| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/circexplorer2/circexplorer2/2.3.8+galaxy0 (this tool) |
| circexplorer2 |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| circexplorer2 | 2.3.8 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
mode|gtf: annotation_01.gtf mode|genome: reference_01.fa mode|fastq: ['reads_01.fastq', 'reads_02.fastq', 'reads_03.fastq'] mode|skip_tophat_fusion: True mode|selector: align |
name: value |
annotation_01.gtf reference_01.fa reads_01.fastq reads_02.fastq reads_03.fastq value |
| Test-2 |
mode|gtf: annotation_01.gtf mode|genome: reference_01.fa mode|fastq: ['reads_01.fastq.gz', 'reads_02.fastq.gz', 'reads_03.fastq.gz'] mode|bw: True mode|scale: True mode|skip_tophat_fusion: True mode|selector: align |
name: value name: value |
annotation_01.gtf reference_01.fa reads_01.fastq.gz reads_02.fastq.gz reads_03.fastq.gz value |
| Test-3 |
mode|aligner|fusion_file: mapsplice_chimeric.junction mode|aligner|selector: MapSplice mode|selector: parse |
name: value |
mapsplice_chimeric.junction value |
| Test-4 |
mode|aligner|fusion_file: STAR_chimeric.junction mode|aligner|f: True mode|aligner|selector: STAR mode|selector: parse |
name: value |
STAR_chimeric.junction value |
| Test-5 |
mode|ref: annotation_02.txt mode|genome: reference_02.fa mode|bed: test_04.bed mode|selector: annotate |
name: value |
annotation_02.txt reference_02.fa test_04.bed value |
| Test-6 |
mode|ref: annotation_02.txt mode|genome: reference_02.fa mode|bed: test_04.bed mode|no_fix: True mode|low_confidence: True mode|selector: annotate |
name: value |
annotation_02.txt reference_02.fa test_04.bed value |
| Test-7 |
mode|ref: annotation_02.txt mode|bed: test_04.bed mode|genome: reference_02.fa mode|assemble_file: assemble.tgz mode|selector: denovo |
name: value name: value name: value name: value |
annotation_02.txt test_04.bed reference_02.fa assemble.tgz value |
| Test-8 |
mode|ref: annotation_02.txt mode|bed: test_04.bed mode|genome: reference_02.fa mode|assemble_file: assemble.tgz mode|abs: True mode|no_fix: True mode|rpkm: True mode|selector: denovo |
name: value name: value name: value name: value name: value name: value |
annotation_02.txt test_04.bed reference_02.fa assemble.tgz value |