Repository revision
6:0db997e4a81d

Repository 'seurat_run_tsne'
hg clone https://toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_tsne

Seurat RunTSNE tool metadata
Miscellaneous
Seurat RunTSNE
run t-SNE dimensionality reduction
seurat_run_tsne
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_tsne/seurat_run_tsne/4.0.4+galaxy0
4.0.4+galaxy0
echo $(R --version | grep version | grep -v GNU)", seurat version" $(R --vanilla --slave -e "library(seurat); cat(sessionInfo()\$otherPkgs\$seurat\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
True
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 (this tool)
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_tsne/seurat_run_tsne/3.2.3+galaxy0
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 4.0.0 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
None
False
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