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