| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/1.0.1 |
| toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/1.0.0 (this tool) |
| cummeRbund |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| CUMMERBUND_SCRIPT_PATH | not provided | set_environment |
| R | 3.1.2 | package |
| cummeRbund | 2.8.2 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
plots_0|width: 1280 plots_0|height: 960 plots_0|plot|x: q1 plots_0|plot|y: q2 plots_0|plot|type: maplot input_database: cuffdiff_out.sqlite |
output: maplot.txt |
cuffdiff_out.sqlite maplot.txt |
| Test-2 |
plots_0|width: 1280 plots_0|height: 960 plots_0|plot|x: q1 plots_0|plot|y: q2 plots_0|plot|type: scatter input_database: cuffdiff_out.sqlite |
output: scatter.txt |
cuffdiff_out.sqlite scatter.txt |
| Test-3 |
plots_0|width: 1280 plots_0|height: 960 input_database: cuffdiff_out.sqlite plots_0|plot|type: dispersion |
output: dispersion.txt |
cuffdiff_out.sqlite dispersion.txt |
| Test-4 |
plots_0|width: 1280 plots_0|height: 960 input_database: cuffdiff_out.sqlite plots_0|plot|type: scatterMatrix |
output: scatterMatrix.txt |
cuffdiff_out.sqlite scatterMatrix.txt |
| Test-5 |
plots_0|width: 1280 plots_0|height: 960 input_database: cuffdiff_out.sqlite plots_0|plot|type: pca |
output: pca.txt |
cuffdiff_out.sqlite pca.txt |
| Test-6 |
plots_0|width: 1280 plots_0|height: 960 plots_0|plot|features: gene plots_0|plot|type: expressionplot input_database: cuffdiff_out.sqlite plots_0|plot|gene_id: XLOC_000059 |
output: expressionplot.txt |
cuffdiff_out.sqlite expressionplot.txt |
| Test-7 |
plots_0|width: 1280 plots_0|height: 960 plots_0|plot|features: gene plots_0|plot|type: expressionbarplot input_database: cuffdiff_out.sqlite plots_0|plot|gene_id: XLOC_000039 |
output: expressionbarplot.txt |
cuffdiff_out.sqlite expressionbarplot.txt |
| Test-8 |
plots_0|width: 1280 plots_0|height: 960 input_database: cuffdiff_out.sqlite plots_0|plot|genes_0|gene_id: XLOC_000078 plots_0|plot|type: heatmap |
output: heatmap.txt |
cuffdiff_out.sqlite heatmap.txt |
| Test-9 |
plots_0|width: 1280 plots_0|height: 960 input_database: cuffdiff_out.sqlite plots_0|plot|type: density |
output: density.txt |
cuffdiff_out.sqlite density.txt |
| Test-10 |
plots_0|width: 1280 plots_0|height: 960 input_database: cuffdiff_out.sqlite plots_0|plot|type: dendrogram |
output: dendrogram.txt |
cuffdiff_out.sqlite dendrogram.txt |
| Test-11 |
plots_0|width: 1280 plots_0|height: 960 plots_0|plot|x: q1 plots_0|plot|y: q2 plots_0|plot|type: volcano input_database: cuffdiff_out.sqlite |
output: volcano.txt |
cuffdiff_out.sqlite volcano.txt |
| Test-12 |
plots_0|width: 1280 plots_0|height: 960 input_database: cuffdiff_out.sqlite plots_0|plot|type: boxplot |
output: boxplot.txt |
cuffdiff_out.sqlite boxplot.txt |
| Test-13 |
plots_0|width: 1280 plots_0|height: 960 input_database: cuffdiff_out.sqlite plots_0|plot|type: fpkmSCV |
output: fpkmSCV.txt |
cuffdiff_out.sqlite fpkmSCV.txt |