view 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

<tool id="kraken-report" name="Kraken-report" version="1.0.0">
    <description>
        View a sample report of your classification
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <command>
        <![CDATA[
        @SET_DATABASE_PATH@ &&
        kraken-report @INPUT_DATABASE@ "${kraken_output}" > "$output_report"
        ]]>
    </command>
    <inputs>
        <param format="tabular" label="Input the Sequenced Kraken Output from your Current History" name="kraken_output" type="data" />
        <expand macro="input_database" />
    </inputs>
    <outputs>
        <data format="tabular" name="output_report" />
    </outputs>
    <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.***



**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

    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 -.

    5)NCBI taxonomy ID

    6)Indented scientific name

The scientific names are indented using spaces, according to the tree
structure specified by the taxonomy.
    ]]>
    </help>
    <expand macro="version_command" />
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="citations" />
</tool>