Mercurial > repos > galaxyp > openms_mssimulator

diff 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
line wrap: on
line diff
--- a/MSSimulator.xml	Mon Feb 12 08:53:36 2018 -0500
+++ b/MSSimulator.xml	Wed May 15 06:02:53 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="MSSimulator" name="MSSimulator" version="2.2.0">
+<tool id="MSSimulator" name="MSSimulator" version="2.3.0">
   <description>A highly configurable simulator for mass spectrometry experiments.</description>
   <macros>
     <token name="@EXECUTABLE@">MSSimulator</token>
@@ -10,7 +10,7 @@
   <expand macro="references"/>
   <expand macro="stdio"/>
   <expand macro="requirements"/>
-  <command>MSSimulator
+  <command detect_errors="aggressive"><![CDATA[MSSimulator
 
 -in
   #for token in $param_in:
@@ -615,7 +615,7 @@
   #end for
 #end if
 #end if
-</command>
+]]></command>
   <inputs>
     <param name="param_in" type="data" format="fasta" multiple="true" optional="False" size="30" label="Input protein sequences" help="(-in) ">
       <sanitizer>
@@ -626,26 +626,31 @@
       </sanitizer>
     </param>
     <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) ">
-      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+      <option value="CNBr">CNBr</option>
       <option value="Trypsin/P">Trypsin/P</option>
+      <option value="Lys-C">Lys-C</option>
       <option value="Formic_acid">Formic_acid</option>
+      <option value="Arg-C/P">Arg-C/P</option>
+      <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+      <option value="proline endopeptidase">proline endopeptidase</option>
+      <option value="Arg-C">Arg-C</option>
+      <option value="unspecific cleavage">unspecific cleavage</option>
+      <option value="Trypsin" selected="true">Trypsin</option>
       <option value="TrypChymo">TrypChymo</option>
-      <option value="V8-DE">V8-DE</option>
-      <option value="CNBr">CNBr</option>
-      <option value="Chymotrypsin">Chymotrypsin</option>
-      <option value="Asp-N">Asp-N</option>
-      <option value="Lys-C">Lys-C</option>
+      <option value="V8-E">V8-E</option>
+      <option value="2-iodobenzoate">2-iodobenzoate</option>
+      <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+      <option value="no cleavage">no cleavage</option>
+      <option value="Asp-N_ambic">Asp-N_ambic</option>
       <option value="PepsinA">PepsinA</option>
+      <option value="Chymotrypsin">Chymotrypsin</option>
+      <option value="V8-DE">V8-DE</option>
+      <option value="Asp-N/B">Asp-N/B</option>
+      <option value="Lys-N">Lys-N</option>
       <option value="Lys-C/P">Lys-C/P</option>
-      <option value="Asp-N_ambic">Asp-N_ambic</option>
-      <option value="Arg-C">Arg-C</option>
-      <option value="proline endopeptidase">proline endopeptidase</option>
-      <option value="Trypsin" selected="true">Trypsin</option>
-      <option value="2-iodobenzoate">2-iodobenzoate</option>
-      <option value="no cleavage">no cleavage</option>
-      <option value="unspecific cleavage">unspecific cleavage</option>
-      <option value="V8-E">V8-E</option>
       <option value="leukocyte elastase">leukocyte elastase</option>
+      <option value="Asp-N">Asp-N</option>
     </param>
     <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)">
       <option value="trained">trained</option>
@@ -1020,5 +1025,5 @@
   <help>A highly configurable simulator for mass spectrometry experiments.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MSSimulator.html</help>
+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_MSSimulator.html</help>
 </tool>