> <import>macros.xml</import> </macros> <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command>Digestor #if $param_in: -in $param_in #end if #if $param_out: -out $param_out #end if #if $param_out_type: -out_type #if " " in str($param_out_type): "$param_out_type" #else $param_out_type #end if #end if #if $param_missed_cleavages: -missed_cleavages $param_missed_cleavages #end if #if $param_min_length: -min_length $param_min_length #end if #if $param_max_length: -max_length $param_max_length #end if #if $param_enzyme: -enzyme $param_enzyme #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force: -force #end if #end if </command> <inputs> <param name="param_in" type="data" format="fasta" optional="False" label="input file" help="(-in) "/> <param name="param_out_type" display="radio" type="select" optional="True" label="Set this if you cannot control the filename of 'out'," help="(-out_type) e.g., in TOPPAS"> <option value="idXML">idXML</option> <option value="fasta">fasta</option> </param> <param name="param_missed_cleavages" type="integer" min="0" optional="True" value="1" label="The number of allowed missed cleavages" help="(-missed_cleavages) "/> <param name="param_min_length" type="integer" value="6" label="Minimum length of peptide" help="(-min_length) "/> <param name="param_max_length" type="integer" value="40" label="Maximum length of peptide" help="(-max_length) "/> <param name="param_enzyme" type="select" optional="False" value="Trypsin" label="The type of digestion enzyme" help="(-enzyme) "> <option value="V8-E">V8-E</option> <option value="TrypChymo">TrypChymo</option> <option value="no cleavage">no cleavage</option> <option value="Lys-C/P">Lys-C/P</option> <option value="Asp-N">Asp-N</option> <option value="Asp-N_ambic">Asp-N_ambic</option> <option value="V8-DE">V8-DE</option> <option value="Lys-C">Lys-C</option> <option value="Trypsin" selected="true">Trypsin</option> <option value="unspecific cleavage">unspecific cleavage</option> <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> <option value="2-iodobenzoate">2-iodobenzoate</option> <option value="leukocyte elastase">leukocyte elastase</option> <option value="proline endopeptidase">proline endopeptidase</option> <option value="CNBr">CNBr</option> <option value="PepsinA">PepsinA</option> <option value="Trypsin/P">Trypsin/P</option> <option value="Arg-C">Arg-C</option> <option value="Formic_acid">Formic_acid</option> <option value="Chymotrypsin">Chymotrypsin</option> </param> <expand macro="advanced_options"> <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> </expand> </inputs> <outputs> <data name="param_out" format="fasta"/> </outputs> <help>Digests a protein database in-silico. For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_Digestor.html</help> </tool>