Mercurial > repos > devteam > fastq_to_fasta

changeset 4:e282bc27be9a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
author iuc
date Thu, 30 Jan 2020 13:29:38 -0500
parents 02a5f43cd5d1
children 8979c288aefb
files fastq_to_fasta.xml macros.xml
diffstat 2 files changed, 4 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- 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" />
--- 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>