| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.3 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.1 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.0 |
| cardinal_quality_report |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bioconductor-cardinal | 1.12.1 | package |
| r-base | 3.5.1 | package |
| r-rcolorbrewer | 1.1_2 | package |
| r-gridextra | 2.3 | package |
| r-ggplot2 | 3.0 | package |
| r-kernsmooth | 2.23_15 | package |
| r-scales | 1.0.0 | package |
| r-pheatmap | 1.0.10 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
infile: processed_cond|units: ppm processed_cond|processed_file: processed tabular_annotation|load_annotation: no_annotation calibrantratio_0|distance: 500 name_column: 1 processed_cond|accuracy: 200 filename: Testfile_imzml calibrantratio_0|filenameratioplot: Ratio of mass1 (328.9) / mass2 (398.8) mz_column: 1 do_pca: True calibrant_file: inputcalibrantfile1.tabular calibrantratio_0|mass2: 398.8 plusminus_ppm: 100 calibrantratio_0|mass1: 328.9 |
attributes: name |
inputcalibrantfile1.tabular name |
| Test-2 |
do_pca: True tabular_annotation|load_annotation: no_annotation infile: filename: Testfile_analyze75 |
attributes: name |
name |
| Test-3 |
infile: 3_files_combined.RData tabular_annotation|column_y: 2 tabular_annotation|tabular_header: True name_column: 1 tabular_annotation|load_annotation: yes_annotation filename: Testfile_rdata calibrant_file: inputcalibrantfile1.tabular tabular_annotation|column_names: 3 tabular_annotation|column_x: 1 do_pca: True tabular_annotation|annotation_file: annotations_rdata.tabular plusminus_ppm: 100 mz_column: 1 |
attributes: name |
3_files_combined.RData annotations_rdata.tabular inputcalibrantfile1.tabular name |
| Test-4 |
tabular_annotation|load_annotation: no_annotation name_column: 2 filename: Testfile_rdata do_pca: False calibrant_file: inputcalibrantfile2.txt infile: empty_spectra.rdata mz_column: 1 |
attributes: name |
empty_spectra.rdata inputcalibrantfile2.txt name |