Mercurial > repos > iuc > hisat2
changeset 27:a86e80d3c09c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ee1e956ad8c2841d6b4861f6b5415f68d84e6ab7"
| author | iuc |
|---|---|
| date | Wed, 04 Nov 2020 20:02:46 +0000 |
| parents | 0c16cad5e03b |
| children | d4b55e2beb12 |
| files | hisat2.xml |
| diffstat | 1 files changed, 6 insertions(+), 8 deletions(-) [+] |
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--- 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.