| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.7a |
| toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.6a |
| toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.5b |
| toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.2b |
| 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 |
| 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 | 2.7.8a | package |
| samtools | 1.9 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
singlePaired|input1: tophat_in2.fastqsanger singlePaired|sPaired: single refGenomeSource|genomeFastaFiles: tophat_test.fa refGenomeSource|genomeSAindexNbases: 5 refGenomeSource|geneSource: history oformat|outSAMattributes: ['NH', 'HI', 'AS', 'nM', 'NM', 'MD', 'jM', 'jI', 'MC', 'ch'] oformat|outSAMmapqUnique: 255 algo|params|settingsType: default |
name: value name: value name: value |
tophat_in2.fastqsanger tophat_test.fa value |
| Test-2 |
singlePaired|input1: tophat_in2.fastqsanger singlePaired|sPaired: single refGenomeSource|GTFconditional|genomeDir: 001 refGenomeSource|GTFconditional|GTFselect: with-gtf refGenomeSource|geneSource: indexed oformat|outSAMattributes: ['NH', 'HI', 'AS', 'nM', 'NM', 'MD', 'jM', 'jI', 'MC', 'ch'] oformat|outSAMmapqUnique: 255 algo|params|settingsType: default |
name: value name: value name: value |
tophat_in2.fastqsanger value |
| Test-3 |
singlePaired|input1: tophat_in2.fastqsanger singlePaired|sPaired: single refGenomeSource|genomeFastaFiles: tophat_test.fa refGenomeSource|genomeSAindexNbases: 5 refGenomeSource|GTFconditional|sjdbGTFfile: test1.gtf refGenomeSource|GTFconditional|sjdbOverhang: 75 refGenomeSource|GTFconditional|GTFselect: with-gtf refGenomeSource|geneSource: history quantmode_output|quantMode: GeneCounts oformat|outSAMattributes: ['NH', 'HI', 'AS', 'nM', 'NM', 'MD', 'jM', 'jI', 'MC', 'ch'] oformat|outSAMmapqUnique: 255 algo|params|settingsType: default |
name: value name: value name: value name: value |
tophat_in2.fastqsanger tophat_test.fa test1.gtf value |
| Test-4 |
singlePaired|input1: tophat_in2.fastqsanger singlePaired|sPaired: single refGenomeSource|genomeFastaFiles: tophat_test.fa refGenomeSource|genomeSAindexNbases: 5 refGenomeSource|GTFconditional|sjdbGTFfile: test1.gtf refGenomeSource|GTFconditional|sjdbOverhang: 75 refGenomeSource|GTFconditional|GTFselect: with-gtf refGenomeSource|geneSource: history quantmode_output|quantMode: TranscriptomeSAM oformat|outSAMattributes: ['NH', 'HI', 'AS', 'nM', 'NM', 'MD', 'jM', 'jI', 'MC', 'ch'] oformat|outSAMmapqUnique: 255 algo|params|settingsType: default |
name: value name: value name: value name: value |
tophat_in2.fastqsanger tophat_test.fa test1.gtf value |
| Test-5 |
singlePaired|input1: tophat_in2.fastqsanger singlePaired|sPaired: single refGenomeSource|genomeFastaFiles: tophat_test.fa refGenomeSource|genomeSAindexNbases: 5 refGenomeSource|geneSource: history oformat|outSAMattributes: ['NH', 'HI', 'AS', 'nM', 'NM', 'MD', 'jM', 'jI', 'MC', 'ch', 'XS'] oformat|outSAMmapqUnique: 255 filter|basic_filters: ['exclude_unmapped', '--outFilterIntronMotifs RemoveNoncanonical'] filter|output_params2|outFilterScoreMinOverLread: 0.9 filter|output_params2|output_select2: yes algo|params|seed|seedSearchStartLmax: 25 algo|params|settingsType: full |
name: value name: value name: value |
tophat_in2.fastqsanger tophat_test.fa value |
| Test-6 |
singlePaired|input1: test3.fastqsanger singlePaired|sPaired: single refGenomeSource|genomeFastaFiles: test3.ref.fa refGenomeSource|genomeSAindexNbases: 5 refGenomeSource|geneSource: history chimOutType: Junctions oformat|outSAMattributes: ['NH', 'HI', 'AS', 'nM', 'NM', 'MD', 'jM', 'jI', 'MC', 'ch', 'XS'] oformat|outSAMmapqUnique: 255 algo|params|settingsType: star_fusion |
name: value |
test3.fastqsanger test3.ref.fa value |
| Test-7 |
singlePaired|input1: test3.fastqsanger.gz singlePaired|sPaired: single refGenomeSource|genomeFastaFiles: test3.ref.fa refGenomeSource|genomeSAindexNbases: 5 refGenomeSource|geneSource: history chimOutType: Junctions oformat|outSAMattributes: ['NH', 'HI', 'AS', 'nM', 'NM', 'MD', 'jM', 'jI', 'MC', 'ch', 'XS'] oformat|outSAMmapqUnique: 255 algo|params|settingsType: star_fusion |
name: value |
test3.fastqsanger.gz test3.ref.fa value |
| Test-8 |
singlePaired|input1: tophat_in2.fastqsanger singlePaired|sPaired: single refGenomeSource|genomeFastaFiles: tophat_test.fa refGenomeSource|genomeSAindexNbases: 5 refGenomeSource|geneSource: history oformat|outSAMattributes: ['NH', 'HI', 'AS', 'nM', 'NM', 'MD', 'jM', 'jI', 'MC', 'ch'] oformat|outSAMmapqUnique: 255 filter|basic_filters: --outFilterIntronMotifs RemoveNoncanonical filter|output_params2|output_select2: yes algo|params|settingsType: full |
name: value name: value name: value |
tophat_in2.fastqsanger tophat_test.fa value |
| Test-9 |
singlePaired|input1: tophat_in2.fastqsanger singlePaired|sPaired: single refGenomeSource|genomeFastaFiles: tophat_test.fa refGenomeSource|genomeSAindexNbases: 5 refGenomeSource|geneSource: history twopass|twopassMode: Basic oformat|outSAMattributes: ['NH', 'HI', 'AS', 'nM', 'NM', 'MD', 'jM', 'jI', 'MC', 'ch'] oformat|outSAMmapqUnique: 255 filter|basic_filters: ['exclude_unmapped', '--outFilterIntronMotifs RemoveNoncanonical'] filter|output_params2|output_select2: yes algo|params|settingsType: full |
name: value name: value name: value |
tophat_in2.fastqsanger tophat_test.fa value |
| Test-10 |
singlePaired|input1: tophat_in2.fastqsanger singlePaired|sPaired: single refGenomeSource|GTFconditional|genomeDir: 000 refGenomeSource|GTFconditional|GTFselect: without-gtf refGenomeSource|geneSource: indexed twopass|twopassMode: Basic oformat|outSAMattributes: ['NH', 'HI', 'AS', 'nM', 'NM', 'MD', 'jM', 'jI', 'MC', 'ch'] oformat|outSAMmapqUnique: 255 filter|basic_filters: ['exclude_unmapped', '--outFilterIntronMotifs RemoveNoncanonical'] filter|output_params2|output_select2: yes algo|params|settingsType: full |
name: value name: value name: value |
tophat_in2.fastqsanger value |
| Test-11 |
singlePaired|input1: tophat_in2.fastqsanger singlePaired|sPaired: single refGenomeSource|genomeFastaFiles: tophat_test.fa refGenomeSource|genomeSAindexNbases: 5 refGenomeSource|geneSource: history twopass|sj_precalculated: rnastar_test_splicejunctions_twopass.bed twopass|twopassMode: None --sjdbFileChrStartEnd oformat|outSAMattributes: ['NH', 'HI', 'AS', 'nM', 'NM', 'MD', 'jM', 'jI', 'MC', 'ch'] oformat|outSAMmapqUnique: 255 filter|basic_filters: ['exclude_unmapped', '--outFilterIntronMotifs RemoveNoncanonicalUnannotated', '--outFilterIntronMotifs RemoveNoncanonical'] filter|output_params2|output_select2: yes algo|params|settingsType: full |
name: value name: value name: value |
tophat_in2.fastqsanger tophat_test.fa rnastar_test_splicejunctions_twopass.bed value |
| Test-12 |
singlePaired|input1: tophat_in2.fastqsanger singlePaired|sPaired: single refGenomeSource|genomeFastaFiles: tophat_test.fa refGenomeSource|genomeSAindexNbases: 14 refGenomeSource|geneSource: history oformat|outSAMattributes: ['NH', 'HI', 'AS', 'nM', 'NM', 'MD', 'jM', 'jI', 'MC', 'ch'] oformat|outSAMmapqUnique: 255 algo|params|settingsType: default |
name: value name: value name: value |
tophat_in2.fastqsanger tophat_test.fa value |
| Test-13 |
singlePaired|input1: tophat_in2.fastqsanger singlePaired|sPaired: single refGenomeSource|genomeFastaFiles: tophat_test.fa refGenomeSource|genomeSAindexNbases: 10 refGenomeSource|geneSource: history oformat|outSAMattributes: ['NH', 'HI', 'AS', 'nM', 'NM', 'MD', 'jM', 'jI', 'MC', 'ch'] oformat|outSAMmapqUnique: 255 algo|params|settingsType: default |
name: value name: value name: value |
tophat_in2.fastqsanger tophat_test.fa value |