Mercurial > repos > devteam > kraken_report
annotate kraken-report.xml @ 1:bb3d55e8ef3d draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit cb1743eafd4ca98be0148d557770ef8635cc8d4c-dirty
| author | devteam |
|---|---|
| date | Tue, 19 May 2015 16:42:26 -0400 |
| parents | 8bbf903bf0cb |
| children | 45ced9c12e18 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="kraken-report" name="Kraken-report" version="1.0.0"> |
| 2 <description> | |
| 3 View a sample report of your classification | |
| 4 </description> | |
| 5 <macros> | |
| 6 <import>macros.xml</import> | |
| 7 </macros> | |
| 8 <command> | |
| 9 <![CDATA[ | |
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bb3d55e8ef3d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit cb1743eafd4ca98be0148d557770ef8635cc8d4c-dirty
devteam
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0
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10 @SET_DATABASE_PATH@ && |
| 0 | 11 kraken-report @INPUT_DATABASE@ "${kraken_output}" > "$output_report" |
| 12 ]]> | |
| 13 </command> | |
| 14 <inputs> | |
| 15 <param format="tabular" label="Input the Sequenced Kraken Output from your Current History" name="kraken_output" type="data" /> | |
| 16 <expand macro="input_database" /> | |
| 17 </inputs> | |
| 18 <outputs> | |
| 19 <data format="tabular" name="output_report" /> | |
| 20 </outputs> | |
| 21 <help> | |
| 22 <![CDATA[ | |
| 23 | |
| 24 ***Note that the database used must be the same as the one used to generate | |
| 25 the output file, or the report script may encounter problems.*** | |
| 26 | |
| 27 | |
| 28 | |
| 29 **The output of kraken-report is tab-delimited, with one line per taxon. The fields of the output, from left-to-right, are as follows:** | |
| 30 | |
| 31 1)Percentage of reads covered by the clade rooted at this taxon | |
| 32 | |
| 33 2)Number of reads covered by the clade rooted at this taxon | |
| 34 | |
| 35 3)Number of reads assigned directly to this taxon | |
| 36 | |
| 37 4)A rank code, indicating (U)nclassified, (D)omain, (K)ingdom, (P)hylum, (C)lass, (O)rder, (F)amily, (G)enus, or (S)pecies. All other ranks are simply -. | |
| 38 | |
| 39 5)NCBI taxonomy ID | |
| 40 | |
| 41 6)Indented scientific name | |
| 42 | |
| 43 The scientific names are indented using spaces, according to the tree | |
| 44 structure specified by the taxonomy. | |
| 45 ]]> | |
| 46 </help> | |
| 47 <expand macro="version_command" /> | |
| 48 <expand macro="requirements" /> | |
| 49 <expand macro="stdio" /> | |
| 50 <expand macro="citations" /> | |
| 51 </tool> |