# HG changeset patch
# User iuc
# Date 1580408910 0
# Node ID 2ff4f91ff5641581c888d715eecfe9820a68112b
# Parent  b962b4efec19f50dabf3cb6d926ad32f2b63c231
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit 4c002e52261da2e7609735883d91fa1610ce6ce7"

diff -r b962b4efec19 -r 2ff4f91ff564 fastx_trimmer.xml
--- a/fastx_trimmer.xml	Wed Aug 22 11:04:02 2018 -0400
+++ b/fastx_trimmer.xml	Thu Jan 30 18:28:30 2020 +0000
@@ -1,16 +1,18 @@
-<tool id="cshl_fastx_trimmer" version="1.0.2" name="Trim sequences">
+<tool id="cshl_fastx_trimmer" version="1.0.2+galaxy0" name="Trim sequences">
     <description></description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="requirements">
+        <requirement type="package" version="1.0.8">bzip2</requirement>
+    </expand>
     <command detect_errors="exit_code"><![CDATA[
 @CATS@ fastx_trimmer -v
 -f $first
 -l $last
--o '$output'
 @FQQUAL@
 @GZIP@
+> '$output'
     ]]></command>
     <inputs>
         <expand macro="fastx_input" />
@@ -36,12 +38,19 @@
             <output name="output" ftype="fastqsolexa" file="fastx_trimmer2.out" />
         </test>
         <test>
-            <!-- Trim a FASTQ.gz file  and output FASTQ.gz -->
+            <!-- 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>
+        <test>
+            <!-- Trim a FASTQ.bz2 file and output FASTQ.bz2 -->
+            <param name="input" value="fastx_trimmer2.fastq.bz2" ftype="fastqsanger.bz2"/>
+            <param name="first" value="1"/>
+            <param name="last" value="27"/>
+            <output name="output" ftype="fastqsanger.bz2" decompress="true" file="fastx_trimmer2.out.bz2" />
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**
diff -r b962b4efec19 -r 2ff4f91ff564 macros.xml
--- a/macros.xml	Wed Aug 22 11:04:02 2018 -0400
+++ b/macros.xml	Thu Jan 30 18:28:30 2020 +0000
@@ -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>
diff -r b962b4efec19 -r 2ff4f91ff564 test-data/fastx_trimmer2.fastq.bz2
Binary file test-data/fastx_trimmer2.fastq.bz2 has changed
diff -r b962b4efec19 -r 2ff4f91ff564 test-data/fastx_trimmer2.out.bz2
Binary file test-data/fastx_trimmer2.out.bz2 has changed
diff -r b962b4efec19 -r 2ff4f91ff564 test-data/fastx_trimmer2.out.gz
Binary file test-data/fastx_trimmer2.out.gz has changed