diff CompNovoCID.xml @ 12:2a753cefc663 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5

--- a/CompNovoCID.xml	Mon Feb 12 08:57:44 2018 -0500
+++ b/CompNovoCID.xml	Wed May 15 06:49:37 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: [Identification]-->
-<tool id="CompNovoCID" name="CompNovoCID" version="2.2.0">
+<tool id="CompNovoCID" name="CompNovoCID" version="2.3.0">
   <description>Performs a de novo peptide identification using the CompNovo engine.</description>
   <macros>
     <token name="@EXECUTABLE@">CompNovoCID</token>
@@ -10,7 +10,7 @@
   <expand macro="references"/>
   <expand macro="stdio"/>
   <expand macro="requirements"/>
-  <command>CompNovoCID
+  <command detect_errors="aggressive"><![CDATA[CompNovoCID
 
 #if $param_in:
   -in $param_in
@@ -104,7 +104,7 @@
   -algorithm:residue_set     "$adv_opts.param_algorithm_residue_set"
 #end if
 #end if
-</command>
+]]></command>
   <inputs>
     <param name="param_in" type="data" format="mzml" optional="False" label="input file in mzML format" help="(-in) "/>
     <param name="param_algorithm_tryptic_only" type="text" size="30" value="true" label="if set to true only tryptic peptides are reported" help="(-tryptic_only) ">
@@ -125,7 +125,7 @@
       <option value="true" selected="true">true</option>
       <option value="false">false</option>
     </param>
-    <repeat name="rep_param_algorithm_fixed_modifications" min="0" max="1" title="param_algorithm_fixed_modifications">
+    <repeat name="rep_param_algorithm_fixed_modifications" min="0" title="param_algorithm_fixed_modifications">
       <param name="param_algorithm_fixed_modifications" type="select" optional="True" label="fixed modifications, specified using UniMod (www.unimod.org) terms," help="(-fixed_modifications) e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
@@ -2658,7 +2658,7 @@
         <option value="trifluoro (L)">trifluoro (L)</option>
       </param>
     </repeat>
-    <repeat name="rep_param_algorithm_variable_modifications" min="0" max="1" title="param_algorithm_variable_modifications">
+    <repeat name="rep_param_algorithm_variable_modifications" min="0" title="param_algorithm_variable_modifications">
       <param name="param_algorithm_variable_modifications" type="select" optional="True" label="variable modifications, specified using UniMod (www.unimod.org) terms," help="(-variable_modifications) e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
@@ -5218,5 +5218,5 @@
   <help>Performs a de novo peptide identification using the CompNovo engine.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_CompNovoCID.html</help>
+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_CompNovoCID.html</help>
 </tool>