Mercurial > repos > devteam > kraken_filter
comparison kraken-filter.xml @ 1:7dfb0218e838 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit 3abfc7eb2999fa588862b84c453012c811fa8350
author | devteam |
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date | Mon, 21 Mar 2016 12:01:56 -0400 |
parents | cbb802a726fd |
children | fe94f318048c |
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0:cbb802a726fd | 1:7dfb0218e838 |
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1 <tool id="kraken-filter" name="Kraken-filter" version="1.1.0"> | 1 <tool id="kraken-filter" name="Kraken-filter" version="1.2.0"> |
2 <description> | 2 <description> |
3 filter classification 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 <expand macro="requirements" /> | |
9 <expand macro="stdio" /> | |
10 <expand macro="version_command" /> | |
8 <command> | 11 <command> |
9 <![CDATA[ | 12 <![CDATA[ |
10 @SET_DATABASE_PATH@ && | 13 @SET_DATABASE_PATH@ && |
11 kraken-filter @INPUT_DATABASE@ --threshold $threshold "${input}" > "$filtered_output" | 14 kraken-filter @INPUT_DATABASE@ --threshold $threshold "${input}" > "$filtered_output" |
12 ]]> | 15 ]]> |
17 <expand macro="input_database" /> | 20 <expand macro="input_database" /> |
18 </inputs> | 21 </inputs> |
19 <outputs> | 22 <outputs> |
20 <data format="tabular" name="filtered_output" /> | 23 <data format="tabular" name="filtered_output" /> |
21 </outputs> | 24 </outputs> |
25 <tests> | |
26 <test> | |
27 <param name="input" value="kraken_filter_test1.tab"/> | |
28 <param name="threshold" value="0"/> | |
29 <param name="kraken_database" value="test_db"/> | |
30 <output name="output" file="kraken_filter_test1_output.tab" ftype="tabular"/> | |
31 </test> | |
32 </tests> | |
33 | |
22 <help> | 34 <help> |
23 <![CDATA[ | 35 <![CDATA[ |
24 | 36 |
25 .. class:: warningmark | 37 .. class:: warningmark |
26 | 38 |
45 the last 3 k-mers mapped to taxonomy ID #562 | 57 the last 3 k-mers mapped to taxonomy ID #562 |
46 | 58 |
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. | 59 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. |
48 ]]> | 60 ]]> |
49 </help> | 61 </help> |
50 <expand macro="version_command" /> | |
51 <expand macro="requirements" /> | |
52 <expand macro="stdio" /> | |
53 <expand macro="citations" /> | 62 <expand macro="citations" /> |
54 </tool> | 63 </tool> |