# HG changeset patch
# User iuc
# Date 1604520166 0
# Node ID a86e80d3c09c543baf908c60740d2154f107ebea
# Parent  0c16cad5e03b09cd84eda43ea8db8e4a5c22f806
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ee1e956ad8c2841d6b4861f6b5415f68d84e6ab7"

diff -r 0c16cad5e03b -r a86e80d3c09c hisat2.xml
--- a/hisat2.xml	Sat Aug 03 06:09:26 2019 -0400
+++ b/hisat2.xml	Wed Nov 04 20:02:46 2020 +0000
@@ -328,7 +328,7 @@
 ##   sorted output to view which only compresses the files (now
 ##   using full parallelism again)
 
-| samtools sort -l 0 -O bam | samtools view -O bam -@ \${GALAXY_SLOTS:-1} -o '${output_alignments}'
+| samtools sort -l 0 -T "\${TMPDIR:-.}" -O bam | samtools view -O bam -@ \${GALAXY_SLOTS:-1} -o '${output_alignments}'
 
 ## Rename any output fastq files
 
@@ -787,7 +787,7 @@
             <param name="unaligned_file" value="true" />
             <param name="history_item" ftype="fasta" value="phiX.fa" />
             <param name="input_1" ftype="fasta" value="test_unaligned_reads.fasta" />
-            <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" />
+            <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" sort="true"/>
         </test>
         <!-- Ensure paired unaligned/aligned output works -->
         <test expect_num_outputs="5">
@@ -799,8 +799,8 @@
             <param name="history_item" ftype="fasta" value="phiX.fa" />
             <param name="input_1" ftype="fasta" value="test_unaligned_reads.fasta" />
             <param name="input_2" ftype="fasta" value="test_unaligned_reads.fasta" />
-            <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" />
-            <output name="output_unaligned_reads_r" file="test_unaligned_reads.fasta" />
+            <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" sort="true"/>
+            <output name="output_unaligned_reads_r" file="test_unaligned_reads.fasta" sort="true"/>
         </test>
         <!-- Ensure fastqsanger.gz works -->
         <test expect_num_outputs="1">
@@ -932,10 +932,8 @@
 supports a paired-end alignment mode. Multiple processors can be used
 simultaneously to achieve greater alignment speed. HISAT outputs
 alignments in `SAM <http://samtools.sourceforge.net/SAM1.pdf>`__ format,
-enabling interoperation with a large number of other tools (e.g.
-`SAMtools <http://samtools.sourceforge.net>`__,
-`GATK <http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit>`__)
-that use SAM. HISAT is distributed under the `GPLv3
+enabling interoperation with a large number of other tools that use SAM.
+HISAT is distributed under the `GPLv3
 license <http://www.gnu.org/licenses/gpl-3.0.html>`__, and it runs on
 the command line under Linux, Mac OS X and Windows.