diff CometAdapter.xml @ 2:999615a63587 draft

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

--- a/CometAdapter.xml	Tue Mar 20 14:49:04 2018 -0400
+++ b/CometAdapter.xml	Wed May 15 08:21:07 2019 -0400
@@ -10,8 +10,9 @@
   <expand macro="references"/>
   <expand macro="stdio"/>
   <expand macro="requirements"/>
-  <command>CometAdapter
+  <command detect_errors="aggressive"><![CDATA[CometAdapter
 
+-comet_executable comet
 #if $param_in:
   -in $param_in
 #end if
@@ -21,9 +22,6 @@
 #if $param_database:
   -database $param_database
 #end if
-#if $param_comet_executable:
-  -comet_executable $param_comet_executable
-#end if
 #if $param_comet_version:
   -comet_version
   #if " " in str($param_comet_version):
@@ -214,11 +212,11 @@
   -force
 #end if
 #end if
-</command>
+-threads "\${GALAXY_SLOTS:-1}"
+]]></command>
   <inputs>
     <param name="param_in" type="data" format="mzml" optional="False" label="Input file" help="(-in) "/>
     <param name="param_database" type="data" format="fasta" optional="False" label="FASTA file" help="(-database) "/>
-    <param name="param_comet_executable" type="data" format="txt" value="comet.exe" label="Comet executable of the installation" help="(-comet_executable) e.g. 'comet.exe'"/>
     <param name="param_comet_version" display="radio" type="select" optional="False" value="2016.01 rev. 2" label="comet version: (year,version,revision)" help="(-comet_version) ">
       <option value="2016.01 rev. 2" selected="true">2016.01 rev. 2</option>
       <option value="2016.01 rev. 3">2016.01 rev. 3</option>
@@ -5414,5 +5412,5 @@
   <help>Annotates MS/MS spectra using Comet.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_CometAdapter.html</help>
+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_CometAdapter.html</help>
 </tool>