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annotate kraken-filter.xml @ 5:d246279116a4 draft

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author devteam
date Wed, 23 Mar 2016 10:59:52 -0400
parents d2c12af1943a
children ccfb9cbfcc72
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1 <tool id="kraken-filter" name="Kraken-filter" version="1.2.1">
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2 <description>
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3 filter classification by confidence score
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="stdio" />
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10 <expand macro="version_command" />
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11 <command>
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12 <![CDATA[
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13 @SET_DATABASE_PATH@ &&
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14 kraken-filter @INPUT_DATABASE@ --threshold $threshold "${input}" > "$filtered_output"
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15 ]]>
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16 </command>
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17 <inputs>
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18 <param format="tabular" label="Kraken output" name="input" type="data" help="Select taxonomy classification produced by kraken"/>
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19 <param label="Confidence threshold" max="1" min="0" name="threshold" type="float" value="0" help="--threshold; A number between 0 and 1; default=0"/>
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20 <expand macro="input_database" />
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21 </inputs>
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22 <outputs>
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23 <data format="tabular" name="filtered_output" />
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="input" value="kraken_filter_test1.tab"/>
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28 <param name="threshold" value="0"/>
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29 <param name="kraken_database" value="test_db"/>
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30 <output name="output" file="kraken_filter_test1_output.tab" ftype="tabular"/>
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31 </test>
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32 </tests>
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33
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34 <help>
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35 <![CDATA[
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37 .. class:: warningmark
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39 **Note**: the database used must be the same as the one used in the original Kraken run
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41 -----
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43 **What it does**
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45 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``.
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47 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::
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49 562:13 561:4 A:31 0:1 562:3
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51 would indicate that::
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53 the first 13 k-mers mapped to taxonomy ID #562
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54 the next 4 k-mers mapped to taxonomy ID #561
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55 the next 31 k-mers contained an ambiguous nucleotide
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56 the next k-mer was not in the database
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57 the last 3 k-mers mapped to taxonomy ID #562
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59 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.
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60 ]]>
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61 </help>
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62 <expand macro="citations" />
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63 </tool>