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comparison kraken-mpa-report.xml @ 0:f2757ab26483 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Thu, 23 Jul 2015 10:56:14 -0400
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children 688428f6800f
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-1:000000000000 0:f2757ab26483
1 <tool id="kraken-mpa-report" name="Kraken-mpa-report" version="1.1.0">
2 <expand macro="version_command" />
3 <expand macro="requirements" />
4 <expand macro="stdio" />
5 <description>
6 view report of classification for multiple samples
7 </description>
8 <macros>
9 <import>macros.xml</import>
10 </macros>
11 <command>
12 <![CDATA[
13
14 #for $input_count, $input_classification in enumerate( $classification ):
15 ln -s "${input_classification}" "sample_${input_count}" &&
16 #end for
17
18 kraken-mpa-report @INPUT_DATABASE@
19
20 #for $input_count, $input_classification in enumerate( $classification ):
21 "sample_${input_count}"
22 #end for
23
24 ${show_zeros}
25 ${header_line}
26
27 > "$output_report"
28
29
30 ]]>
31 </command>
32 <inputs>
33 <param multiple="True" name="classification" type="data" format="tabular" label="Kraken output"/>
34 <param name="show_zeros" type="boolean" truevalue="--show-zeros" falsevalue="" checked="False" label="Display taxa even if they lack a read in any sample" help="--show-zeros"/>
35 <param name="header_line" type="boolean" truevalue="--header-line" falsevalue="" checked="False" label="Display a header line indicating sample IDs" help="--header-line"/>
36 <expand macro="input_database" />
37 </inputs>
38 <outputs>
39 <data format="tabular" name="output_report" />
40 </outputs>
41 <help>
42 <![CDATA[
43
44 .. class:: warningmark
45
46 **Note**: the database used must be the same as the one used in the original Kraken run
47
48 -----
49
50 **What is Does**
51
52 Kraken-mpa-report summarizes read counts across taxonomic ranks for multiple samples. This is convenient for comparing results across multiple expreriments, conditions, locations, etc. It support sthe following parameters::
53
54 --show-zeros Display taxa even if they lack a read in any sample
55 --header-line Display a header line indicating sample IDs
56 (sample IDs are the filenames)
57
58 -----
59
60 **Output**
61
62 The output of kraken-mpa-report is tab-delimited, with one line per taxon.
63
64
65
66
67
68 ]]>
69 </help>
70 <expand macro="citations" />
71 </tool>