| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/recetox/bioconductor_scp/bioconductor_scp/1.16.0+galaxy0 (this tool) |
| bioconductor_scp |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bioconductor-scp | 1.16.0 | package |
| bioconductor-sva | 3.54.0 | package |
| bioconductor-impute | 1.80.0 | package |
| bioconductor-scater | 1.34.0 | package |
| bioconductor-qfeatures | 1.16.0 | package |
| bioconductor-limma | 3.62.1 | package |
| r-ggplot2 | 3.5.1 | package |
| Additional information about this tool |
echo ${run_script} &&
Rscript -e 'source("${__tool_directory__}/utils.r")' -e 'source("${run_script}")'
#if $data_export.export_R_script
&& cat ${run_script} >> $script
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_data: evidence_subset.txt input_annotations: sampleAnnotation.txt runcol: 19 filtering_data|single_cells: ['Macrophage', 'Monocyte'] peptide_aggregation|column_aggregation_peptides: 6 peptide_filtering|samples_to_keep: ['Macrophage', 'Monocyte', 'Blank'] protein_aggregation|column_aggregation_proteins: 17 batch_correction|select_batch_correction|batch_col: 2 dimensionality_reduction|PCA_computation|pca_coloring: 4 |
name: value |
evidence_subset.txt sampleAnnotation.txt value |
| Test-2 |
input_data: evidence_subset.txt input_annotations: sampleAnnotation.txt runcol: 19 filtering_data|single_cells: ['Macrophage', 'Monocyte'] peptide_aggregation|column_aggregation_peptides: 6 peptide_filtering|samples_to_keep: ['Macrophage', 'Monocyte', 'Blank'] protein_aggregation|column_aggregation_proteins: 17 batch_correction|select_batch_correction|batch_col: 2 dimensionality_reduction|PCA_computation|pca_coloring: 4 |
name: value |
evidence_subset.txt sampleAnnotation.txt value |
| Test-3 |
input_data: evidence_subset.txt input_annotations: sampleAnnotation.txt runcol: 19 filtering_data|single_cells: ['Macrophage', 'Monocyte'] peptide_aggregation|column_aggregation_peptides: 6 peptide_filtering|samples_to_keep: ['Macrophage', 'Monocyte', 'Blank'] protein_aggregation|column_aggregation_proteins: 17 batch_correction|select_batch_correction|batch_col: 2 dimensionality_reduction|PCA_computation|pca_coloring: 4 data_export|export_tables: True |
name: value |
evidence_subset.txt sampleAnnotation.txt value |
| Test-4 |
input_data: evidence_subset.txt input_annotations: sampleAnnotation.txt runcol: 19 filtering_data|single_cells: ['Macrophage', 'Monocyte'] peptide_aggregation|column_aggregation_peptides: 6 peptide_filtering|samples_to_keep: ['Macrophage', 'Monocyte', 'Blank'] protein_aggregation|column_aggregation_proteins: 17 batch_correction|select_batch_correction|batch_col: 2 dimensionality_reduction|PCA_computation|pca_coloring: 4 data_export|export_RData: True data_export|export_R_script: True |
name: value name: value |
evidence_subset.txt sampleAnnotation.txt value |