manifest

#AmpliconSuiteAggregator
#Mon Jan 08 08:52:59 PST 2024
JVMLevel=
LSID=urn\:lsid\:genepattern.org\:module.analysis\:00429\:8
author=Edwin Huang;Mesirov Lab
categories=ecdna
commandLine=python3 /opt/genepatt/AmpliconSuiteAggregator.py -s prod --filelist <Amplicon.Architect.Results> --output_name <project_name> <Amplicon.Repository.Email> --upload_only <upload.only>  <run.amplicon.classifier> --accept_license <accept.license>  <reference.genome> <name.map> 
cpuType=any
description=Aggregates individual AmpliconSuite runs. Takes in zip files (or .tar.gz) and aggregates the results. Results can directly be used to load onto AmpliconRepository. 
documentationUrl=https\://github.com/genepattern/AmpliconSuiteAggregator/blob/develop/docs/v1/index.md
fileFormat=
job.cpuCount=1
job.docker.image=genepattern/amplicon-suite-aggregator\:v2.8
job.memory=4GB
job.walltime=01\:00\:00
language=any
name=AmpliconSuiteAggregator
os=any
p1_MODE=IN
p1_TYPE=FILE
p1_default_value=
p1_description=Compressed (.tar.gz, .zip) files of the results from individual or grouped Amplicon Architect runs.
p1_fileFormat=.tar.gz;.zip
p1_flag=
p1_name=Amplicon.Architect.Results
p1_numValues=0+
p1_optional=
p1_prefix=
p1_prefix_when_specified=
p1_type=java.io.File
p1_value=
p2_MODE=
p2_TYPE=TEXT
p2_default_value=output
p2_description=Prefix for output name for resulting '.tar.gz'. Result will be named\: *output_prefix*.tar.gz.
p2_fileFormat=
p2_flag=
p2_name=project_name
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=
p3_description=If wanting to directly transfer results to AmpliconRepository.org, please enter your email. 
p3_fileFormat=
p3_flag=--username 
p3_name=Amplicon.Repository.Email
p3_numValues=0..1
p3_optional=on
p3_prefix=--username 
p3_prefix_when_specified=--username 
p3_type=java.lang.String
p3_value=
p4_MODE=
p4_TYPE=TEXT
p4_default_value=
p4_description=If uploading to Amplicon Repository, you must agree to our <a href \= "https\://raw.githubusercontent.com/AmpliconSuite/AmpliconRepository/main/licenses/CCv4-BY.txt">Creative Commons v4 license </a>
p4_fileFormat=
p4_flag=--accept_license
p4_name=accept.license
p4_numValues=0..1
p4_optional=
p4_prefix=
p4_prefix_when_specified=
p4_type=java.lang.String
p4_value=Yes\=Yes;No\=No
p5_MODE=
p5_TYPE=TEXT
p5_default_value=No
p5_description=Whether or not to re-run Amplicon Classifier
p5_fileFormat=
p5_flag=-c 
p5_name=run.amplicon.classifier
p5_numValues=0..1
p5_optional=on
p5_prefix=-c 
p5_prefix_when_specified=-c 
p5_type=java.lang.String
p5_value=Yes\=Yes;No\=No
p6_MODE=
p6_TYPE=TEXT
p6_default_value=
p6_description=Reference genome used for Amplicon Architect results in the input. 
p6_fileFormat=
p6_flag=--ref 
p6_name=reference.genome
p6_numValues=0..1
p6_optional=on
p6_prefix=--ref 
p6_prefix_when_specified=--ref 
p6_type=java.lang.String
p6_value=GRCh38\=GRCh38;hg38\=hg38;GRCh37\=GRCh37;hg19\=hg19;mm10\=mm10;GRCm38\=GRCm38;GRCh38_viral\=GRCh38_viral
p7_MODE=
p7_TYPE=TEXT
p7_default_value=No
p7_description=Upload only mode. Will skip aggregator and upload to server as is. 
p7_fileFormat=
p7_flag=--upload_only
p7_name=upload.only
p7_numValues=0..1
p7_optional=on
p7_prefix=
p7_prefix_when_specified=
p7_type=java.lang.String
p7_value=No\=No;Yes\=Yes
p8_MODE=IN
p8_TYPE=FILE
p8_default_value=
p8_description=A two column file providing current identifier for each sample (col 1), and a replacement name (col 2). 
p8_fileFormat=
p8_flag=--name_map
p8_name=name.map
p8_numValues=0..1
p8_optional=on
p8_prefix=--name_map
p8_prefix_when_specified=--name_map
p8_type=java.io.File
p8_value=
privacy=public
publicationDate=01/08/2024 02\:11 
quality=production
src.repo=https\://github.com/genepattern/AmpliconSuiteAggregator
taskDoc=
taskType=ecdna
userid=edwin5588
version=added license acceptance & new ecdna tag