| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/1.0.1 |
| toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/1.0.0 (this tool) |
| hisat2 |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| hisat | 2.0 | package |
| samtools | 1.2 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_format|paired|reads_r: hisat_input_1_reverse.fastq input_format|paired|reads_f: hisat_input_1_forward.fastq reference_genome|reference_genome_source: history reference_genome|history_item: phiX.fa input_format|paired|paired_selector: paired input_format|input_format_selector: fastq |
output_alignments: hisat_output_1.bam |
hisat_input_1_forward.fastq hisat_input_1_reverse.fastq phiX.fa hisat_output_1.bam |
| Test-2 |
input_options|input_options_selector: advanced input_format|paired|reads_r: hisat_input_2_reverse.fastq input_format|paired|reads_f: hisat_input_2_forward.fastq reference_genome|reference_genome_source: history input_options|trim_five: 15 reference_genome|history_item: phiX.fa input_format|paired|paired_selector: paired input_format|input_format_selector: fastq input_options|trim_three: 15 |
output_alignments: hisat_output_2.bam |
hisat_input_2_forward.fastq hisat_input_2_reverse.fastq phiX.fa hisat_output_2.bam |
| Test-3 |
input_options|input_options_selector: advanced input_format|paired|reads_r: hisat_input_2_reverse.fastq input_format|paired|reads_f: hisat_input_2_forward.fastq reference_genome|reference_genome_source: history input_format|paired|paired_end_options|no_mixed: True input_options|trim_five: 15 reference_genome|history_item: phiX.fa input_format|paired|paired_selector: paired input_format|input_format_selector: fastq input_options|trim_three: 15 input_format|paired|paired_end_options|no_discordant: True input_format|paired|paired_end_options|paired_end_options_selector: advanced |
output_alignments: hisat_output_3.bam |
hisat_input_2_forward.fastq hisat_input_2_reverse.fastq phiX.fa hisat_output_3.bam |