Mercurial > repos > galaxyp > openms_digestormotif
view DigestorMotif.xml @ 8:87b797e33998 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
author | galaxyp |
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date | Tue, 20 Mar 2018 15:24:42 -0400 |
parents | 2f207d8b1bce |
children | 861833218c65 |
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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 CTDConverter.--> <!--Proposed Tool Section: [Utilities]--> <tool id="DigestorMotif" name="DigestorMotif" version="2.3.0"> <description>digests a protein database in-silico</description> <macros> <token name="@EXECUTABLE@">DigestorMotif</token> <import>macros.xml</import> </macros> <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command>DigestorMotif #if $param_in: -in $param_in #end if #if $param_out: -out $param_out #end if #if $param_missed_cleavages: -missed_cleavages $param_missed_cleavages #end if #if $param_mass_accuracy: -mass_accuracy $param_mass_accuracy #end if #if $param_min_length: -min_length $param_min_length #end if #if $param_out_option: -out_option $param_out_option #end if #if $param_enzyme: -enzyme #if " " in str($param_enzyme): "$param_enzyme" #else $param_enzyme #end if #end if #if $param_motif: -motif "$param_motif" #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="FASTA input file" help="(-in) "/> <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_mass_accuracy" type="integer" value="1000" label="give your mass accuracy in pp" help="(-mass_accuracy) "/> <param name="param_min_length" type="integer" value="6" label="minimum length of peptide" help="(-min_length) "/> <param name="param_out_option" type="integer" value="1" label="indicate 1 (peptide table only), 2 (statistics only) or (both peptide table + statistics)" help="(-out_option) "/> <param name="param_enzyme" type="select" optional="False" value="Trypsin" label="The enzyme used for peptide digestion" help="(-enzyme) "> <option value="Formic_acid">Formic_acid</option> <option value="Alpha-lytic protease">Alpha-lytic protease</option> <option value="V8-E">V8-E</option> <option value="unspecific cleavage">unspecific cleavage</option> <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> <option value="V8-DE">V8-DE</option> <option value="leukocyte elastase">leukocyte elastase</option> <option value="PepsinA">PepsinA</option> <option value="Arg-C">Arg-C</option> <option value="TrypChymo">TrypChymo</option> <option value="no cleavage">no cleavage</option> <option value="CNBr">CNBr</option> <option value="Trypsin/P">Trypsin/P</option> <option value="Chymotrypsin">Chymotrypsin</option> <option value="Chymotrypsin/P">Chymotrypsin/P</option> <option value="Asp-N_ambic">Asp-N_ambic</option> <option value="Lys-C">Lys-C</option> <option value="Trypsin" selected="true">Trypsin</option> <option value="Asp-N">Asp-N</option> <option value="Arg-C/P">Arg-C/P</option> <option value="proline endopeptidase">proline endopeptidase</option> <option value="Asp-N/B">Asp-N/B</option> <option value="Lys-N">Lys-N</option> <option value="2-iodobenzoate">2-iodobenzoate</option> <option value="Lys-C/P">Lys-C/P</option> </param> <param name="param_motif" type="text" size="30" value="M" label="the motif for the restricted peptidome" help="(-motif) "> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </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="idxml"/> </outputs> <help>digests a protein database in-silico For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DigestorMotif.html</help> </tool>