Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_tsne/seurat_run_tsne/4.0.4+galaxy0 |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_tsne/seurat_run_tsne/3.2.3+galaxy0 (this tool) |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_tsne/seurat_run_tsne/3.1.2+galaxy0 |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_tsne/seurat_run_tsne/3.1.1+galaxy1 |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_tsne/seurat_run_tsne/3.1.1_0.0.6+galaxy0 |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_tsne/seurat_run_tsne/2.3.1+galaxy1 |
seurat_run_tsne |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
seurat-scripts | 0.3.0 | package |
Additional information about this tool |
seurat-run-tsne.R #if $input.format == "anndata" --input-object-file input.h5ad --input-format anndata #else if $input.format == "loom" --input-object-file input.loom --input-format loom #else if $input.format == "rds_seurat" --input-object-file '$input.rds_seurat_file' --input-format seurat #else if $input.format == "rds_sce" --input-object-file '$input.rds_sce_file' --input-format singlecellexperiment #else if $input.format == "h5seurat" --input-object-file input.h5seurat --input-format h5seurat #end if #if $genes_use: --genes-use '$genes_use' #end if #if str($adv.dims_use): --dims-use \$(seq -s , 1 '$adv.dims_use') #else --dims-use 1,10 #end if #if not $adv.do_fast: --do-fast '$adv.do_fast' #end if #if $adv.tsne_method --tsne-method '$adv.tsne_method' #end if #if $adv.dim_embed --dim_embed '$adv.dim_embed' #end if #if $adv.random_seed --random-seed '$adv.random_seed' #end if #if $adv.perplexity --perplexity '$adv.perplexity' #end if #if $format == "anndata" --output-object-file '$anndata_file' --output-format anndata #else if $format == "loom" --output-object-file seurat_obj.loom --output-format loom #else if $format == "rds_seurat" --output-object-file '$rds_seurat_file' --output-format seurat #else if $format == "rds_sce" --output-object-file '$rds_sce_file' --output-format singlecellexperiment #end if --output-embeddings-file output_embed
Functional tests |
name | inputs | outputs | required files |
Test-1 |
input|rds_seurat_file: E-MTAB-6077-3k_features_90_cells-clusters.rds |
name: value |
E-MTAB-6077-3k_features_90_cells-clusters.rds value |