Mercurial > repos > iuc > hisat2
comparison hisat2.xml @ 27:a86e80d3c09c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ee1e956ad8c2841d6b4861f6b5415f68d84e6ab7"
author | iuc |
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date | Wed, 04 Nov 2020 20:02:46 +0000 |
parents | 0c16cad5e03b |
children | d4b55e2beb12 |
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26:0c16cad5e03b | 27:a86e80d3c09c |
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326 ## - once hisat is finished sort will start to merge the temporary | 326 ## - once hisat is finished sort will start to merge the temporary |
327 ## files (which should be fast also on a single thread) gives the | 327 ## files (which should be fast also on a single thread) gives the |
328 ## sorted output to view which only compresses the files (now | 328 ## sorted output to view which only compresses the files (now |
329 ## using full parallelism again) | 329 ## using full parallelism again) |
330 | 330 |
331 | samtools sort -l 0 -O bam | samtools view -O bam -@ \${GALAXY_SLOTS:-1} -o '${output_alignments}' | 331 | samtools sort -l 0 -T "\${TMPDIR:-.}" -O bam | samtools view -O bam -@ \${GALAXY_SLOTS:-1} -o '${output_alignments}' |
332 | 332 |
333 ## Rename any output fastq files | 333 ## Rename any output fastq files |
334 | 334 |
335 #if $output_unaligned_reads_l and $output_unaligned_reads_r: | 335 #if $output_unaligned_reads_l and $output_unaligned_reads_r: |
336 #from os.path import splitext | 336 #from os.path import splitext |
785 <param name="history_item" ftype="fasta" value="phiX.fa" /> | 785 <param name="history_item" ftype="fasta" value="phiX.fa" /> |
786 <param name="output_options_selector" value="advanced" /> | 786 <param name="output_options_selector" value="advanced" /> |
787 <param name="unaligned_file" value="true" /> | 787 <param name="unaligned_file" value="true" /> |
788 <param name="history_item" ftype="fasta" value="phiX.fa" /> | 788 <param name="history_item" ftype="fasta" value="phiX.fa" /> |
789 <param name="input_1" ftype="fasta" value="test_unaligned_reads.fasta" /> | 789 <param name="input_1" ftype="fasta" value="test_unaligned_reads.fasta" /> |
790 <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" /> | 790 <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" sort="true"/> |
791 </test> | 791 </test> |
792 <!-- Ensure paired unaligned/aligned output works --> | 792 <!-- Ensure paired unaligned/aligned output works --> |
793 <test expect_num_outputs="5"> | 793 <test expect_num_outputs="5"> |
794 <param name="type" value="paired" /> | 794 <param name="type" value="paired" /> |
795 <param name="source" value="history" /> | 795 <param name="source" value="history" /> |
797 <param name="unaligned_file" value="true" /> | 797 <param name="unaligned_file" value="true" /> |
798 <param name="aligned_file" value="true" /> | 798 <param name="aligned_file" value="true" /> |
799 <param name="history_item" ftype="fasta" value="phiX.fa" /> | 799 <param name="history_item" ftype="fasta" value="phiX.fa" /> |
800 <param name="input_1" ftype="fasta" value="test_unaligned_reads.fasta" /> | 800 <param name="input_1" ftype="fasta" value="test_unaligned_reads.fasta" /> |
801 <param name="input_2" ftype="fasta" value="test_unaligned_reads.fasta" /> | 801 <param name="input_2" ftype="fasta" value="test_unaligned_reads.fasta" /> |
802 <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" /> | 802 <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" sort="true"/> |
803 <output name="output_unaligned_reads_r" file="test_unaligned_reads.fasta" /> | 803 <output name="output_unaligned_reads_r" file="test_unaligned_reads.fasta" sort="true"/> |
804 </test> | 804 </test> |
805 <!-- Ensure fastqsanger.gz works --> | 805 <!-- Ensure fastqsanger.gz works --> |
806 <test expect_num_outputs="1"> | 806 <test expect_num_outputs="1"> |
807 <param name="type" value="paired" /> | 807 <param name="type" value="paired" /> |
808 <param name="source" value="history" /> | 808 <param name="source" value="history" /> |
930 implementation to handle most of the operations on the FM index. In | 930 implementation to handle most of the operations on the FM index. In |
931 addition to spliced alignment, HISAT handles reads involving indels and | 931 addition to spliced alignment, HISAT handles reads involving indels and |
932 supports a paired-end alignment mode. Multiple processors can be used | 932 supports a paired-end alignment mode. Multiple processors can be used |
933 simultaneously to achieve greater alignment speed. HISAT outputs | 933 simultaneously to achieve greater alignment speed. HISAT outputs |
934 alignments in `SAM <http://samtools.sourceforge.net/SAM1.pdf>`__ format, | 934 alignments in `SAM <http://samtools.sourceforge.net/SAM1.pdf>`__ format, |
935 enabling interoperation with a large number of other tools (e.g. | 935 enabling interoperation with a large number of other tools that use SAM. |
936 `SAMtools <http://samtools.sourceforge.net>`__, | 936 HISAT is distributed under the `GPLv3 |
937 `GATK <http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit>`__) | |
938 that use SAM. HISAT is distributed under the `GPLv3 | |
939 license <http://www.gnu.org/licenses/gpl-3.0.html>`__, and it runs on | 937 license <http://www.gnu.org/licenses/gpl-3.0.html>`__, and it runs on |
940 the command line under Linux, Mac OS X and Windows. | 938 the command line under Linux, Mac OS X and Windows. |
941 | 939 |
942 Running HISAT | 940 Running HISAT |
943 ============= | 941 ============= |