# HG changeset patch
# User jjohnson
# Date 1594137454 14400
# Node ID 91343296dbff81acf8724dab0b7fcddb8c68d187
# Parent  b9a2af09b8286b3ab6a44128c7aae8fc739ef978
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"

diff -r b9a2af09b828 -r 91343296dbff encyclopedia_fasta_to_prosit_csv.xml
--- a/encyclopedia_fasta_to_prosit_csv.xml	Thu Jul 02 11:14:11 2020 -0400
+++ b/encyclopedia_fasta_to_prosit_csv.xml	Tue Jul 07 11:57:34 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[
         EncyclopeDIA -convert -fastatoprositcsv 
         -i '$i'
         -minCharge $minCharge
diff -r b9a2af09b828 -r 91343296dbff macros.xml
--- a/macros.xml	Thu Jul 02 11:14:11 2020 -0400
+++ b/macros.xml	Tue Jul 07 11:57:34 2020 -0400
@@ -31,14 +31,12 @@
     #end if
 #end def
 #def clean($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"