Repository revision
4:99d628557c47

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

Seurat FindNeighbours tool metadata
Miscellaneous
Seurat FindNeighbours
constructs a Shared Nearest Neighbor (SNN) Graph
seurat_find_neighbours
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_neighbours/seurat_find_neighbours/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_neighbours/seurat_find_neighbours/4.0.4+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_neighbours/seurat_find_neighbours/3.2.3+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_neighbours/seurat_find_neighbours/3.1.2+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_neighbours/seurat_find_neighbours/3.1.1+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_neighbours/seurat_find_neighbours/3.1.1_0.0.6+galaxy0
seurat_find_neighbours
Requirements (dependencies defined in the <requirements> tag set)
name version type
seurat-scripts 0.3.0 package
Additional information about this tool
seurat-find-neighbours.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
   
$distance_matrix
#if $k_param
  --k-param  '$k_param'
#end if
$compute_snn
#if $prune_snn
  --prune-snn  '$prune_snn'
#end if
#if $nn_method
  --nn-method  '$nn_method'
#end if
#if $annoy_metric
  --annoy-metric  '$annoy_metric'
#end if
#if $graph_name
  --graph-name  '$graph_name'
#end if
#if $nn_eps and $nn_method == "rann"
  --nn-eps '$nn_eps'
#end if
$force_recalc
#if $features_file
  --features '$features_file'
#else if $features
  --features '$features'
#end if
#if $reduction
  --reduction  '$reduction'
#end if
#if $dims
  --dims  '$dims'
#end if
#if $assay
  --assay  '$assay'
#end if
#if $do_plot
  $do_plot
#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
None
False
Functional tests
name inputs outputs required files
Test-1 input|rds_seurat_file: E-MTAB-6077-3k_features_90_cells-pca.rds
reduction: pca
compute_snn: True
 name: value
 E-MTAB-6077-3k_features_90_cells-pca.rds
value