Mercurial > repos > thanhlv > ariba
comparison help-command.txt @ 3:6aabe4f367fd draft
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ariba commit 067b5a6a02d5f04c2155b45eed5df257a1360645-dirty
| author | thanhlv |
|---|---|
| date | Mon, 18 Feb 2019 11:48:39 -0500 |
| parents | 8beb2af51dc5 |
| children |
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| 2:87341275b335 | 3:6aabe4f367fd |
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| 1 usage: ariba <command> <options> | |
| 2 | |
| 3 ARIBA: Antibiotic Resistance Identification By Assembly | |
| 4 | |
| 5 optional arguments: | |
| 6 -h, --help show this help message and exit | |
| 7 | |
| 8 Available commands: | |
| 9 | |
| 10 aln2meta Converts multi-aln fasta and SNPs to metadata | |
| 11 expandflag Expands flag column of report file | |
| 12 flag Translate the meaning of a flag | |
| 13 getref Download reference data | |
| 14 micplot Make violin/dot plots using MIC data | |
| 15 prepareref Prepare reference data for input to "run" | |
| 16 pubmlstget Download species from PubMLST and make db | |
| 17 pubmlstspecies | |
| 18 Get list of available species from PubMLST | |
| 19 refquery Get cluster or sequence info from prepareref output | |
| 20 run Run the local assembly pipeline | |
| 21 summary Summarise multiple reports made by "run" | |
| 22 test Run small built-in test dataset | |
| 23 version Get versions and exit |