# HG changeset patch
# User galaxyp
# Date 1595019911 0
# Node ID 9b5989900a87518d90d0b753ec80cfbb900d67c0
# Parent  851dcf14ee3a79006407c16621fc09db8e8d9825
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 542fee4158c3dbd0c5ad8cd7e97b77f55982e0bf"

diff -r 851dcf14ee3a -r 9b5989900a87 macros.xml
--- a/macros.xml	Wed Jan 22 22:12:14 2020 +0000
+++ b/macros.xml	Fri Jul 17 21:05:11 2020 +0000
@@ -1,5 +1,5 @@
  <macros>
-    <token name="@VERSION@">1.3.0</token>
+    <token name="@VERSION@">1.6.0</token>
     <xml name="modifications">
         <option value="1">HexNAc of T (203.07937251951) modaa</option>
         <option value="2">HexNAc of S (203.07937251951) modaa</option>
diff -r 851dcf14ee3a -r 9b5989900a87 pepquery.xml
--- a/pepquery.xml	Wed Jan 22 22:12:14 2020 +0000
+++ b/pepquery.xml	Fri Jul 17 21:05:11 2020 +0000
@@ -41,6 +41,7 @@
                         #end if
                     #end if
                 #end if
+                -indexType $req_inputs.indexType
                 #if $modifications.fixed_mod
                 -fixMod '$modifications.fixed_mod'
                 #end if
@@ -144,6 +145,10 @@
             </conditional>
             <param name="db_file" type="data" format="fasta" label="Protein Reference Database File" argument="-db" help="an input sequence that matches a reference will be ignored." />
             <param name="spectrum_file" type="data" format="mgf" label="Spectrum File" argument="-ms" help="Spectrum file used for identification, mgf format" />
+            <param name="indexType" type="select" label="Report Spectrum Scan as" argument="-indexType" help="" >
+                <option value="1" selected="true">index (1-based) in MGF</option>
+                <option value="2">spectrum title in MGF</option>
+            </param>
         </section>
         <section name="modifications" title="Modifications" expanded="false">
              <param name="fixed_mod" type="select" label="Fixed modification(s)" multiple="true" argument="-fixMod" help="Fixed modification">