# HG changeset patch
# User iuc
# Date 1664402741 0
# Node ID 8b330a577046d97a1a7549764966cc00a9f1e362
# Parent  f4394bbdf43354ba359b32e64485f71a805bf234
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit 2abcba81319a6f37dfd31270211bd2ab35104510

diff -r f4394bbdf433 -r 8b330a577046 get_organelle_from_reads.xml
--- a/get_organelle_from_reads.xml	Mon Aug 22 09:59:03 2022 +0000
+++ b/get_organelle_from_reads.xml	Wed Sep 28 22:05:41 2022 +0000
@@ -21,7 +21,7 @@
                 #set ext = '.fastq.gz'
             #end if
             #set $in1 = $fastq_input.fastq_input1
-            #set $in1_name = re.sub('[^\w\-\s]', '_', str($fastq_input.fastq_input1.name)) + $ext
+            #set $in1_name = re.sub('[^\w\-\.]', '_', str($fastq_input.fastq_input1.name)) + $ext
             ln -s '$in1' '$in1_name' &&
         #else if str($fastq_input.fastq_input_selector) == 'paired':
             #if $fastq_input.fastq_input1.ext.endswith('.gz'):
@@ -29,8 +29,8 @@
             #end if
             #set $in1 = $fastq_input.fastq_input1
             #set $in2 = $fastq_input.fastq_input2
-            #set $in1_name = re.sub('[^\w\-\s\._]', '_', str($fastq_input.fastq_input1.name)) + $ext
-            #set $in2_name = re.sub('[^\w\-\s\._]', '_', str($fastq_input.fastq_input2.name)) + $ext
+            #set $in1_name = re.sub('[^\w\-\.]', '_', str($fastq_input.fastq_input1.name)) + $ext
+            #set $in2_name = re.sub('[^\w\-\.]', '_', str($fastq_input.fastq_input2.name)) + $ext
             ln -s '$in1' '$in1_name' &&
             ln -s '$in2' '$in2_name' &&
         #else if str($fastq_input.fastq_input_selector) == 'paired_collection':
@@ -39,8 +39,8 @@
             #end if
             #set $in1 = $fastq_input.paired_input.forward
             #set $in2 = $fastq_input.paired_input.reverse
-            #set $in1_name = re.sub('[^\w\-\s\._]', '_', str($fastq_input.paired_input.name)) + $ext
-            #set $in2_name = re.sub('[^\w\-\s\._]', '_', str("%s_%s" % ($fastq_input.paired_input.name, "R2"))) + $ext
+            #set $in1_name = re.sub('[^\w\-\.]', '_', str($fastq_input.paired_input.name)) + $ext
+            #set $in2_name = re.sub('[^\w\-\.]', '_', str("%s_%s" % ($fastq_input.paired_input.name, "R2"))) + $ext
             ln -s '$in1' '$in1_name' &&
             ln -s '$in2' '$in2_name' &&
         #end if