# HG changeset patch
# User jjohnson
# Date 1594137315 14400
# Node ID e191adb34d040a6f20b5e8ff35eef2de24ae6802
# Parent  a3db9a8cf1b599b5e90170e8c01412d6603830dc
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"

diff -r a3db9a8cf1b5 -r e191adb34d04 encyclopedia_encyclopedia.xml
--- a/encyclopedia_encyclopedia.xml	Thu Jul 02 11:02:03 2020 -0400
+++ b/encyclopedia_encyclopedia.xml	Tue Jul 07 11:55:15 2020 -0400
@@ -4,7 +4,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <command detect_errors="exit_code"><![CDATA[
+    <command detect_errors="aggressive"><![CDATA[
         @CMD_IMPORTS@
         @LINK_SCAN_INPUT@
         @LINK_FASTA_INPUT@
diff -r a3db9a8cf1b5 -r e191adb34d04 macros.xml
--- a/macros.xml	Thu Jul 02 11:02:03 2020 -0400
+++ b/macros.xml	Tue Jul 07 11:55:15 2020 -0400
@@ -31,14 +31,12 @@
     #end if
 #end def
 #def clean($name1)
-    ## #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('(?i[.](fa|fasta|imzml|mzml)$)','', $re.sub('.*/','', $name1.rstrip('.gz'))))
-    ## #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('.*/','', $name1.rstrip('.gz')))
-    #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('(?i)[.](fa|fasta|imzml|mzml)$','', $re.sub('.*/','', $name1.rstrip('.gz'))))
+    #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fasta|imzml|mzml)$','', $re.sub('.*/','', $name1.rstrip('.gz'))))
     #return $name_clean
 #end def
 #def ln_name($ds) 
     #set $ext = ''
-    #if $ds.is_of_type('mzml')
+    #if $ds.is_of_type('mzml') or $ds.is_of_type('imzml')
         #set $ext = ".mzML"
     #else if $ds.is_of_type('elib')
         #set $ext = ".elib"