Repository revision
5:249392cd0d99

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

Seurat Export2CellBrowser tool metadata
Miscellaneous
Seurat Export2CellBrowser
produces files for UCSC CellBrowser import.
seurat_export_cellbrowser
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_export_cellbrowser/seurat_export_cellbrowser/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_export_cellbrowser/seurat_export_cellbrowser/4.0.4+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_export_cellbrowser/seurat_export_cellbrowser/3.2.3+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_export_cellbrowser/seurat_export_cellbrowser/3.1.2+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_export_cellbrowser/seurat_export_cellbrowser/3.1.1+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_export_cellbrowser/seurat_export_cellbrowser/3.1.1_0.0.6+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_export_cellbrowser/seurat_export_cellbrowser/2.3.1+galaxy0
seurat_export_cellbrowser
Requirements (dependencies defined in the <requirements> tag set)
name version type
seurat-scripts 0.3.0 package
Additional information about this tool
#if $markers_file:
  cp '$markers_file' markers.csv;
#end if

seurat-export-cellbrowser.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 $markers_file:
-m markers.csv
#end if

-o output_html;

cd output_html && tar -cf '$output' *;
None
False
Functional tests
name inputs outputs required files
Test-1 input|rds_seurat_file: E-MTAB-6077-3k_features_90_cells-tsne.rds
markers_file: E-MTAB-6077-3k_features_90_cells-markers.csv
 name: value
 E-MTAB-6077-3k_features_90_cells-tsne.rds
E-MTAB-6077-3k_features_90_cells-markers.csv
value