Repository revision
5:eefaffdcd441

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

Seurat FindClusters tool metadata
Miscellaneous
Seurat FindClusters
find clusters of cells
seurat_find_clusters
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_clusters/seurat_find_clusters/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_find_clusters/seurat_find_clusters/4.0.4+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_clusters/seurat_find_clusters/3.2.3+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_clusters/seurat_find_clusters/3.1.2+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_clusters/seurat_find_clusters/3.1.1+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_clusters/seurat_find_clusters/3.1.1_0.0.6+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_clusters/seurat_find_clusters/2.3.1+galaxy1
seurat_find_clusters
Requirements (dependencies defined in the <requirements> tag set)
name version type
seurat-scripts 0.3.0 package
Additional information about this tool
seurat-find-clusters.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 $format == "anndata"
        --output-object-file '$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-text-file output_tab

        #if str($adv.resolution):
          --resolution '$adv.resolution'
        #end if

        #if str($adv.algorithm):
          --algorithm '$adv.algorithm'
        #end if

        #if str($adv.modularity_fxn):
          --modularity-fxn '$adv.modularity_fxn'
        #end if

        #if str($adv.method):
          --method '$adv.method'
        #end if

        #if str($adv.graph_name):
          --graph-name '$adv.graph_name'
        #end if

        #if str($adv.nrandom_starts):
          --nrandom-starts '$adv.nrandom_starts'
        #end if

        $adv.group_singletons



  ## TODO add pdf support as optional
None
False
Functional tests
name inputs outputs required files
Test-1 input|rds_seurat_file: E-MTAB-6077-3k_features_90_cells-neighbours.rds
 name: value
name: value
 E-MTAB-6077-3k_features_90_cells-neighbours.rds
value