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comparison kraken-mpa-report.xml @ 1:688428f6800f draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit ce0de4de3fa3fc25c375e378ac84f78452dd61c3
author devteam
date Wed, 05 Aug 2015 12:09:35 -0400
parents f2757ab26483
children c4fb5dc47fce
comparison
equal deleted inserted replaced
0:f2757ab26483 1:688428f6800f
1 <tool id="kraken-mpa-report" name="Kraken-mpa-report" version="1.1.0"> 1 <?xml version="1.0"?>
2 <expand macro="version_command" /> 2 <tool id="kraken-mpa-report" name="Kraken-mpa-report" version="1.1.1">
3 <expand macro="requirements" /> 3 <description>view report of classification for multiple samples</description>
4 <expand macro="stdio" />
5 <description>
6 view report of classification for multiple samples
7 </description>
8 <macros> 4 <macros>
9 <import>macros.xml</import> 5 <import>macros.xml</import>
10 </macros> 6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
11 <command> 10 <command>
12 <![CDATA[ 11 <![CDATA[
13 12
14 #for $input_count, $input_classification in enumerate( $classification ): 13 #for $input_count, $input_classification in enumerate( $classification ):
15 ln -s "${input_classification}" "sample_${input_count}" && 14 ln -s "${input_classification}" "sample_${input_count}" &&
16 #end for 15 #end for
17 16
18 kraken-mpa-report @INPUT_DATABASE@ 17 @SET_DATABASE_PATH@ && kraken-mpa-report @INPUT_DATABASE@
19 18
20 #for $input_count, $input_classification in enumerate( $classification ): 19 #for $input_count, $input_classification in enumerate( $classification ):
21 "sample_${input_count}" 20 "sample_${input_count}"
22 #end for 21 #end for
23 22
24 ${show_zeros} 23 ${show_zeros}
25 ${header_line} 24 ${header_line}
26 25
27 > "$output_report" 26 > "$output_report"
28 27 ]]>
29
30 ]]>
31 </command> 28 </command>
32 <inputs> 29 <inputs>
33 <param multiple="True" name="classification" type="data" format="tabular" label="Kraken output"/> 30 <param format="tabular" label="Kraken output" multiple="True" name="classification" type="data" />
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"/> 31 <param checked="False" falsevalue="" help="--show-zeros" label="Display taxa even if they lack a read in any sample" name="show_zeros" truevalue="--show-zeros" type="boolean" />
35 <param name="header_line" type="boolean" truevalue="--header-line" falsevalue="" checked="False" label="Display a header line indicating sample IDs" help="--header-line"/> 32 <param checked="False" falsevalue="" help="--header-line" label="Display a header line indicating sample IDs" name="header_line" truevalue="--header-line" type="boolean" />
36 <expand macro="input_database" /> 33 <expand macro="input_database" />
37 </inputs> 34 </inputs>
38 <outputs> 35 <outputs>
39 <data format="tabular" name="output_report" /> 36 <data format="tabular" name="output_report" />
40 </outputs> 37 </outputs>
49 46
50 **What is Does** 47 **What is Does**
51 48
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:: 49 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 50
54 --show-zeros Display taxa even if they lack a read in any sample 51 --show-zeros Display taxa even if they lack a read in any sample
55 --header-line Display a header line indicating sample IDs 52 --header-line Display a header line indicating sample IDs
56 (sample IDs are the filenames) 53 (sample IDs are the filenames)
57 54
58 ----- 55 -----
59 56
60 **Output** 57 **Output**
61 58
62 The output of kraken-mpa-report is tab-delimited, with one line per taxon. 59 The output of kraken-mpa-report is tab-delimited, with one line per taxon.
63 60
64 61 ]]>
65
66
67
68 ]]>
69 </help> 62 </help>
70 <expand macro="citations" /> 63 <expand macro="citations" />
71 </tool> 64 </tool>