manifest

#Amplicon.Architect
#Fri Mar 11 19:13:53 UTC 2022
JVMLevel=
LSID=urn\:lsid\:8080.gpserver.ip-172-31-26-71.ip-172-31-26-71.ec2.internal\:genepatternmodules\:587\:3.5
author=Edwin Huang;Mesirov Lab
commandLine=bash /opt/genepatt/run_paa.sh <sample.name> <n.threads> <reference> <BAM.provided> <bam.file> <fastq.r1> <fastq.r2> <RUN.AA> <run.AC> <ploidy> <purity> <cnvkit.segmentation> <cnv.bed> 
cpuType=any
description=A multithread-enabled quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. PrepareAA supports hg19 (or GRCh37), hg38 as well as mouse genome mm10 (or GRCm38). PrepareAA can also be invoked to start at intermediate stages of the data preparation process.\n\nAll credits go to\: https\://github.com/jluebeck/PrepareAA \n
documentationUrl=https\://github.com/jluebeck/PrepareAA
fileFormat=
job.cpuCount=2
job.docker.image=genepattern/amplicon-architect\:v1.1
job.memory=24
job.walltime=03\:00\:00
language=any
name=Amplicon.Architect
os=any
p10_MODE=
p10_TYPE=Floating Point
p10_default_value=-1
p10_description=Specify a tumor purity estimate for CNVKit. Not used by AA itself. Note that specifying low purity may lead to many high copy number seed regions after rescaling is applied consider setting a higher --cn_gain threshold for low purity samples undergoing correction.
p10_fileFormat=
p10_flag=--purity
p10_name=purity
p10_numValues=0..1
p10_optional=on
p10_prefix=
p10_prefix_when_specified=
p10_type=java.lang.Float
p10_value=
p11_MODE=
p11_TYPE=TEXT
p11_default_value=none
p11_description=Segmentation method for CNVKit (if used), defaults to CNVKit default segmentation method (cbs). Use drop down menu to select. 
p11_fileFormat=
p11_flag=--cnvkit.segmentation
p11_name=cnvkit.segmentation
p11_numValues=0..1
p11_optional=on
p11_prefix=
p11_prefix_when_specified=
p11_type=java.lang.String
p11_value=cbs\=cbs;haar\=haar;hmm\=hmm;hmm-tumor\=hmm-tumor;hmm-germline\=hmm-germline;none\=none
p12_MODE=IN
p12_TYPE=FILE
p12_default_value=
p12_description=BED file (or CNVKit .cns file) of CNV changes. Fields in the bed file should be\: chr start end name cngain
p12_fileFormat=bed
p12_flag=--cnv.bed
p12_name=cnv.bed
p12_numValues=0..1
p12_optional=on
p12_prefix=
p12_prefix_when_specified=
p12_type=java.io.File
p12_value=
p13_MODE=IN
p13_TYPE=FILE
p13_default_value=
p13_description=Please provide the BAM file
p13_fileFormat=BAM;bam
p13_flag=--bam
p13_name=bam.file
p13_numValues=0..1
p13_optional=on
p13_prefix=
p13_prefix_when_specified=
p13_type=java.io.File
p13_value=
p1_MODE=
p1_TYPE=TEXT
p1_default_value=
p1_description=Name of the sample being run. 
p1_fileFormat=
p1_flag=-s
p1_name=sample.name
p1_numValues=0..1
p1_optional=
p1_prefix=
p1_prefix_when_specified=
p1_type=java.lang.String
p1_value=
p2_MODE=
p2_TYPE=TEXT
p2_default_value=4
p2_description=Number of threads to be allocated to this run. Higher number of threads may lead to faster runs. 
p2_fileFormat=
p2_flag=-t
p2_name=n.threads
p2_numValues=0..1
p2_optional=
p2_prefix=
p2_prefix_when_specified=
p2_type=java.lang.String
p2_value=
p3_MODE=
p3_TYPE=TEXT
p3_default_value=GRCh38
p3_description=Reference genome. Please use drop down to select. 
p3_fileFormat=
p3_flag=--ref
p3_name=reference
p3_numValues=0..1
p3_optional=
p3_prefix=
p3_prefix_when_specified=
p3_type=java.lang.String
p3_value=hg19\=hg19;GRCh37\=GRCh37;GRCh38\=GRCh38;hg38\=hg38;mm10\=mm10;GRCm38\=GRCm38
p4_MODE=
p4_TYPE=TEXT
p4_default_value=*SELECT AN OPTION*
p4_description=Do you have a BAM file to provide? If not, please upload FASTQ R1 and FASTQ R2 files. If BAM file is available, open parameter group\: BAM INPUT.
p4_fileFormat=
p4_flag=--bamprovided
p4_name=BAM.provided
p4_numValues=0..1
p4_optional=
p4_prefix=
p4_prefix_when_specified=
p4_type=java.lang.String
p4_value=Yes\=Yes;No\=No;*SELECT AN OPTION*\=*SELECT AN ITEM*
p5_MODE=
p5_TYPE=TEXT
p5_default_value=*SELECT AN OPTION*
p5_description=Would you like to run AA at the end? Will return AA results at the end if Yes. If no, will return files necessary to input to AA. 
p5_fileFormat=
p5_flag=--runaa
p5_name=RUN.AA
p5_numValues=0..1
p5_optional=
p5_prefix=
p5_prefix_when_specified=
p5_type=java.lang.String
p5_value=Yes\=Yes;No\=No;*SELECT AN OPTION*\=*SELECT AN OPTION*
p6_MODE=
p6_TYPE=TEXT
p6_default_value=*SELECT AN OPTION*
p6_description=Whether or not to run Amplicon Classifier.
p6_fileFormat=
p6_flag=--ac
p6_name=run.AC
p6_numValues=0..1
p6_optional=
p6_prefix=
p6_prefix_when_specified=
p6_type=java.lang.String
p6_value=Yes\=Yes;No\=No;*SELECT AN OPTION*\=*Select An Option*
p7_MODE=IN
p7_TYPE=FILE
p7_default_value=
p7_description=First FASTQ file.
p7_fileFormat=.fastq.gz
p7_flag=--fastq1
p7_name=fastq.r1
p7_numValues=0..1
p7_optional=on
p7_prefix=
p7_prefix_when_specified=
p7_type=java.io.File
p7_value=
p8_MODE=IN
p8_TYPE=FILE
p8_default_value=
p8_description=Second FASTQ file.
p8_fileFormat=.fastq.gz
p8_flag=--fastq2
p8_name=fastq.r2
p8_numValues=0..1
p8_optional=on
p8_prefix=
p8_prefix_when_specified=
p8_type=java.io.File
p8_value=
p9_MODE=
p9_TYPE=Floating Point
p9_default_value=-1
p9_description=Specify a ploidy estimate of the genome for CNVKit. Not used by AA itself.
p9_fileFormat=
p9_flag=--ploidy
p9_name=ploidy
p9_numValues=0..1
p9_optional=on
p9_prefix=
p9_prefix_when_specified=
p9_type=java.lang.Float
p9_value=
privacy=private
quality=development
src.repo=
taskDoc=
taskType=
userid=edwin5588
version=Changed Module Name