| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| 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 (this tool) |
| 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 | 2.5.2b | package |
| samtools | 0.1.19 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
output_params|output_select: yes params|settingsType: default output_params|outSAMattributes: All refGenomeSource|genomeFastaFiles: tophat_test.fa refGenomeSource|geneSource: history output_params|outSAMstrandField: intronMotif singlePaired|input1: tophat_in2.fastqsanger singlePaired|sPaired: single |
output_log: rnastar_test.log splice_junctions: rnastar_test_splicejunctions.bed mapped_reads: rnastar_test_mapped_reads.bam |
tophat_in2.fastqsanger tophat_test.fa rnastar_test.log rnastar_test_splicejunctions.bed rnastar_test_mapped_reads.bam |
| 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 |
output_log: rnastar_test.log splice_junctions: rnastar_test_splicejunctions.bed mapped_reads: rnastar_test_mapped_reads.bam reads_per_gene: tophat_test_reads_per_gene.txt |
tophat_in2.fastqsanger tophat_test.fa test1.gtf rnastar_test.log rnastar_test_splicejunctions.bed rnastar_test_mapped_reads.bam tophat_test_reads_per_gene.txt |
| 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 |
output_log: rnastar_test2.log splice_junctions: rnastar_test2_splicejunctions.bed mapped_reads: rnastar_test2_mapped_reads.bam |
tophat_in2.fastqsanger tophat_test.fa rnastar_test2.log rnastar_test2_splicejunctions.bed rnastar_test2_mapped_reads.bam |
| Test-4 |
output_params|output_select: yes params|settingsType: star_fusion output_params|outSAMattributes: All refGenomeSource|genomeFastaFiles: test3.ref.fa refGenomeSource|geneSource: history output_params|outSAMstrandField: intronMotif singlePaired|input1: test3.fastqsanger singlePaired|sPaired: single |
chimeric_junctions: test3.chimjunc.tabular |
test3.fastqsanger test3.ref.fa test3.chimjunc.tabular |
| Test-5 |
output_params|output_select: yes params|settingsType: star_fusion output_params|outSAMattributes: All refGenomeSource|genomeFastaFiles: test3.ref.fa refGenomeSource|geneSource: history output_params|outSAMstrandField: intronMotif singlePaired|input1: test3.fastqsanger.gz singlePaired|sPaired: single |
chimeric_junctions: test3.chimjunc.tabular |
test3.fastqsanger.gz test3.ref.fa test3.chimjunc.tabular |
| Test-6 |
output_params|output_select: yes params|settingsType: full output_params|outSAMattributes: All output_params|output_params2|output_select2: yes refGenomeSource|genomeFastaFiles: tophat_test.fa refGenomeSource|geneSource: history output_params|outSAMstrandField: intronMotif output_params|outFilterIntronMotifs: RemoveNoncanonical singlePaired|input1: tophat_in2.fastqsanger singlePaired|sPaired: single |
output_log: rnastar_test.log splice_junctions: rnastar_test_splicejunctions.bed mapped_reads: rnastar_test_mapped_reads.bam |
tophat_in2.fastqsanger tophat_test.fa rnastar_test.log rnastar_test_splicejunctions.bed rnastar_test_mapped_reads.bam |