# HG changeset patch
# User iuc
# Date 1534496766 14400
# Node ID b98f3fa516a30600d60e25fc9f4091f83a92fc46
# Parent  bbb007a39ac24a710b5adaa39eefcfcbc52906cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit f3f313cb59922b945ac9587ff718b231d0f8db5c

diff -r bbb007a39ac2 -r b98f3fa516a3 fastx_trimmer.xml
--- a/fastx_trimmer.xml	Tue May 08 13:28:34 2018 -0400
+++ b/fastx_trimmer.xml	Fri Aug 17 05:06:06 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="cshl_fastx_trimmer" version="1.0.1" name="Trim sequences">
+<tool id="cshl_fastx_trimmer" version="1.0.2" name="Trim sequences">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -10,6 +10,11 @@
 -l $last
 -o '$output'
 @FQQUAL@
+
+#if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
+    -z
+#end if
+
     ]]></command>
     <inputs>
         <expand macro="fastx_input" />
@@ -34,6 +39,13 @@
             <param name="last" value="27"/>
             <output name="output" ftype="fastqsolexa" file="fastx_trimmer2.out" />
         </test>
+        <test>
+            <!-- Trim a FASTQ.gz file  and output FASTQ.gz -->
+            <param name="input" value="fastx_trimmer2.fastq.gz" ftype="fastqsanger.gz"/>
+            <param name="first" value="1"/>
+            <param name="last" value="27"/>
+            <output name="output" ftype="fastqsanger.gz" decompress="true" file="fastx_trimmer2.out.gz" />
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**
diff -r bbb007a39ac2 -r b98f3fa516a3 macros.xml
--- a/macros.xml	Tue May 08 13:28:34 2018 -0400
+++ b/macros.xml	Fri Aug 17 05:06:06 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:
diff -r bbb007a39ac2 -r b98f3fa516a3 test-data/fastx_trimmer2.fastq.gz
Binary file test-data/fastx_trimmer2.fastq.gz has changed
diff -r bbb007a39ac2 -r b98f3fa516a3 test-data/fastx_trimmer2.out.gz
Binary file test-data/fastx_trimmer2.out.gz has changed