comparison 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

1:bb3d55e8ef3d

<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>

        @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>

2:45ced9c12e18

<tool id="kraken-report" name="Kraken-report" version="1.1.0">
    <description>
        view a sample report of your classification
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <command>

        @SET_DATABASE_PATH@ &&
        kraken-report @INPUT_DATABASE@ "${kraken_output}" > "$output_report"
        ]]>
    </command>
    <inputs>
        <param format="tabular" label="Kraken output" name="kraken_output" type="data" help="Select taxonomy classification produced by kraken"/>
        <expand macro="input_database" />
    </inputs>
    <outputs>
        <data format="tabular" name="output_report" />
    </outputs>
    <help>
<![CDATA[

.. class:: warningmark

**Note**: the database used must be the same as the one used in the original Kraken run

-----

**Output**

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 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.
    ]]>
    </help>