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comparison kraken-report.xml @ 7:1c163820e346 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken_report/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
author iuc
date Mon, 07 Aug 2017 17:28:06 -0400
parents 00d6d8350905
children 8ddbdc9cdc57
comparison
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6:00d6d8350905 7:1c163820e346
1 <tool id="kraken-report" name="Kraken-report" version="1.2.1"> 1 <tool id="kraken-report" name="Kraken-report" version="@WRAPPER_VERSION@">
2 <description> 2 <description>view sample report of a classification</description>
3 view a sample report of your classification 3
4 </description>
5
6 <macros> 4 <macros>
7 <import>macros.xml</import> 5 <import>macros.xml</import>
8 </macros> 6 </macros>
9 <expand macro="requirements" /> 7 <expand macro="requirements" />
10 <expand macro="stdio" />
11 <expand macro="version_command" /> 8 <expand macro="version_command" />
12 <command> 9 <command detect_errors="exit_code"><![CDATA[
13 <![CDATA[
14 @SET_DATABASE_PATH@ && 10 @SET_DATABASE_PATH@ &&
15 kraken-report @INPUT_DATABASE@ "${kraken_output}" > "$output_report" 11
16 ]]> 12 kraken-report
17 </command> 13 @INPUT_DATABASE@
14 '${kraken_output}'
15 > '$output_report'
16 ]]></command>
18 <inputs> 17 <inputs>
19 <param format="tabular" label="Kraken output" name="kraken_output" type="data" help="Select taxonomy classification produced by kraken"/> 18 <param name="kraken_output" type="data" format="tabular" label="Kraken output" help="Select taxonomy classification produced by kraken"/>
19
20 <expand macro="input_database" /> 20 <expand macro="input_database" />
21 </inputs> 21 </inputs>
22 <outputs> 22 <outputs>
23 <data format="tabular" name="output_report" /> 23 <data format="tabular" name="output_report" />
24 </outputs> 24 </outputs>
25 <tests> 25 <tests>
26 <test> 26 <test>
27 <param name="kraken_output" value="kraken_report_test1.tab" ftype="tabular"/> 27 <param name="kraken_output" value="kraken_report_test1.tab" ftype="tabular"/>
28 <param name="kraken_database" value="test_db"/> 28 <param name="kraken_database" value="test_db"/>
29 <output name="output_report" file="kraken_report_test1_output.tab" ftype="tabular"/> 29 <output name="output_report" ftype="tabular" file="kraken_report_test1_output.tab"/>
30 </test> 30 </test>
31 </tests> 31 </tests>
32 32
33 <help> 33 <help><![CDATA[
34 <![CDATA[
35 34
36 .. class:: warningmark 35 .. class:: warningmark
37 36
38 **Note**: the database used must be the same as the one used in the original Kraken run 37 **Note**: the database used must be the same as the one used in the original Kraken run
39 38
50 5. NCBI taxonomy ID 49 5. NCBI taxonomy ID
51 6. Indented scientific name 50 6. Indented scientific name
52 51
53 The scientific names are indented using spaces, according to the tree 52 The scientific names are indented using spaces, according to the tree
54 structure specified by the taxonomy. 53 structure specified by the taxonomy.
55 ]]> 54 ]]></help>
56 </help>
57 <expand macro="citations" /> 55 <expand macro="citations" />
58 </tool> 56 </tool>