| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db/1.22.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db/1.16.1.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db/1.16.0.1 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db/1.16.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db/1.14.0 |
| custom_pro_db |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bioconductor-rgalaxy | 1.26.0 | package |
| bioconductor-variantannotation | 1.28.3 | package |
| r-devtools | 2.0.1 | package |
| r-testthat | 2.0.1 | package |
| r-getoptlong | 0.1.7 | package |
| r-data.table | 1.12.0 | package |
| r-sqldf | 0.4_11 | package |
| r-plyr | 1.8.4 | package |
| r-rmysql | 0.10.13 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
outputIndels: False genome_annotation|bamInput: hg19/test1_sort.bam outputSQLite: True outputRData: True genome_annotation|ids: hg19/ids.RData genome_annotation|proCodingSeq: hg19/procodingseq.RData genome_annotation|proteinSeq: hg19/proseq.RData genome_annotation|vcfInput: hg19/test1.vcf genome_annotation|source: history genome_annotation|exonAnno: hg19/exon_anno.RData rpkmCutoff: 1 |
attributes: name attributes: name attributes: name attributes: name attributes: name |
hg19/exon_anno.RData hg19/proseq.RData hg19/procodingseq.RData hg19/ids.RData hg19/test1_sort.bam hg19/test1.vcf name |
| Test-2 |
outputIndels: True genome_annotation|bamInput: hg19/test1_sort.bam outputSQLite: True genome_annotation|cosmic: hg19/cosmic.RData genome_annotation|ids: hg19/ids.RData genome_annotation|proCodingSeq: hg19/procodingseq.RData genome_annotation|proteinSeq: hg19/proseq.RData genome_annotation|vcfInput: hg19/test1.vcf genome_annotation|source: history genome_annotation|dbsnpInCoding: hg19/dbsnpinCoding.RData genome_annotation|exonAnno: hg19/exon_anno.RData rpkmCutoff: 0 |
attributes: name attributes: name attributes: name attributes: name attributes: name |
hg19/exon_anno.RData hg19/proseq.RData hg19/procodingseq.RData hg19/ids.RData hg19/test1_sort.bam hg19/test1.vcf hg19/dbsnpinCoding.RData hg19/cosmic.RData name |
| Test-3 |
outputIndels: True genome_annotation|bamInput: hg19/test1_sort.bam genome_annotation|ids: hg19/ids.RData genome_annotation|proCodingSeq: hg19/procodingseq.RData genome_annotation|exonAnno: hg19/exon_anno.RData genome_annotation|vcfInput: hg19/test1.vcf genome_annotation|source: history genome_annotation|proteinSeq: hg19/proseq.RData rpkmCutoff: 1000 |
attributes: name attributes: name attributes: name |
hg19/exon_anno.RData hg19/proseq.RData hg19/procodingseq.RData hg19/ids.RData hg19/test1_sort.bam hg19/test1.vcf name |