# HG changeset patch
# User iuc
# Date 1491880676 14400
# Node ID e926afbd9e10242d3fb6ee57c1fa354aafff67ad
# Parent  da8d655e215431ab35d78bf3c10954cc6ea06864
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 2d92a777711babd19c84dfa0db806d33e386afc7-dirty

diff -r da8d655e2154 -r e926afbd9e10 hisat2.xml
--- a/hisat2.xml	Mon Apr 10 17:40:42 2017 -0400
+++ b/hisat2.xml	Mon Apr 10 23:17:56 2017 -0400
@@ -40,7 +40,7 @@
                 #if $compressed == "GZ":
                     --un-gz '$output_unaligned_reads_l'
                 #else if $compressed == "BZ2":
-                    --un-gz '$output_unaligned_reads_l'
+                    --un-bz2 '$output_unaligned_reads_l'
                 #else:
                     --un '$output_unaligned_reads_l'
                 #end if
diff -r da8d655e2154 -r e926afbd9e10 hisat2_macros.xml
--- a/hisat2_macros.xml	Mon Apr 10 17:40:42 2017 -0400
+++ b/hisat2_macros.xml	Mon Apr 10 23:17:56 2017 -0400
@@ -62,13 +62,17 @@
         #if str( $input_format.paired.unaligned_file ) == "true":
             #if $compressed == "GZ":
                 --un-conc-gz '${output_unaligned_reads_l}'
+            #else if $compressed == "BZ2":
+                --un-conc-bz2 '${output_unaligned_reads_l}'
             #else:
                 --un-conc '${output_unaligned_reads_l}'
             #end if
         #end if
         #if str( $input_format.paired.aligned_file ) == "true":
             #if $compressed == "GZ":
-                --al-conc '${output_aligned_reads_l}'
+                --al-conc-gz '${output_aligned_reads_l}'
+            #else if $compressed == "BZ2"
+                --al-conc-bz2 '${output_aligned_reads_l}'
             #else:
                 --al-conc '${output_aligned_reads_l}'
             #end if
@@ -98,7 +102,7 @@
             #else:
                 #set read1 = "input_f.fastq"
             #end if
-            ln -f -s "${input_format.paired.reads_f}" "${read1}" &&
+            ln -f -s '${input_format.paired.reads_f}' ${read1} &&
 
             #if $input_format.paired.reads_r.is_of_type("fastq.gz", "fastqsanger.gz"):
                 #set read2 = "input_r.fastq.gz"
@@ -109,7 +113,7 @@
             #else:
                 #set read2 = "input_r.fastq"
             #end if
-            ln -f -s "${input_format.paired.reads_r}" "${read2}" &&
+            ln -f -s '${input_format.paired.reads_r}' ${read2} &&
         #else if str($input_format.paired.paired_selector) == 'paired_collection':
             #if $input_format.paired.reads.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
                 #set read1 = "input_f.fastq.gz"
@@ -120,7 +124,7 @@
             #else:
                 #set read1 = "input_f.fastq"
             #end if
-            ln -s "${input_format.paired.reads.forward}" "${read1}" &&
+            ln -s '${input_format.paired.reads.forward}' ${read1} &&
 
             #if $input_format.paired.reads.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
                 #set read2 = "input_r.fastq.gz"
@@ -131,7 +135,7 @@
             #else:
                 #set read2 = "input_r.fastq"
             #end if
-            ln -s "${input_format.paired.reads.reverse}" "${read2}" &&
+            ln -s '${input_format.paired.reads.reverse}' ${read2} &&
         #else:
             #if $input_format.paired.reads.is_of_type("fastq.gz", "fastqsanger.gz"):
                 #set read1 = "input_f.fastq.gz"
@@ -142,7 +146,7 @@
             #else:
                 #set read1 = "input_f.fastq"
             #end if
-            ln -s "${input_format.paired.reads}" "${read1}" &&
+            ln -s '${input_format.paired.reads}' ${read1} &&
         #end if
 ]]>
     </token>