comparison kraken-filter.xml @ 0:60d9479c58d6 draft

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0:60d9479c58d6

<tool id="kraken-filter" name="Filter Kraken" version="1.0.0">
    <description>
        by confidence score
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <command>
        <![CDATA[
        kraken-filter @INPUT_DATABASE@ --threshold $threshold "${input}" > "$filtered_output"
        ]]>
    </command>
    <inputs>
        <param format="tabular" label="Kraken classified output" name="input" type="data" />
        <param label="Confidence threshold" max="1" min="0" name="threshold" type="float" value="0" />
        <expand macro="input_database" />
    </inputs>
    <outputs>
        <data format="tabular" name="filtered_output" />
    </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.***

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 given earlier:

"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="version_command" />
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="citations" />
</tool>