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1 <tool id="kraken-filter" name="Filter Kraken" version="1.0.0">
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2 <description>
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3 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 <command>
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9 <![CDATA[
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10 kraken-filter @INPUT_DATABASE@ --threshold $threshold "${input}" > "$filtered_output"
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11 ]]>
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12 </command>
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13 <inputs>
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14 <param format="tabular" label="Kraken classified output" name="input" type="data" />
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15 <param label="Confidence threshold" max="1" min="0" name="threshold" type="float" value="0" />
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16 <expand macro="input_database" />
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17 </inputs>
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18 <outputs>
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19 <data format="tabular" name="filtered_output" />
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20 </outputs>
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21 <help>
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22 <![CDATA[
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23
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24 ***Note that the database used must be the same as the one used to generate
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25 the output file, or the report script may encounter problems.***
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26
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27 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:
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28
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29 "562:13 561:4 A:31 0:1 562:3" would indicate that:
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30
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31 the first 13 k-mers mapped to taxonomy ID #562
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32 the next 4 k-mers mapped to taxonomy ID #561
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33 the next 31 k-mers contained an ambiguous nucleotide
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34 the next k-mer was not in the database
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35 the last 3 k-mers mapped to taxonomy ID #562
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36
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37 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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38 ]]>
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39 </help>
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40 <expand macro="version_command" />
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41 <expand macro="requirements" />
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42 <expand macro="stdio" />
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43 <expand macro="citations" />
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44 </tool>
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