Repository revision
5:301cf1b4b43d

Repository 'seurat_read10x'
hg clone https://toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x

Seurat Read10x tool metadata
Miscellaneous
Loads Tabular or 10x data into a serialized seurat R object
seurat_read10x
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/3.2.3+galaxy0
3.2.3+galaxy0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/4.0.4+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/3.2.3+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/3.1.2+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/3.1.1+galaxy1
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/3.1.1_0.0.6+galaxy0
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/2.3.1+galaxy1
seurat_read10x
Requirements (dependencies defined in the <requirements> tag set)
name version type
seurat-scripts 0.3.0 package
Additional information about this tool
#if str($input.format) == "mtx":
    ln -s "$matrix" matrix.mtx;
    ln -s "$genes" genes.tsv;
    ln -s "$barcodes" barcodes.tsv;
#end if

seurat-read-10x.R
#if str($input.format) == "mtx":
 -d ./
#else
 -f $input.file
#end if
#if $metadata
  --metadata '$metadata'
#end if
#if $min_cells
  --min-cells '$min_cells'
#end if
#if $min_features
  --min-features '$min_features'
#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|matrix: E-MTAB-6077_3k_features_90_cells_matrix.txt
input|genes: E-MTAB-6077_3k_features_90_cells_genes.tsv
input|barcodes: E-MTAB-6077_3k_features_90_cells_barcodes.tsv
input|format: mtx
name: value
E-MTAB-6077_3k_features_90_cells_matrix.txt
E-MTAB-6077_3k_features_90_cells_genes.tsv
E-MTAB-6077_3k_features_90_cells_barcodes.tsv
value