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comparison kraken-report.xml @ 2:45ced9c12e18 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit cb6ebb843c71dcfc73aa05cc616f8e3229170108-dirty
author devteam
date Wed, 15 Jul 2015 15:22:27 -0400
parents bb3d55e8ef3d
children 9709eedcff4b
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1:bb3d55e8ef3d 2:45ced9c12e18
1 <tool id="kraken-report" name="Kraken-report" version="1.0.0"> 1 <tool id="kraken-report" name="Kraken-report" version="1.1.0">
2 <description> 2 <description>
3 View a sample report of your classification 3 view a sample report of your classification
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-report @INPUT_DATABASE@ "${kraken_output}" > "$output_report" 11 kraken-report @INPUT_DATABASE@ "${kraken_output}" > "$output_report"
12 ]]> 12 ]]>
13 </command> 13 </command>
14 <inputs> 14 <inputs>
15 <param format="tabular" label="Input the Sequenced Kraken Output from your Current History" name="kraken_output" type="data" /> 15 <param format="tabular" label="Kraken output" name="kraken_output" type="data" help="Select taxonomy classification produced by kraken"/>
16 <expand macro="input_database" /> 16 <expand macro="input_database" />
17 </inputs> 17 </inputs>
18 <outputs> 18 <outputs>
19 <data format="tabular" name="output_report" /> 19 <data format="tabular" name="output_report" />
20 </outputs> 20 </outputs>
21 <help> 21 <help>
22 <![CDATA[ 22 <![CDATA[
23 23
24 ***Note that the database used must be the same as the one used to generate 24 .. class:: warningmark
25 the output file, or the report script may encounter problems.***
26 25
26 **Note**: the database used must be the same as the one used in the original Kraken run
27 27
28 -----
28 29
29 **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:** 30 **Output**
30 31
31 1)Percentage of reads covered by the clade rooted at this taxon 32 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::
32 33
33 2)Number of reads covered by the clade rooted at this taxon 34 1. Percentage of reads covered by the clade rooted at this taxon
34 35 2. Number of reads covered by the clade rooted at this taxon
35 3)Number of reads assigned directly to this taxon 36 3. Number of reads assigned directly to this taxon
36 37 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 filled with a dash.
37 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 -. 38 5. NCBI taxonomy ID
38 39 6. Indented scientific name
39 5)NCBI taxonomy ID
40
41 6)Indented scientific name
42 40
43 The scientific names are indented using spaces, according to the tree 41 The scientific names are indented using spaces, according to the tree
44 structure specified by the taxonomy. 42 structure specified by the taxonomy.
45 ]]> 43 ]]>
46 </help> 44 </help>