Repository revision
5:5be60722113a

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

Seurat FindVariableGenes tool metadata
Miscellaneous
Seurat FindVariableGenes
identify variable genes
seurat_find_variable_genes
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_variable_genes/seurat_find_variable_genes/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_variable_genes/seurat_find_variable_genes/4.0.4+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_variable_genes/seurat_find_variable_genes/3.2.3+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_variable_genes/seurat_find_variable_genes/3.1.2+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_variable_genes/seurat_find_variable_genes/3.1.1+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_variable_genes/seurat_find_variable_genes/3.1.1_0.0.6+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_variable_genes/seurat_find_variable_genes/2.3.1+galaxy1
seurat_find_variable_genes
Requirements (dependencies defined in the <requirements> tag set)
name version type
seurat-scripts 0.3.0 package
Additional information about this tool
seurat-find-variable-genes.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 $mean:
    --mean-function '$mean'
#end if
#if $selection_method
  --selection-method '$selection_method'
#end if
#if $disp:
--dispersion-function $disp
#end if
#if $xlow:
--x-low-cutoff $xlow
#end if
#if $xhigh:
--x-high-cutoff $xhigh
#end if
#if $ylow:
--y-low-cutoff $ylow
#end if
#if $yhigh:
--y-high-cutoff $yhigh
#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'
None
False
Functional tests
name inputs outputs required files
Test-1 input|rds_seurat_file: E-MTAB-6077-3k_features_90_cells-normalised.rds
 name: value
 E-MTAB-6077-3k_features_90_cells-normalised.rds
value