comparison kraken-report.xml @ 0:8bbf903bf0cb draft

Uploaded
author devteam
date Wed, 22 Apr 2015 13:04:06 -0400
parents
children bb3d55e8ef3d
comparison
equal deleted inserted replaced
-1:000000000000 0:8bbf903bf0cb
1 <tool id="kraken-report" name="Kraken-report" version="1.0.0">
2 <description>
3 View a sample report of your classification
4 </description>
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8 <command>
9 <![CDATA[
10 kraken-report @INPUT_DATABASE@ "${kraken_output}" > "$output_report"
11 ]]>
12 </command>
13 <inputs>
14 <param format="tabular" label="Input the Sequenced Kraken Output from your Current History" name="kraken_output" type="data" />
15 <expand macro="input_database" />
16 </inputs>
17 <outputs>
18 <data format="tabular" name="output_report" />
19 </outputs>
20 <help>
21 <![CDATA[
22
23 ***Note that the database used must be the same as the one used to generate
24 the output file, or the report script may encounter problems.***
25
26
27
28 **The output of kraken-report is tab-delimited, with one line per taxon. The fields of the output, from left-to-right, are as follows:**
29
30 1)Percentage of reads covered by the clade rooted at this taxon
31
32 2)Number of reads covered by the clade rooted at this taxon
33
34 3)Number of reads assigned directly to this taxon
35
36 4)A rank code, indicating (U)nclassified, (D)omain, (K)ingdom, (P)hylum, (C)lass, (O)rder, (F)amily, (G)enus, or (S)pecies. All other ranks are simply -.
37
38 5)NCBI taxonomy ID
39
40 6)Indented scientific name
41
42 The scientific names are indented using spaces, according to the tree
43 structure specified by the taxonomy.
44 ]]>
45 </help>
46 <expand macro="version_command" />
47 <expand macro="requirements" />
48 <expand macro="stdio" />
49 <expand macro="citations" />
50 </tool>