| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1 (this tool) |
| 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 |
| 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 | 2.2.1 | package |
| samtools | 1.12 | 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 |