# HG changeset patch
# User jjohnson
# Date 1594137362 14400
# Node ID 602d01de42b44afbb5b826d9a698a543040c69f0
# Parent  7d58a052411a9d5f25858fcf9b38c766cb127876
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"

diff -r 7d58a052411a -r 602d01de42b4 encyclopedia_prosit_csv_to_library.xml
--- a/encyclopedia_prosit_csv_to_library.xml	Thu Jul 02 11:07:21 2020 -0400
+++ b/encyclopedia_prosit_csv_to_library.xml	Tue Jul 07 11:56:02 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 -prositcsvtolibrary
         -i '$i'
         -f '$f'
diff -r 7d58a052411a -r 602d01de42b4 macros.xml
--- a/macros.xml	Thu Jul 02 11:07:21 2020 -0400
+++ b/macros.xml	Tue Jul 07 11:56:02 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"