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Option Type: FILELIST

Argument: batch batchrun classify compare filelist fixendings gbatch haqdb nwklist oma parseparam resfiles vbatch virusgb xrefdata

Modules: gopherbench revert rje_pacbio rje_taxamap file_monster rje_mysql rje_samtools rje_xref fiesta pagsat_V1 pagsat picsi seqsuite slimfinder slimmutant slimprob smrtscape_V1 smrtscape

ModuleOptionDescriptionDefault
fiesta haqdb=FILELIST Optional extra databases to search for HAQESAC analysis
file_monster fixendings=FILELIST Replace Mac with UNIX line endings for FILELIST (wildcards allowed)
gopherbench oma=FILELIST List of OMA pairwise orthology files (wildcards allowed)
pagsat compare=FILES Compare assemblies selected using a list of *.Summary.tdt files (wildcards allowed).
pagsat_V1 compare=FILES Compare assemblies selected using a list of *.Summary.tdt files (wildcards allowed).
picsi resfiles=FILES List of CSV MASCOT output files
revert gbatch=FILELIST Run REVERT on a list of genome files (over-rides genome=FILE). Wildcards allowed.
revert vbatch=FILELIST Run REVERT on a list of virusgb files (over-rides virusgb=FILE). Wildcards allowed.
revert virusgb=FILE/LIST Either a genbank download (must end *.gb) or a list of GenBank viral nuccore UIDs virus.gb
rje_mysql filelist=FILE(s) Input file or files. May be comma-separated (FILE1,FILE2) and include wildcards. *.tdt,*.csv
rje_pacbio parseparam=FILES Parse parameter settings from 1+ assembly runs
rje_samtools batch=FILELIST List of MPileup/SAM files to be parsed and filtered (e.g. *.pileup)
rje_taxamap classify=FILELIST List of files containing protein IDs (first column) for additional taxsum outputs *.class
rje_taxamap nwklist=FILES List of Newick format files. (*.nwk names must match accnum.) Wildcards allowed. *.nwk
rje_xref xrefdata=FILES List of files with delimited data of identifier cross-referencing (wildcards allowed)
seqsuite batchrun=FILELIST Batch run the program on selected files (wildcards allowed)
slimfinder batch=FILELIST 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
smrtscape batch=FILELIST Batch input of multiple subread fasta files (wildcards allowed) if seqin=None basefile.fofn
smrtscape parseparam=FILES Parse parameter settings from 1+ assembly runs
smrtscape_V1 batch=FILELIST Batch input of multiple subread fasta files (wildcards allowed) if seqin=None
smrtscape_V1 parseparam=FILES Parse parameter settings from 1+ assembly runs

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