Mercurial > repos > galaxyp > pepquery

diff pepquery.xml @ 1:528bcf03e561 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 542fee4158c3dbd0c5ad8cd7e97b77f55982e0bf"
author galaxyp
date Fri, 17 Jul 2020 17:05:41 -0400
parents 32d3818fc635
children 5b5a9f59e2c7
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line diff
--- a/pepquery.xml	Wed Jan 22 17:12:37 2020 -0500
+++ b/pepquery.xml	Fri Jul 17 17:05:41 2020 -0400
@@ -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">