annotate kraken-filter.xml @ 4:3d6570bffdb1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"

<tool id="kraken-filter" name="Kraken-filter" version="@WRAPPER_VERSION@">
    <description>filter classification by confidence score</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
        @SET_DATABASE_PATH@ &&

        kraken-filter
            @INPUT_DATABASE@
            --threshold $threshold
            '${input}'
            > '$filtered_output'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="tabular" label="Kraken output" help="Select taxonomy classification produced by kraken"/>
        <param argument="--threshold" type="float" value="0" min="0" max="1"
               label="Confidence threshold" help="A floating point number between 0 and 1; default=0"/>

        <expand macro="input_database" />
    </inputs>
    <outputs>
        <data format="tabular" name="filtered_output" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="kraken-filter/kraken_filter_test1.tab"/>
            <param name="threshold" value="0"/>
            <param name="kraken_database" value="new_style_test_entry"/>

            <output name="filtered_output" file="kraken-filter/kraken_filter_test1_output.tab" ftype="tabular"/>
        </test>
    </tests>

    <help>
<![CDATA[

.. class:: warningmark

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

-----

**What it does**

At present, we have not yet developed a confidence score with a solid probabilistic interpretation for Kraken. However, we have developed a simple scoring scheme that has yielded good results for us, and we've made that available in the kraken-filter script. The approach we use allows a user to specify a threshold score in the [0,1] interval; the ``kraken-filter`` script then will adjust labels up the tree until the label's score (described below) meets or exceeds that threshold. If a label at the root of the taxonomic tree would not have a score exceeding the threshold, the sequence is called unclassified by ``kraken-filter``.

A sequence label's score is a fraction C/Q, where C is the number of k-mers mapped to LCA values in the clade rooted at the label, and Q is the number of k-mers in the sequence that lack an ambiguous nucleotide (i.e., they were queried against the database). Consider the example of the LCA mappings in Kraken's output::

 562:13 561:4 A:31 0:1 562:3

would indicate that::

 the first 13 k-mers mapped to taxonomy ID #562
 the next 4 k-mers mapped to taxonomy ID #561
 the next 31 k-mers contained an ambiguous nucleotide
 the next k-mer was not in the database
 the last 3 k-mers mapped to taxonomy ID #562

In this case, ID #561 is the parent node of #562. Here, a label of #562 for this sequence would have a score of C/Q = (13+3)/(13+4+1+3) = 16/21. A label of #561 would have a score of C/Q = (13+4+3)/(13+4+1+3) = 20/21. If a user specified a threshold over 16/21, kraken-filter would adjust the original label from #562 to #561; if the threshold was greater than 20/21, the sequence would become unclassified.
    ]]>
    </help>
    <expand macro="citations" />
</tool>