# HG changeset patch
# User iuc
# Date 1643623950 0
# Node ID f5643712dca7ab49ba02ad10b54373dc9a759ac3
# Parent  f212134e204c185ca40c7fb1b73d3e67b0001c21
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"

diff -r f212134e204c -r f5643712dca7 artic_minion.xml
--- a/artic_minion.xml	Wed Oct 06 12:04:58 2021 +0000
+++ b/artic_minion.xml	Mon Jan 31 10:12:30 2022 +0000
@@ -34,8 +34,13 @@
             --medaka-model '$medaka_model'
             $bwa
             'name/V1'
-            '${read_file.element_identifier}'
+            ## enclose the sample name in extra single quotes because
+            ## the minion pipeline script doesn't care about passing
+            ## its arguments safely.
+            "'"'${read_file.element_identifier}'"'"
         && bgzip -f '${read_file.element_identifier}.fail.vcf'
+        ## remove enclosing single-quotes from header of output consensus fasta
+        && sed -i "1s/'${read_file.element_identifier}'/${read_file.element_identifier}/" ${read_file.element_identifier}.consensus.fasta
     ]]></command>
     <inputs>
         <param argument="--read-file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Input Read File"/>
diff -r f212134e204c -r f5643712dca7 macros.xml
--- a/macros.xml	Wed Oct 06 12:04:58 2021 +0000
+++ b/macros.xml	Mon Jan 31 10:12:30 2022 +0000
@@ -1,5 +1,6 @@
 <macros>
     <token name="@PACKAGE_VERSION@">1.2.1</token>
+    <token name="@FASTQ_FORMATS@">fastq,fastq.gz,fastqsanger,fastqsanger.gz</token>
     <xml name="citations">
         <citations>
             <citation type="bibtex">