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comparison metaphlan2krona.xml @ 31:83f06bee818c draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
author bebatut
date Tue, 21 Feb 2017 12:29:37 -0500
parents 99fe591b59fb
children
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30:99fe591b59fb 31:83f06bee818c
1 <tool id="metaphlan2krona" name="Format MetaPhlAn2" version="2.5.0"> 1 <tool id="metaphlan2krona" name="Format MetaPhlAn2" version="@WRAPPER_VERSION@.0">
2 2
3 <description>output for Krona</description> 3 <description>output for Krona</description>
4 4
5 <macros> 5 <macros>
6 <import>metaphlan2_macros.xml</import> 6 <import>metaphlan2_macros.xml</import>
7 </macros> 7 </macros>
8 8
9 <expand macro="requirements"/> 9 <expand macro="requirements"/>
10 <expand macro="stdio"/> 10 <expand macro="stdio"/>
11 11
12 <version_command> 12 <version_command>metaphlan2krona.py -v</version_command>
13 <![CDATA[
14 metaphlan2krona.py -v
15 ]]>
16 </version_command>
17 13
18 <command> 14 <command>
19 <![CDATA[ 15 <![CDATA[
20 metaphlan2krona.py 16 metaphlan2krona.py
21 -p $input_file 17 --profile '$profile'
22 -k $krona 18 -k '$krona'
23 ]]> 19 ]]>
24 </command> 20 </command>
25 21
26 <inputs> 22 <inputs>
27 <param name="input_file" type="data" format="tabular,txt" label="Input file (MetaPhlAN2 output)" help="(--profile)"/> 23 <param argument="--profile" type="data" format="tabular,txt" label="Input file (MetaPhlAN2 output)"/>
28 </inputs> 24 </inputs>
29 25
30 <outputs> 26 <outputs>
31 <data format="tabular" name="krona" label="${tool.name} on ${on_string}: Formatted file for Krona" /> 27 <data format="tabular" name="krona" label="${tool.name} on ${on_string}: Formatted file for Krona" />
32 </outputs> 28 </outputs>
33 29
34 <tests> 30 <tests>
35 <test> 31 <test>
36 <param name="input_file" value="community_profile.tabular"/> 32 <param name="profile" value="community_profile.tabular"/>
37 <output name="krona" file="formatted_to_krona.tabular"/> 33 <output name="krona" file="formatted_to_krona.tabular"/>
38 </test> 34 </test>
39 </tests> 35 </tests>
40 36
41 <help><![CDATA[ 37 <help><![CDATA[
46 42
47 This tool formats MetaPhlAn2 output to be ready for Krona. 43 This tool formats MetaPhlAn2 output to be ready for Krona.
48 44
49 ]]></help> 45 ]]></help>
50 46
51 <citations> 47 <expand macro="citations"/>
52 <citation type="doi">10.1038/nmeth.3589</citation>
53 </citations>
54 </tool> 48 </tool>