| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/ebi-gxa/sceasy_convert/sceasy_convert/0.0.5+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/ebi-gxa/sceasy_convert/sceasy_convert/0.0.5+galaxy0 |
| sceasy_convert |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| r-sceasy | 0.0.5 | package |
| Additional information about this tool |
#if str($conversion['direction']).startswith("loom")
ln -s ${conversion.input_object_file} input.loom &&
#else if str($conversion['direction']).startswith("anndata")
ln -s ${conversion.input_object_file} input.h5ad &&
#else
ln -s ${conversion.input_object_file} input.rds &&
#end if
Rscript -e 'library(sceasy)'
#if $conversion.direction == "loom2sce"
-e 'sce <- sceasy::convertFormat("input.loom", from="loom", to="sce", main_layer_name="${conversion.assay_name}")'
-e 'saveRDS(sce, "output.rds")'
-e 'print(sce)'
#else if $conversion.direction == "sce2loom"
-e 'sce <- readRDS("input.rds")'
-e 'sceasy::convertFormat(sce, outFile="output.loom", from="sce", to="loom", main_layer="${conversion.assay}")'
#else if $conversion.direction == "sce2anndata"
-e 'sce <- readRDS("input.rds")'
-e 'sceasy::convertFormat(sce, outFile="output.h5ad", from="sce", to="anndata", main_layer="${conversion.assay}")'
-e 'print(sce)'
#else if $conversion.direction == "seurat2anndata"
-e 'srt <- readRDS("input.rds")'
-e 'sceasy::convertFormat(srt, outFile="output.h5ad", from="seurat", to="anndata", assay="${conversion.assay}", main_layer="${conversion.dtype}")'
-e 'print(srt)'
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
conversion|direction: loom2sce conversion|input_object_file: input.loom |
attributes: name |
input.loom name |