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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
| Module | Option | Description | Default |
|---|---|---|---|
| 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.