Mercurial > repos > devteam > kraken_report
comparison kraken-report.xml @ 0:f2757ab26483 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
| author | devteam |
|---|---|
| date | Thu, 23 Jul 2015 10:56:14 -0400 |
| parents | |
| children | c4fb5dc47fce |
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| -1:000000000000 | 0:f2757ab26483 |
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| 1 <tool id="kraken-report" name="Kraken-report" version="1.1.0"> | |
| 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[ | |
| 10 @SET_DATABASE_PATH@ && | |
| 11 kraken-report @INPUT_DATABASE@ "${kraken_output}" > "$output_report" | |
| 12 ]]> | |
| 13 </command> | |
| 14 <inputs> | |
| 15 <param format="tabular" label="Kraken output" name="kraken_output" type="data" help="Select taxonomy classification produced by kraken"/> | |
| 16 <expand macro="input_database" /> | |
| 17 </inputs> | |
| 18 <outputs> | |
| 19 <data format="tabular" name="output_report" /> | |
| 20 </outputs> | |
| 21 <help> | |
| 22 <![CDATA[ | |
| 23 | |
| 24 .. class:: warningmark | |
| 25 | |
| 26 **Note**: the database used must be the same as the one used in the original Kraken run | |
| 27 | |
| 28 ----- | |
| 29 | |
| 30 **Output** | |
| 31 | |
| 32 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:: | |
| 33 | |
| 34 1. Percentage of reads covered by the clade rooted at this taxon | |
| 35 2. Number of reads covered by the clade rooted at this taxon | |
| 36 3. Number of reads assigned directly to this taxon | |
| 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 filled with a dash. | |
| 38 5. NCBI taxonomy ID | |
| 39 6. Indented scientific name | |
| 40 | |
| 41 The scientific names are indented using spaces, according to the tree | |
| 42 structure specified by the taxonomy. | |
| 43 ]]> | |
| 44 </help> | |
| 45 <expand macro="version_command" /> | |
| 46 <expand macro="requirements" /> | |
| 47 <expand macro="stdio" /> | |
| 48 <expand macro="citations" /> | |
| 49 </tool> |