Mercurial > repos > galaxyp > openms_digestor

diff Digestor.xml @ 12:eeeb3e9a9538 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 06:53:31 -0400
parents 0edfa495299f
children abf7c4154f1e
line wrap: on
line diff
--- a/Digestor.xml	Mon Feb 12 08:59:21 2018 -0500
+++ b/Digestor.xml	Wed May 15 06:53:31 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="Digestor" name="Digestor" version="2.2.0">
+<tool id="Digestor" name="Digestor" version="2.3.0">
   <description>Digests a protein database in-silico.</description>
   <macros>
     <token name="@EXECUTABLE@">Digestor</token>
@@ -10,7 +10,7 @@
   <expand macro="references"/>
   <expand macro="stdio"/>
   <expand macro="requirements"/>
-  <command>Digestor
+  <command detect_errors="aggressive"><![CDATA[Digestor
 
 #if $param_in:
   -in $param_in
@@ -48,7 +48,7 @@
   -force
 #end if
 #end if
-</command>
+]]></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">
@@ -59,26 +59,31 @@
     <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="proline endopeptidase">proline endopeptidase</option>
+      <option value="V8-DE">V8-DE</option>
+      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+      <option value="no cleavage">no cleavage</option>
+      <option value="2-iodobenzoate">2-iodobenzoate</option>
+      <option value="leukocyte elastase">leukocyte elastase</option>
       <option value="V8-E">V8-E</option>
-      <option value="Trypsin/P">Trypsin/P</option>
-      <option value="PepsinA">PepsinA</option>
+      <option value="unspecific cleavage">unspecific cleavage</option>
+      <option value="Arg-C">Arg-C</option>
       <option value="CNBr">CNBr</option>
-      <option value="Lys-C/P">Lys-C/P</option>
+      <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+      <option value="Chymotrypsin">Chymotrypsin</option>
+      <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+      <option value="TrypChymo">TrypChymo</option>
       <option value="Asp-N_ambic">Asp-N_ambic</option>
-      <option value="Arg-C">Arg-C</option>
-      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-      <option value="2-iodobenzoate">2-iodobenzoate</option>
+      <option value="Lys-C">Lys-C</option>
       <option value="Trypsin" selected="true">Trypsin</option>
-      <option value="TrypChymo">TrypChymo</option>
-      <option value="Chymotrypsin">Chymotrypsin</option>
+      <option value="Trypsin/P">Trypsin/P</option>
       <option value="Asp-N">Asp-N</option>
+      <option value="Lys-N">Lys-N</option>
       <option value="Formic_acid">Formic_acid</option>
-      <option value="V8-DE">V8-DE</option>
-      <option value="Lys-C">Lys-C</option>
-      <option value="no cleavage">no cleavage</option>
-      <option value="leukocyte elastase">leukocyte elastase</option>
-      <option value="proline endopeptidase">proline endopeptidase</option>
-      <option value="unspecific cleavage">unspecific cleavage</option>
+      <option value="Lys-C/P">Lys-C/P</option>
+      <option value="Asp-N/B">Asp-N/B</option>
+      <option value="PepsinA">PepsinA</option>
+      <option value="Arg-C/P">Arg-C/P</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) "/>
@@ -90,5 +95,5 @@
   <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>
+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_Digestor.html</help>
 </tool>