| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/3.4.3+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/2.10.0.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/2.6.0.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/2.4.0.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/1.12.1.2 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/1.12.1.1 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/1.12.1.0 |
| cardinal_data_exporter |
| 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 $infile infile.RData &&
#end if
cat '${cardinal_imzml_exporter}' &&
Rscript '${cardinal_imzml_exporter}'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
infile: output_options: ['int_matrix', 'mz_tabular'] |
name: value name: value |
value |
| Test-2 |
infile: output_options: pixel_tabular tabular_annotation|annotation_file: annotations.tabular tabular_annotation|column_x: 1 tabular_annotation|column_y: 2 tabular_annotation|column_names: 4 tabular_annotation|tabular_header: True tabular_annotation|summary_type: ['mean', 'sd'] tabular_annotation|load_annotation: yes_annotation |
name: value name: value name: value |
annotations.tabular value |
| Test-3 |
infile: output_options: ['int_matrix', 'pixel_tabular', 'mz_tabular'] counting_calibrants|mz_tabular: inputcalibrantfile2.txt counting_calibrants|feature_column: 1 counting_calibrants|feature_header: False counting_calibrants|plusminus_ppm: 200 counting_calibrants|pixel_with_calibrants: yes_calibrants |
name: value name: value name: value |
inputcalibrantfile2.txt value |
| Test-4 |
infile: processed_cond|accuracy: 200 processed_cond|units: ppm processed_cond|processed_file: processed output_options: ['pixel_tabular', 'mz_tabular'] counting_calibrants|mz_tabular: featuresofinterest5.tabular counting_calibrants|feature_column: 1 counting_calibrants|feature_header: False counting_calibrants|plusminus_ppm: 200 counting_calibrants|pixel_with_calibrants: yes_calibrants |
name: value name: value |
featuresofinterest5.tabular value |