| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0 (this tool) |
| tophat |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| samtools | 0.1.18 | package |
| bowtie | 0.12.7 | package |
| tophat | 1.4.0 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
singlePaired|sParams|sSettingsType: preSet refGenomeSource|genomeSource: indexed refGenomeSource|index: tophat_test input1: tophat_in2.fastqsanger singlePaired|sPaired: single |
junctions: tophat_out1j.bed accepted_hits: tophat_out1h.bam |
tophat_in2.fastqsanger tophat_out1j.bed tophat_out1h.bam |
| Test-2 |
input1: tophat_in2.fastqsanger singlePaired|input2: tophat_in3.fastqsanger refGenomeSource|genomeSource: history refGenomeSource|ownFile: tophat_in1.fasta singlePaired|sPaired: paired singlePaired|pParams|pSettingsType: preSet singlePaired|mate_inner_distance: 20 |
junctions: tophat_out2j.bed accepted_hits: tophat_out2h.bam |
tophat_in2.fastqsanger tophat_in1.fasta tophat_in3.fastqsanger tophat_out2j.bed tophat_out2h.bam |
| Test-3 |
singlePaired|sParams|closure_search|max_closure_intron: 5000 input1: tophat_in2.fastqsanger singlePaired|sParams|max_intron_length: 500000 singlePaired|sParams|max_multihits: 40 singlePaired|sParams|min_intron_length: 70 singlePaired|sParams|splice_mismatches: 0 singlePaired|sParams|anchor_length: 8 singlePaired|sParams|max_segment_intron: 500000 singlePaired|sPaired: single singlePaired|sParams|indel_search|max_deletion_length: 3 singlePaired|sParams|closure_search|min_closure_intron: 50 singlePaired|sParams|indel_search|max_insertion_length: 3 singlePaired|sParams|seg_length: 25 singlePaired|sParams|microexon_search: Yes singlePaired|sParams|closure_search|use_search: Yes singlePaired|sParams|seg_mismatches: 2 singlePaired|sParams|min_segment_intron: 50 singlePaired|sParams|indel_search|allow_indel_search: Yes singlePaired|sParams|own_junctions|gene_model_ann|use_annotations: No singlePaired|sParams|sSettingsType: full singlePaired|sParams|own_junctions|use_junctions: Yes singlePaired|sParams|coverage_search|max_coverage_intron: 20000 singlePaired|sParams|own_junctions|raw_juncs|use_juncs: No singlePaired|sParams|coverage_search|use_search: Yes singlePaired|sParams|own_junctions|no_novel_juncs: No refGenomeSource|genomeSource: history refGenomeSource|ownFile: tophat_in1.fasta singlePaired|sParams|library_type: fr-unstranded singlePaired|sParams|closure_search|min_closure_exon: 50 singlePaired|sParams|coverage_search|min_coverage_intron: 50 |
insertions: tophat_out3i.bed deletions: tophat_out3d.bed junctions: tophat_out3j.bed accepted_hits: tophat_out3h.bam |
tophat_in2.fastqsanger tophat_in1.fasta tophat_out3i.bed tophat_out3d.bed tophat_out3j.bed tophat_out3h.bam |
| Test-4 |
singlePaired|pParams|mate_std_dev: 20 input1: tophat_in2.fastqsanger singlePaired|pParams|min_intron_length: 70 singlePaired|pParams|own_junctions|gene_model_ann|use_annotations: No singlePaired|pParams|own_junctions|use_junctions: Yes singlePaired|pParams|anchor_length: 8 singlePaired|pParams|max_multihits: 40 singlePaired|pParams|own_junctions|no_novel_juncs: No singlePaired|pParams|max_intron_length: 500000 singlePaired|input2: tophat_in3.fastqsanger singlePaired|pParams|closure_search|use_search: No singlePaired|pParams|own_junctions|raw_juncs|use_juncs: No singlePaired|pParams|seg_mismatches: 2 singlePaired|pParams|microexon_search: Yes singlePaired|pParams|min_segment_intron: 50 singlePaired|mate_inner_distance: 20 singlePaired|pParams|splice_mismatches: 0 singlePaired|pParams|indel_search|allow_indel_search: No singlePaired|pParams|pSettingsType: full singlePaired|pParams|library_type: fr-unstranded refGenomeSource|index: tophat_test singlePaired|sPaired: paired singlePaired|pParams|seg_length: 25 singlePaired|pParams|max_segment_intron: 500000 refGenomeSource|genomeSource: indexed |
junctions: tophat_out4j.bed accepted_hits: tophat_out4h.bam |
tophat_in2.fastqsanger tophat_in3.fastqsanger tophat_out4j.bed tophat_out4h.bam |