# HG changeset patch
# User galaxy-australia
# Date 1668579555 0
# Node ID 03acc0e3772eecfefcf56bc2f3b8851f0dee20e6
# Parent  41f5b4a4eac092a6b977df63006da39512f09563
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit db087ed782a52833a02df3bfef0793b4dd909081"

diff -r 41f5b4a4eac0 -r 03acc0e3772e hifiadapterfilt.xml
--- a/hifiadapterfilt.xml	Wed Sep 14 02:37:39 2022 +0000
+++ b/hifiadapterfilt.xml	Wed Nov 16 06:19:15 2022 +0000
@@ -10,17 +10,15 @@
     <expand macro="stdio" />
     <command><![CDATA[
 
-	    @CLEAN_EXT@
-
 	    #if $input_file.is_of_type("fastq.gz"):
-	    	#set $inputfile = $clean_ext($input_file.element_identifier) + '.fastq.gz'
-		#set prefix = $clean_ext($input_file.element_identifier)
+	    	#set $inputfile = "input" + '.fastq.gz'
+		#set prefix = "input"
 	    #elif $input_file.is_of_type("fastq"):
-	        #set $inputfile = $clean_ext($input_file.element_identifier) + '.fastq'
-	        #set prefix = $clean_ext($input_file.element_identifier)
+	        #set $inputfile = "input" + '.fastq'
+	        #set prefix = "input"
 	    #elif $input_file.is_of_type("bam"):
-	    	#set $inputfile = $clean_ext($input_file.element_identifier) + '.bam'
-                #set prefix = $clean_ext($input_file.element_identifier)
+	    	#set $inputfile = "input" + '.bam'
+                #set prefix = "input"
 	    #end if
 	    ln -s '${input_file}' '${inputfile}' &&
 
@@ -86,7 +84,7 @@
 
 **Contributor**
 
-Galaxy Australia wrapped the HiFiadapterFilt: the original software is available in this Github repository `Github <https://github.com/sheinasim/HiFiAdapterFilt>`_.
+Galaxy Australia wrapped the HiFiadapterFilt: the original software is available in this `Github repository <https://github.com/sheinasim/HiFiAdapterFilt>`_.
 
 **References**
 	    
diff -r 41f5b4a4eac0 -r 03acc0e3772e macros.xml
--- a/macros.xml	Wed Sep 14 02:37:39 2022 +0000
+++ b/macros.xml	Wed Nov 16 06:19:15 2022 +0000
@@ -14,16 +14,4 @@
          <exit_code range="1:"  level="fatal" description="Error" />
       </stdio>
     </xml>	
-    <token name="@CLEAN_EXT@">
-        <![CDATA[
-        #from os.path import splitext
-        #import re
-        #def clean_ext($identifier)
-            #while $identifier.endswith(('.fq','.fastq', '.fastq.gz','.bam'))
-                #set $identifier = splitext($identifier)[0]
-            #end while
-$identifier#slurp
-        #end def
-        ]]>
-    </token>
 </macros>