| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.1.0.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.0.2.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.0.1.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.0.0.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.5.7.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.5.1.1.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.5.1.0.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.5.0.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.4.2.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.4.1.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.3.6.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.3.5.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.2.3.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.2.2.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.1.0.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.0.1.0 |
| deeptools_bam_coverage |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| deeptools | 3.0.2 | package |
| samtools | 1.7 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
advancedOpt|showAdvancedOpt: no bamInput: bowtie2 test1.bam scaling|type: no outFileFormat: bigwig binSize: 10 |
outFileName: bamCoverage_result1.bw |
bowtie2 test1.bam bamCoverage_result1.bw |
| Test-2 |
scaling|effectiveGenomeSize|effectiveGenomeSize: 2451960000 outFileFormat: bigwig advancedOpt|showAdvancedOpt: no bamInput: bowtie2 test1.bam binSize: 10 scaling|effectiveGenomeSize|effectiveGenomeSize_opt: specific |
outFileName: bamCoverage_result2.bw |
bowtie2 test1.bam bamCoverage_result2.bw |
| Test-3 |
scaling|effectiveGenomeSize|effectiveGenomeSize: 2451960000 outFileFormat: bedgraph advancedOpt|showAdvancedOpt: no bamInput: bowtie2 test1.bam binSize: 10 scaling|effectiveGenomeSize|effectiveGenomeSize_opt: specific |
outFileName: bamCoverage_result3.bg |
bowtie2 test1.bam bamCoverage_result3.bg |
| Test-4 |
scaling|effectiveGenomeSize|effectiveGenomeSize: 2451960000 outFileFormat: bigwig advancedOpt|showAdvancedOpt: no bamInput: phiX.bam binSize: 10 scaling|effectiveGenomeSize|effectiveGenomeSize_opt: specific |
outFileName: bamCoverage_result4.bw |
phiX.bam bamCoverage_result4.bw |
| Test-5 |
scaling|effectiveGenomeSize|effectiveGenomeSize: 2451960000 outFileFormat: bedgraph advancedOpt|showAdvancedOpt: yes bamInput: phiX.bam binSize: 10 scaling|effectiveGenomeSize|effectiveGenomeSize_opt: specific |
outFileName: bamCoverage_result4.bg |
phiX.bam bamCoverage_result4.bg |
| Test-6 |
scaling|effectiveGenomeSize|effectiveGenomeSize: 2451960000 advancedOpt|showAdvancedOpt: yes advancedOpt|filterRNAstrand: reverse scaling|effectiveGenomeSize|effectiveGenomeSize_opt: specific outFileFormat: bigwig bamInput: phiX.bam binSize: 10 |
outFileName: bamCoverage_result5.bw |
phiX.bam bamCoverage_result5.bw |
| Test-7 |
advancedOpt|showAdvancedOpt: yes advancedOpt|Offset: -4 -1 advancedOpt|minMappingQuality: 0 outFileFormat: bigwig advancedOpt|doExtendCustom|doExtend: yes bamInput: bowtie2 test1.bam scaling|type: no binSize: 10 |
outFileName: bamCoverage_result6.bw |
bowtie2 test1.bam bamCoverage_result6.bw |