# HG changeset patch
# User iuc
# Date 1665751764 0
# Node ID b55bb7e06429d721f68353d26dcf4b0546ed7e6f
# Parent  d734212462caa96517b2f11a1694441ac5685a3c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 7143af903be8405ca77d524b343e0973304be693

diff -r d734212462ca -r b55bb7e06429 cutadapt.xml
--- a/cutadapt.xml	Wed Jun 22 07:10:50 2022 +0000
+++ b/cutadapt.xml	Fri Oct 14 12:49:24 2022 +0000
@@ -18,10 +18,16 @@
 #set library_type = str($library.type)
 #if $library_type == 'paired':
     #set paired = True
+    #set input_1 = $library.input_1
+    #set input_2 = $library.input_2
+    ## Avoid the paired read input files sharing the same name, else the program still runs but 
+    ## uses inaccurate results by using only 1 of 2 files.
     #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier))
     #set read2 = re.sub('[^\w\-\s]', '_', str($library.input_2.element_identifier))
-    #set input_1 = $library.input_1
-    #set input_2 = $library.input_2
+    #if read1 == read2:
+        #set read1 = read1 + "_1"
+        #set read2 = read2 + "_2"
+    #end if
 #else if $library_type == 'paired_collection'
     #set paired = True
     #set input_1 = $library.input_1.forward
diff -r d734212462ca -r b55bb7e06429 macros.xml
--- a/macros.xml	Wed Jun 22 07:10:50 2022 +0000
+++ b/macros.xml	Fri Oct 14 12:49:24 2022 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">4.0</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@FASTQ_TYPES@">fastq.gz,fastq,fasta</token>
     <xml name="edam_ontology">
         <edam_topics>