# HG changeset patch
# User jjohnson
# Date 1594137409 14400
# Node ID 2f36eba0b8779a2ab6bf54f36deb4a6364db7e64
# Parent  e37e3c4a87a985abc31421b1e4729b53ff68cb05
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"

diff -r e37e3c4a87a9 -r 2f36eba0b877 encyclopedia_walnut.xml
--- a/encyclopedia_walnut.xml	Thu Jul 02 11:10:14 2020 -0400
+++ b/encyclopedia_walnut.xml	Tue Jul 07 11:56:49 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 e37e3c4a87a9 -r 2f36eba0b877 macros.xml
--- a/macros.xml	Thu Jul 02 11:10:14 2020 -0400
+++ b/macros.xml	Tue Jul 07 11:56:49 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"