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#Tue, 17 Dec 2019 13:14:51 -0800
JVMLevel=
LSID=urn\:lsid\:broad.mit.edu\:cancer.software.genepattern.module.analysis\:00408\:999999999
author=Satija Lab New York Genome Canter, Wrapped as a module by Ted Liefeld, UCSD School of Medicine.
categories=SingleCell
commandLine=/opt/R3.6/bin/Rscript --no-save --quiet --slave --no-restore /seurat/run-seurat-clustering.R --input.file\=<input.seurat.rds.file> --output.file\=<output.filename>.rds --max_dim\=<maximum_dimension> --resolution\=<resolution> --reduction\=<reduction> --seed\=<seed>
cpuType=any
description=performs clustering on Seurat RDS objects
fileFormat=pdf,rds
language=any
minGenePatternVersion=3.9.13
name=SeuratClustering
os=any
job.docker.image=genepattern/seurat-clustering:3.2
p1_MODE=IN
p1_TYPE=FILE
p1_default_value=
p1_description=RDS file containing a seurat object
p1_fileFormat=rds
p1_flag=
p1_name=input.seurat.rds.file
p1_numValues=1
p1_optional=
p1_prefix=
p1_prefix_when_specified=
p1_type=java.io.File
p1_value=
p2_MODE=
p2_TYPE=TEXT
p2_default_value=<input.seurat.rds.file_basename>.clustered
p2_description=Name for output rds file
p2_fileFormat=
p2_flag=
p2_name=output.filename
p2_numValues=1..1
p2_optional=
p2_prefix=
p2_prefix_when_specified=
p2_type=java.lang.String
p2_value=
p3_MODE=IN
p3_TYPE=
p3_default_value=10
p3_description=Max num dimensions to cluster
p3_fileFormat=
p3_flag=
p3_name=maximum_dimension
p3_numValues=1
p3_optional=on
p3_prefix=
p3_prefix_when_specified=
p3_type=java.lang.String
p3_value=
# <gene.sets.database> <link.to.msigdb> <url.in.description>
p4_MODE=IN
p4_TYPE=
p4_default_value=0.5
p4_description=resolution
p4_fileFormat=
p4_numValues=1
p4_flag=
p4_name=resolution
p4_optional=
p4_prefix=
p4_prefix_when_specified=
p4_type=java.lang.String
p4_value=
p5_MODE=
p5_TYPE=TEXT
p5_default_value=umap
p5_description=The reduction to use (umap/tsne)
p5_fileFormat=
p5_flag=
p5_name=reduction
p5_numValues=1..1
p5_optional=
p5_prefix=
p5_prefix_when_specified=
p5_type=java.lang.String
p5_value=umap;tsne
p6_MODE=IN
p6_TYPE=
p6_default_value=17
p6_description=Random number seed.
p6_fileFormat=
p6_flag=
p6_name=seed
p6_numValues=1
p6_optional=on
p6_prefix=
p6_prefix_when_specified=
p6_type=java.lang.String
p6_value=
privacy=public
publicationDate=12/17/2019 13\:14
quality=${quality.level}
requiredPatchLSIDs=
requiredPatchURLs=
taskDoc=doc.html
taskType=SingleCell
version=Initial Revision