SLiMSuite REST Server


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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.