Repository revision
29:26371a1df031

Repository 'hisat2'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/hisat2

HISAT2 tool metadata
Miscellaneous
HISAT2
A fast and sensitive alignment program
hisat2
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7
2.1.0+galaxy7
hisat2 --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy6
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy5
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy4
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy3
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.5.2
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.5.1
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.5
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3.3
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3.2
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3.1
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/1.0.1
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/1.0.0
hisat2
Requirements (dependencies defined in the <requirements> tag set)
name version type
hisat2 2.1.0 package
samtools 1.11 package
seqtk 1.3 package
Functional tests
name inputs outputs required files
Test-1 reference_genome|history_item: phiX.fa
reference_genome|source: history
library|input_1: hisat_input_1_forward.fastq
library|input_2: hisat_input_1_reverse.fastq
library|type: paired
adv|reporting_options|reporting_options_selector: advanced
name: value
phiX.fa
hisat_input_1_forward.fastq
hisat_input_1_reverse.fastq
value
Test-2 reference_genome|history_item: phiX.fa
reference_genome|source: history
library|input_1: hisat_input_1_forward.fastq
library|input_2: hisat_input_1_reverse.fastq
library|type: paired
name: value
phiX.fa
hisat_input_1_forward.fastq
hisat_input_1_reverse.fastq
value
Test-3 reference_genome|source: indexed
library|input_1: hisat_input_1_forward.fastq
library|input_2: hisat_input_1_reverse.fastq
library|type: paired
name: value
hisat_input_1_forward.fastq
hisat_input_1_reverse.fastq
value
Test-4 reference_genome|history_item: phiX.fa
reference_genome|source: history
library|input_1: hisat_input_2_forward.fastq
library|input_2: hisat_input_2_reverse.fastq
library|type: paired
adv|input_options|trim5: 15
adv|input_options|trim3: 15
adv|input_options|input_options_selector: advanced
name: value
phiX.fa
hisat_input_2_forward.fastq
hisat_input_2_reverse.fastq
value
Test-5 reference_genome|history_item: phiX.fa
reference_genome|source: history
library|input_1: hisat_input_2_forward.fastq
library|input_2: hisat_input_2_reverse.fastq
library|paired_options|no_mixed: True
library|paired_options|no_discordant: True
library|paired_options|paired_options_selector: advanced
library|type: paired
adv|input_options|trim5: 15
adv|input_options|trim3: 15
adv|input_options|input_options_selector: advanced
name: value
phiX.fa
hisat_input_2_forward.fastq
hisat_input_2_reverse.fastq
value
Test-6 reference_genome|history_item: phiX.fa
reference_genome|source: history
library|input_1: test_unaligned_reads.fasta
library|type: single
adv|output_options|unaligned_file: True
adv|output_options|output_options_selector: advanced
name: value
phiX.fa
test_unaligned_reads.fasta
value
Test-7 reference_genome|history_item: phiX.fa
reference_genome|source: history
library|input_1: test_unaligned_reads.fasta
library|input_2: test_unaligned_reads.fasta
library|type: paired
adv|output_options|unaligned_file: True
adv|output_options|aligned_file: True
adv|output_options|output_options_selector: advanced
name: value
name: value
phiX.fa
test_unaligned_reads.fasta
value
Test-8 reference_genome|history_item: phiX.fa
reference_genome|source: history
library|input_1: hisat_input_2_forward.fastq.gz
library|input_2: hisat_input_2_reverse.fastq.gz
library|paired_options|no_mixed: True
library|paired_options|no_discordant: True
library|paired_options|paired_options_selector: advanced
library|type: paired
adv|input_options|trim5: 15
adv|input_options|trim3: 15
adv|input_options|input_options_selector: advanced
name: value
phiX.fa
hisat_input_2_forward.fastq.gz
hisat_input_2_reverse.fastq.gz
value
Test-9 reference_genome|history_item: phiX.fa
reference_genome|source: history
library|input_1: hisat_input_2_forward.fastq.bz2
library|input_2: hisat_input_2_reverse.fastq.bz2
library|paired_options|no_mixed: True
library|paired_options|no_discordant: True
library|paired_options|paired_options_selector: advanced
library|type: paired
adv|input_options|trim5: 15
adv|input_options|trim3: 15
adv|input_options|input_options_selector: advanced
name: value
phiX.fa
hisat_input_2_forward.fastq.bz2
hisat_input_2_reverse.fastq.bz2
value
Test-10 reference_genome|history_item: phiX.fa
reference_genome|source: history
library|input_1: hisat_input_1_forward.fastq
library|input_2: hisat_input_1_reverse.fastq
library|rna_strandness: FR
library|type: paired
name: value
phiX.fa
hisat_input_1_forward.fastq
hisat_input_1_reverse.fastq
value
Test-11 reference_genome|history_item: phiX.fa
reference_genome|source: history
library|input_1: hisat_input_1_forward.fastq
library|rna_strandness: R
library|type: single
sum|new_summary: True
sum|summary_file: True
name: value
phiX.fa
hisat_input_1_forward.fastq
value
Test-12 reference_genome|history_item: phiX.fa
reference_genome|source: history
library|input_1: hisat_input_1_interleaved.fastq
library|type: paired_interleaved
name: value
phiX.fa
hisat_input_1_interleaved.fastq
value
Test-13 reference_genome|history_item: phiX.fa
reference_genome|source: history
library|input_1: hisat_input_1_interleaved.fastq.bz2
library|type: paired_interleaved
name: value
phiX.fa
hisat_input_1_interleaved.fastq.bz2
value
Test-14 reference_genome|history_item: phiX.fa
reference_genome|source: history
library|input_1: hisat_input_1_interleaved.fastq.gz
library|type: paired_interleaved
name: value
phiX.fa
hisat_input_1_interleaved.fastq.gz
value
Test-15 reference_genome|history_item: phiX.fa
reference_genome|source: history
library|input_1: hisat_input_1_interleaved.fasta
library|type: paired_interleaved
name: value
phiX.fa
hisat_input_1_interleaved.fasta
value
Test-16 reference_genome|history_item: phiX.fa
reference_genome|source: history
library|input_1: hisat_input_1_split_forward.fastq
library|rna_strandness: R
library|type: single
adv|spliced_options|novel_splicesite_outfile: True
adv|spliced_options|spliced_options_selector: advanced
name: value
name: value
phiX.fa
hisat_input_1_split_forward.fastq
value
Test-17 reference_genome|history_item: phiX.fa
reference_genome|source: history
library|input_1: hisat_input_1_interleaved.fastq.bz2
library|type: paired_interleaved
adv|sam_options|no_unal: True
adv|sam_options|read_groups|read_groups_0|rg: BC:test1
adv|sam_options|read_groups|read_groups_1|rg: CN:test2
adv|sam_options|read_groups|rg_labels: Yes
adv|sam_options|chr_text: --add-chrname
adv|sam_options|omit_sec_seq: True
adv|sam_options|sam_options_selector: advanced
name: value
phiX.fa
hisat_input_1_interleaved.fastq.bz2
value