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

planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit cb6ebb843c71dcfc73aa05cc616f8e3229170108-dirty
author devteam
date Wed, 15 Jul 2015 15:22:22 -0400
parents f093ba52debe
children 7fb926851f66
comparison
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1:f093ba52debe 2:317726be0703
1 <tool id="kraken-filter" name="Filter Kraken" version="1.0.0"> 1 <tool id="kraken-filter" name="Kraken-filter" version="1.1.0">
2 <description> 2 <description>
3 by confidence score 3 filter classification by confidence score
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
8 <command> 8 <command>
10 @SET_DATABASE_PATH@ && 10 @SET_DATABASE_PATH@ &&
11 kraken-filter @INPUT_DATABASE@ --threshold $threshold "${input}" > "$filtered_output" 11 kraken-filter @INPUT_DATABASE@ --threshold $threshold "${input}" > "$filtered_output"
12 ]]> 12 ]]>
13 </command> 13 </command>
14 <inputs> 14 <inputs>
15 <param format="tabular" label="Kraken classified output" name="input" type="data" /> 15 <param format="tabular" label="Kraken output" name="input" type="data" help="Select taxonomy classification produced by kraken"/>
16 <param label="Confidence threshold" max="1" min="0" name="threshold" type="float" value="0" /> 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"/>
17 <expand macro="input_database" /> 17 <expand macro="input_database" />
18 </inputs> 18 </inputs>
19 <outputs> 19 <outputs>
20 <data format="tabular" name="filtered_output" /> 20 <data format="tabular" name="filtered_output" />
21 </outputs> 21 </outputs>
22 <help> 22 <help>
23 <![CDATA[ 23 <![CDATA[
24 24
25 ***Note that the database used must be the same as the one used to generate 25 .. class:: warningmark
26 the output file, or the report script may encounter problems.***
27 26
28 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: 27 **Note**: the database used must be the same as the one used in the original Kraken run
29 28
30 "562:13 561:4 A:31 0:1 562:3" would indicate that: 29 -----
31 30
32 the first 13 k-mers mapped to taxonomy ID #562 31 **What it does**
33 the next 4 k-mers mapped to taxonomy ID #561 32
34 the next 31 k-mers contained an ambiguous nucleotide 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``.
35 the next k-mer was not in the database 34
36 the last 3 k-mers mapped to taxonomy ID #562 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::
36
37 562:13 561:4 A:31 0:1 562:3
38
39 would indicate that::
40
41 the first 13 k-mers mapped to taxonomy ID #562
42 the next 4 k-mers mapped to taxonomy ID #561
43 the next 31 k-mers contained an ambiguous nucleotide
44 the next k-mer was not in the database
45 the last 3 k-mers mapped to taxonomy ID #562
37 46
38 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. 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.
39 ]]> 48 ]]>
40 </help> 49 </help>
41 <expand macro="version_command" /> 50 <expand macro="version_command" />