Mercurial > repos > devteam > kraken_report
diff kraken-report.xml @ 2:45ced9c12e18 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit cb6ebb843c71dcfc73aa05cc616f8e3229170108-dirty
| author | devteam |
|---|---|
| date | Wed, 15 Jul 2015 15:22:27 -0400 |
| parents | bb3d55e8ef3d |
| children | 9709eedcff4b |
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--- a/kraken-report.xml Tue May 19 16:42:26 2015 -0400 +++ b/kraken-report.xml Wed Jul 15 15:22:27 2015 -0400 @@ -1,6 +1,6 @@ -<tool id="kraken-report" name="Kraken-report" version="1.0.0"> +<tool id="kraken-report" name="Kraken-report" version="1.1.0"> <description> - View a sample report of your classification + view a sample report of your classification </description> <macros> <import>macros.xml</import> @@ -12,7 +12,7 @@ ]]> </command> <inputs> - <param format="tabular" label="Input the Sequenced Kraken Output from your Current History" name="kraken_output" type="data" /> + <param format="tabular" label="Kraken output" name="kraken_output" type="data" help="Select taxonomy classification produced by kraken"/> <expand macro="input_database" /> </inputs> <outputs> @@ -21,24 +21,22 @@ <help> <![CDATA[ -***Note that the database used must be the same as the one used to generate -the output file, or the report script may encounter problems.*** +.. class:: warningmark +**Note**: the database used must be the same as the one used in the original Kraken run +----- -**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:** - - 1)Percentage of reads covered by the clade rooted at this taxon +**Output** - 2)Number of reads covered by the clade rooted at this taxon - - 3)Number of reads assigned directly to this taxon +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:: - 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 -. - - 5)NCBI taxonomy ID - - 6)Indented scientific name + 1. Percentage of reads covered by the clade rooted at this taxon + 2. Number of reads covered by the clade rooted at this taxon + 3. Number of reads assigned directly to this taxon + 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. + 5. NCBI taxonomy ID + 6. Indented scientific name The scientific names are indented using spaces, according to the tree structure specified by the taxonomy.