# HG changeset patch
# User iuc
# Date 1580408778 0
# Node ID 5dbca5fbdc45459c30a216e8e71de0dc31359907
# Parent  4498e994e31b002cc89364363781fec7b09d35da
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit 4c002e52261da2e7609735883d91fa1610ce6ce7"

diff -r 4498e994e31b -r 5dbca5fbdc45 fastq_to_fasta.xml
--- a/fastq_to_fasta.xml	Wed Aug 22 11:02:27 2018 -0400
+++ b/fastq_to_fasta.xml	Thu Jan 30 18:26:18 2020 +0000
@@ -8,9 +8,8 @@
 @CATS@ fastq_to_fasta
 $SKIPN
 $RENAMESEQ
--o '$output'
 -v @FQQUAL@
-@GZIP@
+@GZIP@ > '$output'
     ]]></command>
     <inputs>
         <expand macro="fastq_input" />
diff -r 4498e994e31b -r 5dbca5fbdc45 macros.xml
--- a/macros.xml	Wed Aug 22 11:02:27 2018 -0400
+++ b/macros.xml	Thu Jan 30 18:26:18 2020 +0000
@@ -21,7 +21,9 @@
     <token name="@GZIP@">
         <![CDATA[
             #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
-                -z
+                | gzip -c
+            #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
+                | bzip2 -c
             #end if
         ]]>
     </token>