# HG changeset patch
# User iuc
# Date 1534950147 14400
# Node ID 4498e994e31b002cc89364363781fec7b09d35da
# Parent  44ed3f74ea7ad2d0e1fcff2df7dc4f4070b39f6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a

diff -r 44ed3f74ea7a -r 4498e994e31b fastq_to_fasta.xml
--- a/fastq_to_fasta.xml	Tue May 08 12:50:22 2018 -0400
+++ b/fastq_to_fasta.xml	Wed Aug 22 11:02:27 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA" version="1.0.1">
+<tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA" version="1.0.2">
     <description>converter from FASTX-toolkit</description>
     <macros>
         <import>macros.xml</import>
@@ -10,6 +10,7 @@
 $RENAMESEQ
 -o '$output'
 -v @FQQUAL@
+@GZIP@
     ]]></command>
     <inputs>
         <expand macro="fastq_input" />
diff -r 44ed3f74ea7a -r 4498e994e31b macros.xml
--- a/macros.xml	Tue May 08 12:50:22 2018 -0400
+++ b/macros.xml	Wed Aug 22 11:02:27 2018 -0400
@@ -2,7 +2,7 @@
 <macros>
     <token name="@CATS@">
         #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
-            zcat -f '$input' |
+            gunzip -c -f '$input' |
         #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
             bzcat -f '$input' |
         #else:
@@ -18,6 +18,13 @@
             #end if
         ]]>
     </token>
+    <token name="@GZIP@">
+        <![CDATA[
+            #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
+                -z
+            #end if
+        ]]>
+    </token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">fastx_toolkit</requirement>