# HG changeset patch
# User iuc
# Date 1626630620 0
# Node ID 4a826a536dcbc6e4f75fd3700a5ca2a0faa066a2
# Parent  aac14659f53c8fb276f3f4ce8d7bd43540e14a3f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 591f9e8e46a9429bf28b64bae6f27f744bf08b3c"

diff -r aac14659f53c -r 4a826a536dcb hisat2.xml
--- a/hisat2.xml	Mon Jan 25 17:28:43 2021 +0000
+++ b/hisat2.xml	Sun Jul 18 17:50:20 2021 +0000
@@ -1,11 +1,11 @@
-<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy7" profile="17.01">
+<tool id="hisat2" name="HISAT2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
     <description>A fast and sensitive alignment program</description>
     <macros>
         <import>hisat2_macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="2.1.0">hisat2</requirement>
-        <requirement type="package" version="1.11">samtools</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">hisat2</requirement>
+        <requirement type="package" version="1.12">samtools</requirement>
         <requirement type="package" version="1.3">seqtk</requirement>
     </requirements>
     <stdio>
@@ -15,6 +15,7 @@
     </stdio>
     <version_command>hisat2 --version</version_command>
     <command><![CDATA[
+set -o pipefail;    
 ## Prepare HISAT2 index
 
 #if $reference_genome.source == "history":
@@ -96,24 +97,20 @@
     ln -s '${library.input_1.reverse}' ${read2} &&
 #elif str( $library.type ) == "paired_interleaved":
     #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
-        #set interleaved_reads = "input_f.fastq.gz"
         #set compressed = "GZ"
     #elif $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-        #set interleaved_reads = "input_f.fastq.bz2"
         #set compressed = "BZ2"
     #elif $library.input_1.is_of_type('fasta'):
         #set reads_are_fastq = False
-        #set interleaved_reads = "input_f.fasta"
-    #else:
-        #set interleaved_reads = "input_f.fastq"
     #end if
-    ln -f -s '${library.input_1}' ${interleaved_reads} &&
+    #set read1 = "input_f.fastq" if reads_are_fastq else "input_f.fasta"
+    #set read2 = "input_r.fastq" if reads_are_fastq else "input_r.fasta"
     #if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-        #set read1 = "<(bzcat input_f.fastq.bz2 | seqtk seq -1 /dev/stdin)"
-        #set read2 = "<(bzcat input_f.fastq.bz2 | seqtk seq -2 /dev/stdin)"
-    #else:
-        #set read1 = "<(seqtk seq -1 %s)" % $interleaved_reads
-        #set read2 = "<(seqtk seq -2 %s)" % $interleaved_reads
+        bzcat '${library.input_1}' | seqtk seq -1 /dev/stdin > $read1 &&
+        bzcat '${library.input_1}' | seqtk seq -2 /dev/stdin > $read2 &&
+    #else
+        seqtk seq -1 '${library.input_1}' > $read1 &&
+        seqtk seq -2 '${library.input_1}' > $read2 &&
     #end if
 #else:
     #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
@@ -348,7 +345,7 @@
 ##   sorted output to view which only compresses the files (now
 ##   using full parallelism again)
 
-| samtools sort -l 0 -T "\${TMPDIR:-.}" -O bam | samtools view -O bam -@ \${GALAXY_SLOTS:-1} -o '${output_alignments}'
+| samtools sort --no-PG -l 0 -T "\${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ \${GALAXY_SLOTS:-1} -o '${output_alignments}'
 
 ## Rename any output fastq files
 
diff -r aac14659f53c -r 4a826a536dcb hisat2_macros.xml
--- a/hisat2_macros.xml	Mon Jan 25 17:28:43 2021 +0000
+++ b/hisat2_macros.xml	Sun Jul 18 17:50:20 2021 +0000
@@ -1,4 +1,7 @@
 <macros>
+    <token name="@TOOL_VERSION@">2.2.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    
     <xml name="paired_end_options">
 
         <param name="rna_strandness" argument="--rna-strandness" type="select" label="Specify strand information"
diff -r aac14659f53c -r 4a826a536dcb test-data/hisat_output_5.bam
Binary file test-data/hisat_output_5.bam has changed
diff -r aac14659f53c -r 4a826a536dcb test-data/hisat_output_spliced_1.bam
Binary file test-data/hisat_output_spliced_1.bam has changed