manifest

#Fri, 22 Jun 2018 09:09:40 -0700
# STREAM
#Tues Jun 11 21:02:09 UTC 2019
JVMLevel=
LSID=urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00405:999999999
author=Ted Liefeld, UCSD School of Medicine.
categories=SingleCell

commandLine=python /stream/viz2d_command_line.py -m <data.file> -of <output.filename> <percent.neighbor.cells> <perplexity> <color.by>  <method> <use.precomputed> <figure.width> <figure.height> <figure.legend.num.columns> 

cpuType=any
description=STREAM.Plot2DVisualization is used to check if there is clear meaningful trajectory pattern via TSNE or UMAP 2-D plots. If so, we can continue the STREAM analysis; If not, go back to previous steps (preprocessing, feature selection and dimension reduction) to modify the parameters.
fileFormat=pkl
language=any
minGenePatternVersion=3.9.13
name=STREAM.Plot2DVisualization
os=any
job.docker.image=genepattern/stream_plot2dvisualization:0.12
job.cpuCount=2
job.memory=8 Gb
job.walltime=1\:00\:00

p1_MODE=IN
p1_TYPE=FILE
p1_default_value=
p1_description=A STREAM pkl file containing gene expression data.
p1_fileFormat=pkl
p1_flag=
p1_name=data.file
p1_numValues=1..1
p1_optional=
p1_prefix=
p1_prefix_when_specified=
p1_type=java.io.File
p1_value=

p2_MODE=
p2_TYPE=CHOICE
p2_default_value=0.1
p2_description=The percentage of neighbor cells (only valid when 'umap' is specified). 
p2_fileFormat=
p2_flag=
p2_name=percent.neighbor.cells
p2_numValues=0..1
p2_optional=on
p2_prefix=
p2_prefix_when_specified=-nb_pct   
p2_type=java.lang.String
p2_value=

p3_MODE=
p3_TYPE=CHOICE
p3_default_value=30
p3_description=The perplexity used (only valid when tSNE is specified).
p3_fileFormat=
p3_flag=
p3_name=perplexity
p3_numValues=1..1
p3_optional=
p3_prefix=
p3_prefix_when_specified=-perplexity   
p3_type=java.lang.String
p3_value=

p4_MODE=
p4_TYPE=CHOICE
p4_default_value=
p4_description=Specify how to color cells. 'label': the cell labels, 'branch': the branch id identifed by STREAM.
p4_fileFormat=
p4_flag=
p4_name=color.by
p4_numValues=1..1
p4_optional=on
p4_prefix=
p4_prefix_when_specified=-color_by   
p4_type=java.lang.String
p4_value=label;branch

p5_MODE=
p5_TYPE=CHOICE
p5_default_value=umap
p5_description=Method used for visualization.  Choose from; 'umap': Uniform Manifold Approximation and Projection; 'tsne': t-Distributed Stochastic Neighbor Embedding.
p5_fileFormat=
p5_flag=
p5_name=method
p5_numValues=1..1
p5_optional=
p5_prefix=
p5_prefix_when_specified=-method 
p5_type=java.lang.String
p5_value=umap\=Uniform Manifold Approximation and Projection (UMAP);tsne\=TSNE

p6_default_value=
p6_description=If True, the visualization coordinates from previous computation stored in the input pkl file will be used.
p6_fileFormat=
p6_flag=
p6_name=use.precomputed
p6_numValues=0..1
p6_optional=on
p6_prefix=
p6_prefix_when_specified=  
p6_type=java.lang.String
p6_value=\=FALSE;--flag_useprecomputed\=TRUE

p7_MODE=
p7_TYPE=TEXT
p7_default_value=8
p7_description=figure width.
p7_fileFormat=
p7_flag=
p7_name=figure.width
p7_numValues=0..1
p7_optional=on
p7_prefix=
p7_prefix_when_specified=-fig_width   
p7_type=java.lang.String
p7_value=

p8_MODE=
p8_TYPE=TEXT
p8_default_value=3
p8_description=The number of columns that the legend has.
p8_fileFormat=
p8_flag=
p8_name=figure.legend.num.columns
p8_numValues=1..1
p8_optional=
p8_prefix=
p8_prefix_when_specified=-fig_legend_ncol  
p8_type=java.lang.String
p8_value=

p9_MODE=
p9_TYPE=TEXT
p9_default_value=8
p9_description=figure height.
p9_fileFormat=
p9_flag=
p9_name=figure.height
p9_numValues=0..1
p9_optional=on
p9_prefix=
p9_prefix_when_specified=-fig_height  
p9_type=java.lang.String
p9_value=

p10_MODE=
p10_TYPE=TEXT
p10_default_value=
p10_description=output file name prefix.
p10_fileFormat=
p10_flag=
p10_name=output.filename
p10_numValues=1..1
p10_optional=
p10_prefix=
p10_prefix_when_specified=
p10_type=java.lang.String
p10_value=

privacy=public
publicationDate=06/11/2019 09\:09 
quality=beta
requiredPatchLSIDs=
requiredPatchURLs=
taskDoc=doc.html
taskType=ScRnaSeq
userid=ted
version=inital revision