comparison hisat2.xml @ 27:a86e80d3c09c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ee1e956ad8c2841d6b4861f6b5415f68d84e6ab7"

26:0c16cad5e03b

## - once hisat is finished sort will start to merge the temporary
##   files (which should be fast also on a single thread) gives the
##   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}'

## Rename any output fastq files

#if $output_unaligned_reads_l and $output_unaligned_reads_r:
    #from os.path import splitext

            <param name="history_item" ftype="fasta" value="phiX.fa" />
            <param name="output_options_selector" value="advanced" />
            <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" />
        </test>
        <!-- Ensure paired unaligned/aligned output works -->
        <test expect_num_outputs="5">
            <param name="type" value="paired" />
            <param name="source" value="history" />

            <param name="unaligned_file" value="true" />
            <param name="aligned_file" value="true" />
            <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" />
        </test>
        <!-- Ensure fastqsanger.gz works -->
        <test expect_num_outputs="1">
            <param name="type" value="paired" />
            <param name="source" value="history" />

implementation to handle most of the operations on the FM index. In
addition to spliced alignment, HISAT handles reads involving indels and
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
license <http://www.gnu.org/licenses/gpl-3.0.html>`__, and it runs on
the command line under Linux, Mac OS X and Windows.

Running HISAT
=============

27:a86e80d3c09c

## - once hisat is finished sort will start to merge the temporary
##   files (which should be fast also on a single thread) gives the
##   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}'

## Rename any output fastq files

#if $output_unaligned_reads_l and $output_unaligned_reads_r:
    #from os.path import splitext

            <param name="history_item" ftype="fasta" value="phiX.fa" />
            <param name="output_options_selector" value="advanced" />
            <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" sort="true"/>
        </test>
        <!-- Ensure paired unaligned/aligned output works -->
        <test expect_num_outputs="5">
            <param name="type" value="paired" />
            <param name="source" value="history" />

            <param name="unaligned_file" value="true" />
            <param name="aligned_file" value="true" />
            <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" 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">
            <param name="type" value="paired" />
            <param name="source" value="history" />

implementation to handle most of the operations on the FM index. In
addition to spliced alignment, HISAT handles reads involving indels and
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 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.

Running HISAT
=============