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annotate kraken-filter.xml @ 6:ccfb9cbfcc72 draft

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author iuc
date Mon, 07 Aug 2017 17:27:49 -0400
parents d246279116a4
children 6e690205b306
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1 <tool id="kraken-filter" name="Kraken-filter" version="@WRAPPER_VERSION@">
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2 <description>filter classification by confidence score</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version_command" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 @SET_DATABASE_PATH@ &&
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11 kraken-filter
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12 @INPUT_DATABASE@
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13 --threshold $threshold
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14 '${input}'
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15 > '$filtered_output'
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16 ]]></command>
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17 <inputs>
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18 <param name="input" type="data" format="tabular" label="Kraken output" help="Select taxonomy classification produced by kraken"/>
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19 <param argument="--threshold" type="float" value="0" min="0" max="1"
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20 label="Confidence threshold" help="A floating point number between 0 and 1; default=0"/>
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21
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22 <expand macro="input_database" />
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23 </inputs>
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24 <outputs>
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25 <data format="tabular" name="filtered_output" />
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="input" value="kraken_filter_test1.tab"/>
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30 <param name="threshold" value="0"/>
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31 <param name="kraken_database" value="test_db"/>
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33 <output name="filtered_output" file="kraken_filter_test1_output.tab" ftype="tabular"/>
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34 </test>
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35 </tests>
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36
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37 <help>
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38 <![CDATA[
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40 .. class:: warningmark
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42 **Note**: the database used must be the same as the one used in the original Kraken run
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44 -----
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46 **What it does**
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48 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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49
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50 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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52 562:13 561:4 A:31 0:1 562:3
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54 would indicate that::
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56 the first 13 k-mers mapped to taxonomy ID #562
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57 the next 4 k-mers mapped to taxonomy ID #561
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58 the next 31 k-mers contained an ambiguous nucleotide
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59 the next k-mer was not in the database
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60 the last 3 k-mers mapped to taxonomy ID #562
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62 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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63 ]]>
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64 </help>
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65 <expand macro="citations" />
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66 </tool>