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annotate kraken-filter.xml @ 2:317726be0703 draft

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author devteam
date Wed, 15 Jul 2015 15:22:22 -0400
parents f093ba52debe
children 7fb926851f66
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1 <tool id="kraken-filter" name="Kraken-filter" version="1.1.0">
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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 <command>
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9 <![CDATA[
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10 @SET_DATABASE_PATH@ &&
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11 kraken-filter @INPUT_DATABASE@ --threshold $threshold "${input}" > "$filtered_output"
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12 ]]>
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13 </command>
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14 <inputs>
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15 <param format="tabular" label="Kraken output" name="input" type="data" help="Select taxonomy classification produced by kraken"/>
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16 <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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17 <expand macro="input_database" />
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18 </inputs>
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19 <outputs>
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20 <data format="tabular" name="filtered_output" />
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21 </outputs>
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22 <help>
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23 <![CDATA[
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25 .. class:: warningmark
317726be0703 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit cb6ebb843c71dcfc73aa05cc616f8e3229170108-dirty
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27 **Note**: the database used must be the same as the one used in the original Kraken run
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29 -----
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31 **What it does**
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33 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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35 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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37 562:13 561:4 A:31 0:1 562:3
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39 would indicate that::
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41 the first 13 k-mers mapped to taxonomy ID #562
317726be0703 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit cb6ebb843c71dcfc73aa05cc616f8e3229170108-dirty
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42 the next 4 k-mers mapped to taxonomy ID #561
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43 the next 31 k-mers contained an ambiguous nucleotide
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44 the next k-mer was not in the database
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45 the last 3 k-mers mapped to taxonomy ID #562
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47 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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48 ]]>
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49 </help>
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50 <expand macro="version_command" />
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51 <expand macro="requirements" />
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52 <expand macro="stdio" />
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53 <expand macro="citations" />
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54 </tool>