diff PeptideIndexer.xml @ 7:96dcf92f992d draft

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

--- a/PeptideIndexer.xml	Tue Mar 20 15:04:14 2018 -0400
+++ b/PeptideIndexer.xml	Fri May 17 04:39:57 2019 -0400
@@ -10,7 +10,7 @@
   <expand macro="references"/>
   <expand macro="stdio"/>
   <expand macro="requirements"/>
-  <command>PeptideIndexer
+  <command detect_errors="aggressive"><![CDATA[PeptideIndexer
 
 #if $param_in:
   -in $param_in
@@ -88,7 +88,8 @@
   -force
 #end if
 #end if
-</command>
+-threads "\${GALAXY_SLOTS:-1}"
+]]></command>
   <inputs>
     <param name="param_in" type="data" format="idxml" optional="False" label="Input idXML file containing the identifications" help="(-in) "/>
     <param name="param_fasta" type="data" format="fasta" optional="False" label="Input sequence database in FASTA format" help="(-fasta) Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'"/>
@@ -159,5 +160,5 @@
   <help>Refreshes the protein references for all peptide hits.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeptideIndexer.html</help>
+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_PeptideIndexer.html</help>
 </tool>