Repository revision
5:9547ebb03f6f

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

Seurat RunPCA tool metadata
Miscellaneous
Seurat RunPCA
run a PCA dimensionality reduction
seurat_run_pca
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_pca/seurat_run_pca/3.2.3+galaxy0
3.2.3+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_pca/seurat_run_pca/4.0.4+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_pca/seurat_run_pca/3.2.3+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_pca/seurat_run_pca/3.1.2+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_pca/seurat_run_pca/3.1.1+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_pca/seurat_run_pca/3.1.1_0.0.6+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_pca/seurat_run_pca/2.3.1+galaxy1
seurat_run_pca
Requirements (dependencies defined in the <requirements> tag set)
name version type
seurat-scripts 0.3.0 package
Additional information about this tool
seurat-run-pca.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 $pc_genes:
    --pc-genes '$pc_genes'
#end if
#if $pc_cells
  --pc-cells '$pc_cells'
#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
--output-loadings-file output_load
--output-stdev-file output_sdev
#if $pcs_compute:
    --pcs-compute '$pcs_compute'
#end if
#if $reverse_pca
  '$reverse_pca'
#end if
None
False
Functional tests
name inputs outputs required files
Test-1 input|rds_seurat_file: E-MTAB-6077-3k_features_90_cells-scaled.rds
 name: value
name: value
name: value
name: value
 E-MTAB-6077-3k_features_90_cells-scaled.rds
value