-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathmanifest
102 lines (102 loc) · 4.54 KB
/
manifest
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
#TCGA.SampleSelection
#Thu Feb 25 19:28:34 UTC 2021
JVMLevel=
LSID=urn:lsid:genepattern.org:module.analysis:00417
author=Anthony S. Castanza;UCSD-MesirovLab
categories=preprocess & utilities;gsea
commandLine=Rscript /TCGA_SS/TCGA_Datasets.R --id <TCGA.Collection> --symbol <Gene.Symbol> --high <High.Expression> --low <Low.Expression> --type <Output.Type> --msigdb <MSigDB.Version>
cpuType=any
description=Retrieve TCGA data from Broad FireBrowse and perform sample selection on the basis of expression levels for specific genes of interest for analysis using GSEA tools.
fileFormat=cls;gct
job.docker.image=genepattern/tcga-sampleselection:beta6
src.repo=https://github.com/genepattern/TCGA.SampleSelection/tree/v0.14
language=any
job.memory=4 Gb
name=TCGA.SampleSelection
os=any
p1_MODE=
p1_TYPE=TEXT
p1_default_value=GBM
p1_description=TCGA Study for sample selection
p1_fileFormat=
p1_flag=--id
p1_name=TCGA.Collection
p1_numValues=1..1
p1_optional=
p1_prefix=
p1_prefix_when_specified=
p1_type=java.lang.String
p1_value=LAML\=Acute Myeloid Leukemia (LAML);ACC\=Adrenocortical carcinoma (ACC);BLCA\=Bladder urothelial carcinoma (BLCA);LGG\=Brain Lower Grade Glioma (LGG);BRCA\=Breast invasive carcinoma (BRCA);CESC\=Cervical and endocervical cancers (CESC);CHOL\=Cholangiocarcinoma (CHOL);COAD\=Colon adenocarcinoma (COAD);COADREAD\=Colorectal adenocarcinoma (COADREAD);ESCA\=Esophageal carcinoma (ESCA);GBM\=Glioblastoma multiforme (GBM);GBMLGG\=Glioma (GBMLGG);HNSC\=Head and Neck squamous cell carcinoma (HNSC);KICH\=Kidney Chromophobe (KICH);KIRC\=Kidney renal clear cell carcinoma (KIRC);KIRP\=Kidney renal papillary cell carcinoma (KIRP);LIHC\=Liver hepatocellular carcinoma (LIHC);LUAD\=Lung adenocarcinoma (LUAD);LUSC\=Lung squamous cell carcinoma (LUSC);DLBC\=Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (DLBC);MESO\=Mesothelioma (MESO);OV\=Ovarian serous cystadenocarcinoma (OV);KIPAN\=Pan-kidney cohort (KICH+KIRC+KIRP) (KIPAN);PAAD\=Pancreatic adenocarcinoma (PAAD);PCPG\=Pheochromocytoma and Paraganglioma (PCPG);PRAD\=Prostate adenocarcinoma (PRAD);READ\=Rectum adenocarcinoma (READ);SARC\=Sarcoma (SARC);SKCM\=Skin Cutaneous Melanoma (SKCM);STAD\=Stomach adenocarcinoma (STAD);STES\=Stomach and Esophageal carcinoma (STES);TGCT\=Testicular Germ Cell Tumors (TGCT);THYM\=Thymoma (THYM);THCA\=Thyroid carcinoma (THCA);UCS\=Uterine Carcinosarcoma (UCS);UCEC\=Uterine Corpus Endometrial Carcinoma (UCEC);UVM\=Uveal Melanoma (UVM)
p2_MODE=
p2_TYPE=TEXT
p2_default_value=
p2_description=HGNC Gene Symbol to use for expression level thresholding
p2_fileFormat=
p2_flag=--symbol
p2_name=Gene.Symbol
p2_numValues=1..1
p2_optional=
p2_prefix=
p2_prefix_when_specified=
p2_type=java.lang.String
p2_value=
p3_MODE=
p3_TYPE=Floating Point
p3_default_value=1
p3_description=mRNA expression is greater than or equal to x standard deviations above the mean. <br>\n(mRNA expression z-scores relative to all samples)
p3_fileFormat=
p3_flag=--high
p3_name=High.Expression
p3_numValues=1..1
p3_optional=
p3_prefix=
p3_prefix_when_specified=
p3_range=0+
p3_type=java.lang.Float
p3_value=
p4_MODE=
p4_TYPE=Floating Point
p4_default_value=-1
p4_description=mRNA expression is less than or equal to x standard deviations below the mean. <br>\n(mRNA expression z-scores relative to all samples)
p4_fileFormat=
p4_flag=--low
p4_name=Low.Expression
p4_numValues=1..1
p4_optional=
p4_prefix=
p4_prefix_when_specified=
p4_range=0-
p4_type=java.lang.Float
p4_value=
p5_MODE=
p5_TYPE=TEXT
p5_default_value=scaled_estimate
p5_description=Type of RSEM quantifications to output\:\n<br>TPM (transcripts per million, within sample normalization, useful for ssGSEA)\n<br> Raw counts (unnormalized counts, usable with DESeq2 or other DEG calculations).
p5_fileFormat=
p5_flag=--type
p5_name=Output.Type
p5_numValues=1..1
p5_optional=
p5_prefix=
p5_prefix_when_specified=
p5_type=java.lang.String
p5_value=scaled_estimate\=TPM;raw_count\=Raw Counts
p6_MODE=
p6_TYPE=TEXT
p6_default_value=latest
p6_description=MSigDB version to use for Gene Symbol lookup.<br>\nThis version should match the version of the gene sets intended for all downstream analysis.<br><a href="https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Release_Notes" target="_blank">Click here for a current listing of all MSigDB versions.</a>
p6_fileFormat=
p6_flag=--msigdb
p6_name=MSigDB.Version
p6_numValues=1..1
p6_optional=
p6_prefix=
p6_prefix_when_specified=
p6_type=java.lang.String
p6_value=
privacy=public
quality=preproduction
taskDoc=TCGA.SampleSelection.pdf
taskType=preprocess & utilities
userid=acastanza
version= Update for non-float MSigDB version numbers