# HG changeset patch
# User iuc
# Date 1580408978 18000
# Node ID e282bc27be9ad6e7221f522c62778f207ff8179c
# Parent  02a5f43cd5d171e5d5c8988862b77ffa7f88315b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit 4c002e52261da2e7609735883d91fa1610ce6ce7"

diff -r 02a5f43cd5d1 -r e282bc27be9a fastq_to_fasta.xml
--- a/fastq_to_fasta.xml	Wed Aug 22 11:04:47 2018 -0400
+++ b/fastq_to_fasta.xml	Thu Jan 30 13:29:38 2020 -0500
@@ -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 02a5f43cd5d1 -r e282bc27be9a macros.xml
--- a/macros.xml	Wed Aug 22 11:04:47 2018 -0400
+++ b/macros.xml	Thu Jan 30 13:29:38 2020 -0500
@@ -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>