Mercurial > repos > devteam > kraken_filter
comparison kraken-filter.xml @ 0:60d9479c58d6 draft
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| author | devteam |
|---|---|
| date | Wed, 22 Apr 2015 13:03:54 -0400 |
| parents | |
| children | f093ba52debe |
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| -1:000000000000 | 0:60d9479c58d6 |
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| 1 <tool id="kraken-filter" name="Filter Kraken" version="1.0.0"> | |
| 2 <description> | |
| 3 by confidence score | |
| 4 </description> | |
| 5 <macros> | |
| 6 <import>macros.xml</import> | |
| 7 </macros> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 kraken-filter @INPUT_DATABASE@ --threshold $threshold "${input}" > "$filtered_output" | |
| 11 ]]> | |
| 12 </command> | |
| 13 <inputs> | |
| 14 <param format="tabular" label="Kraken classified output" name="input" type="data" /> | |
| 15 <param label="Confidence threshold" max="1" min="0" name="threshold" type="float" value="0" /> | |
| 16 <expand macro="input_database" /> | |
| 17 </inputs> | |
| 18 <outputs> | |
| 19 <data format="tabular" name="filtered_output" /> | |
| 20 </outputs> | |
| 21 <help> | |
| 22 <![CDATA[ | |
| 23 | |
| 24 ***Note that the database used must be the same as the one used to generate | |
| 25 the output file, or the report script may encounter problems.*** | |
| 26 | |
| 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: | |
| 28 | |
| 29 "562:13 561:4 A:31 0:1 562:3" would indicate that: | |
| 30 | |
| 31 the first 13 k-mers mapped to taxonomy ID #562 | |
| 32 the next 4 k-mers mapped to taxonomy ID #561 | |
| 33 the next 31 k-mers contained an ambiguous nucleotide | |
| 34 the next k-mer was not in the database | |
| 35 the last 3 k-mers mapped to taxonomy ID #562 | |
| 36 | |
| 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. | |
| 38 ]]> | |
| 39 </help> | |
| 40 <expand macro="version_command" /> | |
| 41 <expand macro="requirements" /> | |
| 42 <expand macro="stdio" /> | |
| 43 <expand macro="citations" /> | |
| 44 </tool> |