# HG changeset patch
# User thanhlv
# Date 1645657022 0
# Node ID 4d3e54bace617565a8219d10b207238dacda1e90
# Parent  d1df295495a9ddf184ef08288f8be02e41297e85
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 5eecf52d4fc6e1875235924568afde1d90789cb0-dirty"

diff -r d1df295495a9 -r 4d3e54bace61 metamlst.xml
--- a/metamlst.xml	Wed Feb 23 10:17:46 2022 +0000
+++ b/metamlst.xml	Wed Feb 23 22:57:02 2022 +0000
@@ -42,10 +42,8 @@
             #end if
             ln -f -s '${library.input_2}' ${read2} &&
         #else if str($library.type) == 'paired_collection':
-                #set pe_input_1 = $library.input_1.forward
-                #set pe_input_2 = $library.input_1.reverse
-                #set name_1 = re.sub('[^\w\-\s]', '_', str($library.pe_input_1.name)) + "_1"
-                #set name_2 = re.sub('[^\w\-\s]', '_', str($library.pe_input_2.name)) + "_2"
+                #set name_1 = re.sub('[^\w\-\s]', '_', str($library.input_1.forward.name)) + "_1"
+                #set name_2 = re.sub('[^\w\-\s]', '_', str($library.input_1.reverse.name)) + "_2"
             #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
                 #set read1 = $name_1 + '.fastq.gz'
                 #set compressed = "GZ"
@@ -151,8 +149,9 @@
             cat ./out/*.out > log.txt &&
         #end if
         #if $write_sequences
-            cat ./out/*.nfo > sequences.txt
+            cat ./out/*.nfo > sequences.txt && 
         #end if
+        echo "Finished"
     ]]>    </command>
 
     <inputs>