# HG changeset patch
# User iuc
# Date 1534950273 14400
# Node ID 7b4468117008b719c044619a7e60e3a4c5a04def
# Parent  43a7370aa0101ad9253fa940aaf8c34c30689e8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a

diff -r 43a7370aa010 -r 7b4468117008 fastq_quality_filter.xml
--- a/fastq_quality_filter.xml	Tue May 08 13:26:35 2018 -0400
+++ b/fastq_quality_filter.xml	Wed Aug 22 11:04:33 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="cshl_fastq_quality_filter" version="1.0.1" name="Filter by quality">
+<tool id="cshl_fastq_quality_filter" version="1.0.2" name="Filter by quality">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -11,6 +11,7 @@
 -v
 -o '$output'
 @FQQUAL@
+@GZIP@
     ]]></command>
 
     <inputs>
diff -r 43a7370aa010 -r 7b4468117008 macros.xml
--- a/macros.xml	Tue May 08 13:26:35 2018 -0400
+++ b/macros.xml	Wed Aug 22 11:04:33 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>