# HG changeset patch
# User galaxyp
# Date 1715188333 0
# Node ID d39a43a076fce7965d8193262fe480282b4d3af8
# Parent  8671cf7c1671fc101135201af8dd53c784cec699
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 22916ed24dfb8452c8142e5d6b282d0e931af91f

diff -r 8671cf7c1671 -r d39a43a076fc macros.xml
--- a/macros.xml	Wed Oct 18 06:40:48 2023 +0000
+++ b/macros.xml	Wed May 08 17:12:13 2024 +0000
@@ -1,6 +1,6 @@
  <macros>
     <token name="@TOOL_VERSION@">2.0.2</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1101/gr.235028.118</citation>
@@ -20,7 +20,7 @@
     #end if
 #end def
 #def clean($name1)
-    #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fas|fasta|imzml|mzml|mzxml|mgf|raw)$','', $re.sub('.*/','', $name1.rstrip('.gz'))))
+    #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fas|fasta|imzml|mzml|mzxml|mgf)$','', $re.sub('.*/','', $name1.rstrip('.gz'))))
     #return $name_clean
 #end def
 #def ln_name($ds)
@@ -31,8 +31,6 @@
         #set $ext = ".mzXML"
     #else if $ds.is_of_type('mgf')
         #set $ext = ".mgf"
-    #else if $ds.is_of_type('thermo.raw')
-        #set $ext = ".raw"
     #else if $ds.is_of_type('fasta')
         #set $ext = ".fasta"
     #end if
diff -r 8671cf7c1671 -r d39a43a076fc pepquery2_show_sets.xml
--- a/pepquery2_show_sets.xml	Wed Oct 18 06:40:48 2023 +0000
+++ b/pepquery2_show_sets.xml	Wed May 08 17:12:13 2024 +0000
@@ -45,7 +45,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <output name="pepquerydb">
                 <assert_contents>
                     <has_text text="CPTAC_PDA_Discovery_Study_Proteome_PDC000270" />