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comparison kraken-filter.xml @ 3:7fb926851f66 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
author devteam
date Fri, 18 Dec 2015 19:41:19 -0500
parents 317726be0703
children d2c12af1943a
comparison
equal deleted inserted replaced
2:317726be0703 3:7fb926851f66
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>