Mercurial > repos > galaxyp > openms_digestormotif
diff DigestorMotif.xml @ 12:661cb880129a draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author | galaxyp |
---|---|
date | Wed, 15 May 2019 06:56:13 -0400 |
parents | e6f171ddbca4 |
children | 38106b5b3bc6 |
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--- a/DigestorMotif.xml Mon Feb 12 09:01:09 2018 -0500 +++ b/DigestorMotif.xml Wed May 15 06:56:13 2019 -0400 @@ -1,7 +1,7 @@ <?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.--> +<!--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="2.2.0"> +<tool id="DigestorMotif" name="DigestorMotif" version="2.3.0"> <description>digests a protein database in-silico</description> <macros> <token name="@EXECUTABLE@">DigestorMotif</token> @@ -10,7 +10,7 @@ <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> - <command>DigestorMotif + <command detect_errors="aggressive"><![CDATA[DigestorMotif #if $param_in: -in $param_in @@ -46,7 +46,7 @@ -force #end if #end if -</command> +]]></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) "/> @@ -54,26 +54,31 @@ <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="Trypsin/P">Trypsin/P</option> + <option value="V8-DE">V8-DE</option> + <option value="leukocyte elastase">leukocyte elastase</option> <option value="PepsinA">PepsinA</option> - <option value="Lys-C/P">Lys-C/P</option> - <option value="Lys-C">Lys-C</option> + <option value="Arg-C">Arg-C</option> <option value="TrypChymo">TrypChymo</option> - <option value="Asp-N_ambic">Asp-N_ambic</option> - <option value="Arg-C">Arg-C</option> - <option value="Trypsin" selected="true">Trypsin</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="Formic_acid">Formic_acid</option> - <option value="V8-DE">V8-DE</option> - <option value="CNBr">CNBr</option> + <option value="Arg-C/P">Arg-C/P</option> <option value="proline endopeptidase">proline endopeptidase</option> - <option value="unspecific cleavage">unspecific cleavage</option> - <option value="no cleavage">no cleavage</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="V8-E">V8-E</option> - <option value="leukocyte elastase">leukocyte elastase</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> @@ -93,5 +98,5 @@ <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> +For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_DigestorMotif.html</help> </tool>