SLiMSuite REST Server


Links
REST Home
EdwardsLab Homepage
EdwardsLab Blog
SLiMSuite Blog
SLiMSuite
Webservers
Genomes
REST Pages
REST Status
REST Help
REST Tools
REST Alias Data
REST API
REST News
REST Sitemap

SLiMSuite Documentation

Please note that command documentation sometimes lags behind the latest module versions. Click on module names to check current documentation.

cmd: batch

Option Type: [?]{docs:?} FILELIST GLIST LIST

Modules: orcfinder rje_misc rje_paml rje_price rje_teaching qslimfinder_V1.9 slimfinder_V4.9 slimprob_V1.4 rje_iridis rje_samtools rje_slimcore snp_mapper fiesta qslimfinder slimfarmer slimfinder slimmutant slimprob slimsearch smrtscape_V1 smrtscape


ModuleOptionDescriptionDefault
fiesta batch=LIST List of EST libraries to search (will use seqin if none given)
orcfinder batch=LIST List of files to search, wildcards allowed. (Over-ruled by seqin=FILE.) *.dat,*.fas
qslimfinder batch=LIST List of files to search, wildcards allowed. (Over-ruled by seqin=FILE.) *.dat,*.fas
qslimfinder_V1.9 batch=LIST List of files to search, wildcards allowed. (Over-ruled by seqin=FILE.) *.dat,*.fas
rje_iridis [batch=?]{docs:?} ?
rje_misc batch=GLIST List of files to process for relevant task
rje_paml batch=LIST List of files to batch run on '*.fas'
rje_price batch=LIST List of alignment files to use as input *.fas,*.fasta
rje_samtools batch=FILELIST List of MPileup/SAM files to be parsed and filtered (e.g. *.pileup)
rje_slimcore batch=LIST List of files to search, wildcards allowed. *.dat,*.fas
rje_teaching [batch=?]{docs:?} ?
slimfarmer [batch=?]{docs:?} ?
slimfinder batch=FILELIST List of files to search, wildcards allowed. (Over-ruled by seqin=FILE.) *.dat,*.fas
slimfinder_V4.9 batch=LIST List of files to search, wildcards allowed. (Over-ruled by seqin=FILE.) *.dat,*.fas
slimmutant batch=FILELIST List of mutfiles to run in batch mode. Wildcards allowed.
slimprob batch=FILELIST List of files to search, wildcards allowed. (Over-ruled by seqin=FILE.) *.dat,*.fas
slimprob_V1.4 batch=LIST List of sequence files for batch input (wildcard * permitted)
slimsearch batch=LIST List of sequence files for batch input (wildcard * permitted)
smrtscape batch=FILELIST Batch input of multiple subread fasta files (wildcards allowed) if seqin=None basefile.fofn
smrtscape_V1 batch=FILELIST Batch input of multiple subread fasta files (wildcards allowed) if seqin=None
snp_mapper batch=LIST List of alignment files to read X.aln - must have X_polymorphisms.txt too *.aln

© 2015 RJ Edwards. Contact: richard.edwards@unsw.edu.au.