Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
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 (this tool) |
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 | 1.9 | package |
seqtk | 1.3 | package |
Functional tests |
name | inputs | outputs | required files |
Test-1 |
reference_genome|history_item: phiX.fa library|input_2: hisat_input_1_reverse.fastq library|input_1: hisat_input_1_forward.fastq library|type: paired reference_genome|source: history |
attributes: name |
phiX.fa hisat_input_1_forward.fastq hisat_input_1_reverse.fastq name |
Test-2 |
reference_genome|history_item: phiX.fa library|input_2: hisat_input_1_reverse.fastq library|input_1: hisat_input_1_forward.fastq library|type: paired reference_genome|source: history |
attributes: name |
phiX.fa hisat_input_1_forward.fastq hisat_input_1_reverse.fastq name |
Test-3 |
library|input_2: hisat_input_1_reverse.fastq library|input_1: hisat_input_1_forward.fastq library|type: paired reference_genome|source: indexed |
attributes: name |
hisat_input_1_forward.fastq hisat_input_1_reverse.fastq name |
Test-4 |
library|input_2: hisat_input_2_reverse.fastq library|input_1: hisat_input_2_forward.fastq reference_genome|history_item: phiX.fa library|type: paired reference_genome|source: history adv|input_options|input_options_selector: advanced adv|input_options|trim5: 15 adv|input_options|trim3: 15 |
attributes: name |
phiX.fa hisat_input_2_forward.fastq hisat_input_2_reverse.fastq name |
Test-5 |
library|input_2: hisat_input_2_reverse.fastq library|input_1: hisat_input_2_forward.fastq library|paired_options|no_discordant: True library|paired_options|paired_options_selector: advanced library|paired_options|no_mixed: True reference_genome|history_item: phiX.fa library|type: paired reference_genome|source: history adv|input_options|input_options_selector: advanced adv|input_options|trim5: 15 adv|input_options|trim3: 15 |
attributes: name |
phiX.fa hisat_input_2_forward.fastq hisat_input_2_reverse.fastq name |
Test-6 |
library|input_1: test_unaligned_reads.fasta adv|output_options|output_options_selector: advanced reference_genome|history_item: phiX.fa adv|output_options|unaligned_file: True library|type: single reference_genome|source: history |
attributes: name |
phiX.fa test_unaligned_reads.fasta name |
Test-7 |
library|input_2: test_unaligned_reads.fasta library|input_1: test_unaligned_reads.fasta adv|output_options|output_options_selector: advanced reference_genome|history_item: phiX.fa adv|output_options|unaligned_file: True library|type: paired adv|output_options|aligned_file: True reference_genome|source: history |
attributes: name attributes: name |
phiX.fa test_unaligned_reads.fasta name |
Test-8 |
library|input_2: hisat_input_2_reverse.fastq.gz library|input_1: hisat_input_2_forward.fastq.gz library|paired_options|no_discordant: True library|paired_options|paired_options_selector: advanced library|paired_options|no_mixed: True reference_genome|history_item: phiX.fa library|type: paired reference_genome|source: history adv|input_options|input_options_selector: advanced adv|input_options|trim5: 15 adv|input_options|trim3: 15 |
attributes: name |
phiX.fa hisat_input_2_forward.fastq.gz hisat_input_2_reverse.fastq.gz name |
Test-9 |
library|input_2: hisat_input_2_reverse.fastq.bz2 library|input_1: hisat_input_2_forward.fastq.bz2 library|paired_options|no_discordant: True library|paired_options|paired_options_selector: advanced library|paired_options|no_mixed: True reference_genome|history_item: phiX.fa library|type: paired reference_genome|source: history adv|input_options|input_options_selector: advanced adv|input_options|trim5: 15 adv|input_options|trim3: 15 |
attributes: name |
phiX.fa hisat_input_2_forward.fastq.bz2 hisat_input_2_reverse.fastq.bz2 name |
Test-10 |
library|input_2: hisat_input_1_reverse.fastq library|input_1: hisat_input_1_forward.fastq reference_genome|history_item: phiX.fa library|type: paired library|rna_strandness: FR reference_genome|source: history |
attributes: name |
phiX.fa hisat_input_1_forward.fastq hisat_input_1_reverse.fastq name |
Test-11 |
library|input_1: hisat_input_1_forward.fastq sum|new_summary: True reference_genome|history_item: phiX.fa library|type: single library|rna_strandness: R sum|summary_file: True reference_genome|source: history |
attributes: name |
phiX.fa hisat_input_1_forward.fastq name |
Test-12 |
reference_genome|history_item: phiX.fa library|input_1: hisat_input_1_interleaved.fastq library|type: paired_interleaved reference_genome|source: history |
attributes: name |
phiX.fa hisat_input_1_interleaved.fastq name |
Test-13 |
reference_genome|history_item: phiX.fa library|input_1: hisat_input_1_interleaved.fastq.bz2 library|type: paired_interleaved reference_genome|source: history |
attributes: name |
phiX.fa hisat_input_1_interleaved.fastq.bz2 name |
Test-14 |
reference_genome|history_item: phiX.fa library|input_1: hisat_input_1_interleaved.fastq.gz library|type: paired_interleaved reference_genome|source: history |
attributes: name |
phiX.fa hisat_input_1_interleaved.fastq.gz name |
Test-15 |
reference_genome|history_item: phiX.fa library|input_1: hisat_input_1_interleaved.fasta library|type: paired_interleaved reference_genome|source: history |
attributes: name |
phiX.fa hisat_input_1_interleaved.fasta name |