| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.2a |
| toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.6.0b-2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.6.0b-1 |
| toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2 |
| toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-1 |
| toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-0 |
| toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.4.0d-2 |
| toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.4.0d |
| rna_star |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| star | 2.6.0b | package |
| samtools | 1.8 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
output_params|output_select: yes params|settingsType: default refGenomeSource|genomeFastaFiles: tophat_test.fa refGenomeSource|geneSource: history singlePaired|sPaired: single output_params|outSAMattributes: All singlePaired|input1: tophat_in2.fastqsanger output_params|outSAMstrandField: intronMotif |
attributes: name attributes: name attributes: name |
tophat_in2.fastqsanger tophat_test.fa name |
| Test-2 |
output_params|output_select: yes refGenomeSource|sjdbOverhang: 75 refGenomeSource|genomeFastaFiles: tophat_test.fa refGenomeSource|geneSource: history refGenomeSource|sjdbGTFfile: test1.gtf params|settingsType: default singlePaired|sPaired: single output_params|outSAMattributes: All singlePaired|input1: tophat_in2.fastqsanger output_params|outSAMstrandField: intronMotif quantMode: True |
attributes: name attributes: name attributes: name attributes: name |
tophat_in2.fastqsanger tophat_test.fa test1.gtf name |
| Test-3 |
output_params|output_select: yes params|settingsType: full output_params|output_params2|output_select2: yes refGenomeSource|genomeFastaFiles: tophat_test.fa refGenomeSource|geneSource: history params|seed|seedSearchStartLmax: 25 singlePaired|sPaired: single output_params|outSAMattributes: All singlePaired|input1: tophat_in2.fastqsanger output_params|outSAMstrandField: intronMotif output_params|outFilterIntronMotifs: RemoveNoncanonical output_params|output_params2|outFilterScoreMinOverLread: 0.9 |
attributes: name attributes: name attributes: name |
tophat_in2.fastqsanger tophat_test.fa name |
| Test-4 |
output_params|output_select: yes params|settingsType: star_fusion refGenomeSource|genomeFastaFiles: test3.ref.fa refGenomeSource|geneSource: history singlePaired|sPaired: single output_params|outSAMattributes: All singlePaired|input1: test3.fastqsanger output_params|outSAMstrandField: intronMotif |
attributes: name |
test3.fastqsanger test3.ref.fa name |
| Test-5 |
output_params|output_select: yes params|settingsType: star_fusion refGenomeSource|genomeFastaFiles: test3.ref.fa refGenomeSource|geneSource: history singlePaired|sPaired: single output_params|outSAMattributes: All singlePaired|input1: test3.fastqsanger.gz output_params|outSAMstrandField: intronMotif |
attributes: name |
test3.fastqsanger.gz test3.ref.fa name |
| Test-6 |
output_params|output_select: yes params|settingsType: full output_params|output_params2|output_select2: yes refGenomeSource|genomeFastaFiles: tophat_test.fa refGenomeSource|geneSource: history singlePaired|sPaired: single output_params|outSAMattributes: All singlePaired|input1: tophat_in2.fastqsanger output_params|outSAMstrandField: intronMotif output_params|outFilterIntronMotifs: RemoveNoncanonical |
attributes: name attributes: name attributes: name |
tophat_in2.fastqsanger tophat_test.fa name |
| Test-7 |
output_params|output_select: yes params|settingsType: full output_params|output_params2|output_select2: yes refGenomeSource|genomeFastaFiles: tophat_test.fa refGenomeSource|geneSource: history singlePaired|sPaired: single output_params|outSAMattributes: All params|twopass|twopassMode: True singlePaired|input1: tophat_in2.fastqsanger output_params|outSAMstrandField: intronMotif output_params|outFilterIntronMotifs: RemoveNoncanonical |
attributes: name attributes: name attributes: name |
tophat_in2.fastqsanger tophat_test.fa name |