| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/3.4.3+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/2.10.0.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/2.6.0.2 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/2.6.0.1 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/2.6.0.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/2.4.0.1 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/2.4.0.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/1.12.1.3 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/1.12.1.2 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/1.12.1.1 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/1.12.1.0 |
| cardinal_classification |
| 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_segmentation}' &&
Rscript '${MSI_segmentation}'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
infile: testfile_squares.rdata type_cond|annotation_file: pixel_annotation_file1.tabular type_cond|column_x: 1 type_cond|column_y: 2 type_cond|column_response: 4 type_cond|column_fold: 3 type_cond|tabular_header: False type_cond|method_cond|analysis_cond|plscv_comp: 2:4 type_cond|method_cond|analysis_cond|PLS_method: cvapply type_cond|method_cond|class_method: PLS type_cond|type_method: training |
name: value |
testfile_squares.rdata pixel_annotation_file1.tabular value |
| Test-2 |
infile: testfile_squares.rdata type_cond|annotation_file: pixel_annotation_file1.tabular type_cond|column_x: 1 type_cond|column_y: 2 type_cond|column_response: 4 type_cond|tabular_header: False type_cond|method_cond|analysis_cond|pls_comp: 2 type_cond|method_cond|analysis_cond|pls_scale: True type_cond|method_cond|analysis_cond|PLS_Yweights: True type_cond|method_cond|analysis_cond|PLS_method: PLS_analysis type_cond|method_cond|class_method: PLS type_cond|type_method: training output_rdata: True |
name: value name: value name: value name: value name: value |
testfile_squares.rdata pixel_annotation_file1.tabular value |
| Test-3 |
infile: testfile_squares.rdata type_cond|annotation_file: random_factors.tabular type_cond|column_x: 1 type_cond|column_y: 2 type_cond|column_response: 4 type_cond|column_fold: 3 type_cond|tabular_header: False type_cond|method_cond|opls_analysis_cond|opls_cvcomp: 1:2 type_cond|method_cond|opls_analysis_cond|opls_method: opls_cvapply type_cond|method_cond|class_method: OPLS type_cond|type_method: training |
name: value |
testfile_squares.rdata random_factors.tabular value |
| Test-4 |
infile: testfile_squares.rdata type_cond|annotation_file: random_factors.tabular type_cond|column_x: 1 type_cond|column_y: 2 type_cond|column_response: 4 type_cond|tabular_header: False type_cond|method_cond|opls_analysis_cond|opls_comp: 3 type_cond|method_cond|opls_analysis_cond|opls_scale: False type_cond|method_cond|opls_analysis_cond|opls_method: opls_analysis type_cond|method_cond|class_method: OPLS type_cond|type_method: training output_rdata: True |
name: value name: value name: value name: value name: value |
testfile_squares.rdata random_factors.tabular value |
| Test-5 |
infile: testfile_squares.rdata type_cond|annotation_file: pixel_annotation_file1.tabular type_cond|column_x: 1 type_cond|column_y: 2 type_cond|column_response: 3 type_cond|column_fold: 4 type_cond|tabular_header: False type_cond|method_cond|ssc_analysis_cond|write_best_params: True type_cond|method_cond|ssc_analysis_cond|ssc_method: ssc_cvapply type_cond|method_cond|class_method: spatialShrunkenCentroids type_cond|type_method: training |
name: value name: value name: value |
testfile_squares.rdata pixel_annotation_file1.tabular value |
| Test-6 |
infile: testfile_squares.rdata type_cond|annotation_file: random_factors.tabular type_cond|column_x: 1 type_cond|column_y: 2 type_cond|column_response: 4 type_cond|method_cond|ssc_analysis_cond|ssc_toplabels: 20 type_cond|method_cond|ssc_analysis_cond|ssc_method: ssc_analysis type_cond|method_cond|ssc_r: 2 type_cond|method_cond|ssc_s: 2 type_cond|method_cond|ssc_kernel_method: adaptive type_cond|method_cond|class_method: spatialShrunkenCentroids type_cond|type_method: training output_rdata: True |
name: value name: value name: value name: value |
testfile_squares.rdata random_factors.tabular value |
| Test-7 |
infile: testfile_squares.rdata type_cond|training_result: test2.rdata type_cond|new_y_values_cond|new_response_file: pixel_annotation_file1.tabular type_cond|new_y_values_cond|column_new_x: 1 type_cond|new_y_values_cond|column_new_y: 2 type_cond|new_y_values_cond|column_new_response: 4 type_cond|new_y_values_cond|new_tabular_header: False type_cond|new_y_values_cond|new_y_values: new_response type_cond|type_method: prediction output_rdata: True |
name: value name: value name: value name: value name: value |
testfile_squares.rdata test2.rdata pixel_annotation_file1.tabular value |