diff MSGFPlusAdapter.xml @ 7:f0761deada39 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb

--- a/MSGFPlusAdapter.xml	Mon Feb 12 13:05:04 2018 -0500
+++ b/MSGFPlusAdapter.xml	Tue Mar 20 15:08:17 2018 -0400
@@ -143,12 +143,13 @@
   -force
 #end if
 #end if
+-threads "\${GALAXY_SLOTS:-1}"
  ]]>
 </command>
   <inputs>
     <param name="param_in" type="data" format="mzml,mzxml,mgf,ms2" optional="False" label="Input file (MS-GF+ parameter '-s')" help="(-in) "/>
     <param name="param_database" type="data" format="fasta" optional="False" label="Protein sequence database (FASTA file; MS-GF+ parameter '-d')" help="(-database) Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'"/>
-    <param name="param_add_decoys" display="radio" type="boolean" truevalue="-add_decoys" falsevalue="" checked="false" optional="True" label="Create decoy proteins (reversed sequences) and append them to the database for the search (MS-GF+ parameter '-tda')" help="(-add_decoys) This allows the calculation of FDRs, but should only be used if the database does not already contain decoys"/>
+    <param name="param_add_decoys" display="radio" type="boolean" truevalue="-add_decoys" falsevalue="" checked="false" optional="True" label="Create decoy proteins (reversed sequences) and append them to the database for the search (MS-GF+ parameter '-tda')" help="(-add_decoys) This allows the calculation of FDRs, but should only be used if the database does not already contain decoys. Decoys are marked by the prefix XXX_"/>
     <param name="param_precursor_mass_tolerance" type="float" value="10.0" label="Precursor monoisotopic mass tolerance (MS-GF+ parameter '-t')" help="(-precursor_mass_tolerance) "/>
     <param name="param_precursor_error_units" display="radio" type="select" optional="False" value="ppm" label="Unit of precursor mass tolerance (MS-GF+ parameter '-t')" help="(-precursor_error_units) ">
       <option value="Da">Da</option>
@@ -5277,8 +5278,8 @@
     </expand>
   </inputs>
   <outputs>
-    <data name="param_out" format="idxml"/>
-    <data name="param_mzid_out" format="mzid"/>
+    <data name="param_out" format="idxml" label="${tool.name} on ${on_string}: idxml"/>
+    <data name="param_mzid_out" format="mzid" label=" ${tool.name} on ${on_string}: mzid"/>
   </outputs>
   <help>MS/MS database search using MS-GF+.