| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/3.4.3+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.10.0.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.6.0.3 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.6.0.2 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.6.0.1 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.6.0.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.4.0.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/1.12.1.3 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/1.12.1.2 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/1.12.1.1 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/1.12.1.0 |
| cardinal_spectra_plots |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bioconductor-cardinal | 3.4.3 | package |
| r-gridextra | 2.3 | package |
| r-ggplot2 | 3.5.1 | package |
| r-maldiquantforeign | 0.14.1 | package |
| r-maldiquant | 1.22.2 | package |
| bioconductor-sva | 3.50.0 | package |
| r-randomcolor | 1.1.0.1 | package |
| r-rcolorbrewer | 1.1_3 | package |
| r-kernsmooth | 2.23_24 | package |
| r-scales | 1.3.0 | package |
| r-pheatmap | 1.0.12 | package |
| Additional information about this tool |
#if $infile.ext == 'imzml'
cp '${infile.extra_files_path}/imzml' infile.imzML &&
cp '${infile.extra_files_path}/ibd' infile.ibd &&
#elif $infile.ext == 'analyze75'
cp '${infile.extra_files_path}/hdr' infile.hdr &&
cp '${infile.extra_files_path}/img' infile.img &&
cp '${infile.extra_files_path}/t2m' infile.t2m &&
#else
ln -s $infile infile.RData &&
#end if
cat '${MSI_mzplots}' &&
Rscript '${MSI_mzplots}'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
infile: pixel_conditional|pixel_file: spectra_1_pixel.tabular pixel_conditional|column_pixel_x: 1 pixel_conditional|column_pixel_y: 2 pixel_conditional|tabular_pixel_header: False pixel_conditional|pixel_type: tabular_pixel fullmz: True mz_range|zoomed_sample_0|xlimmin: 310 mz_range|zoomed_sample_0|xlimmax: 320 mz_range|zoomed_sample_1|xlimmin: 350 mz_range|zoomed_sample_1|xlimmax: 400 mz_range|zoomed_sample_2|xlimmin: 360 mz_range|zoomed_sample_2|xlimmax: 360.8 mz_range|mz_range_options: manual_mz grid_variable: True |
name: value |
spectra_1_pixel.tabular value |
| Test-2 |
infile: pixel_conditional|pixel_file: spectra_1_pixel.tabular pixel_conditional|column_pixel_x: 1 pixel_conditional|column_pixel_y: 2 pixel_conditional|tabular_pixel_header: True pixel_conditional|pixel_type: tabular_pixel fullmz: True mz_range|zoomed_sample_0|xlimmin: 840 mz_range|zoomed_sample_0|xlimmax: 850 mz_range|mz_range_options: manual_mz grid_variable: False |
name: value |
spectra_1_pixel.tabular value |
| Test-3 |
infile: pixel_conditional|pixel_file: annotations.tabular pixel_conditional|column_pixel_x: 1 pixel_conditional|column_pixel_y: 2 pixel_conditional|tabular_pixel_header: True pixel_conditional|single_or_overlaid|column_pixel_annotation: 4 pixel_conditional|single_or_overlaid|plot_type: overlaid_plots pixel_conditional|pixel_type: tabular_pixel fullmz: False mz_range|zoomed_sample_0|xlimmin: 1250 mz_range|zoomed_sample_0|xlimmax: 1270 mz_range|mz_range_options: manual_mz grid_variable: False |
name: value |
annotations.tabular value |
| Test-4 |
infile: 3_files_combined.RData pixel_conditional|pixel_type: all_pixel fullmz: True mz_range|zoomed_sample_0|xlimmin: 350 mz_range|zoomed_sample_0|xlimmax: 360 mz_range|mz_range_options: manual_mz grid_variable: False |
name: value |
3_files_combined.RData value |
| Test-5 |
infile: processed_cond|accuracy: 100 processed_cond|units: ppm processed_cond|processed_file: processed pixel_conditional|pixel_type: all_pixel fullmz: False mz_range|zoomed_sample_0|xlimmin: 350 mz_range|zoomed_sample_0|xlimmax: 350.5 mz_range|zoomed_sample_1|xlimmin: 600 mz_range|zoomed_sample_1|xlimmax: 650 mz_range|mz_range_options: manual_mz grid_variable: True |
name: value |
value |
| Test-6 |
infile: centroids: True pixel_conditional|pixel_type: all_pixel fullmz: True mz_range|zoomed_sample_0|xlimmin: 328 mz_range|zoomed_sample_0|xlimmax: 330 mz_range|zoomed_sample_1|xlimmin: 335 mz_range|zoomed_sample_1|xlimmax: 340 mz_range|mz_range_options: manual_mz grid_variable: True |
name: value |
value |