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comparison metaphlan2krona.xml @ 28:1d993cca38e3 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit b467108d731001d89920aee31433a5b0a623c251-dirty
author bebatut
date Thu, 28 Apr 2016 07:04:50 -0400
parents fb2dc25a832d
children 713a83023626
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27:fb2dc25a832d 28:1d993cca38e3
1 <tool id="metaphlan2krona" name="Format MetaPhlAn2" version="0.1.0"> 1 <tool id="metaphlan2krona" name="Format MetaPhlAn2" version="2.5.0">
2 2
3 <description>output for Krona</description> 3 <description>output for Krona</description>
4 4
5 <requirements> 5 <macros>
6 <requirement type="package" version="2.2.5">bowtie2</requirement> 6 <import>metaphlan2_macros.xml</import>
7 <requirement type="package" version="2.2.0">metaphlan2</requirement> 7 </macros>
8 </requirements>
9 8
10 <stdio> 9 <expand macro="requirements"/>
11 <exit_code range="1:" level="fatal" description="" /> 10 <expand macro="stdio"/>
12 <regex match="ERROR"
13 source="stderr"
14 level="fatal"
15 description="" />
16 <regex match="WARNING"
17 source="stderr"
18 level="warning"
19 description="" />
20 </stdio>
21 11
22 <version_command> 12 <version_command>
23 <![CDATA[ 13 <![CDATA[
24 metaphlan2krona.py -v 14 metaphlan2krona.py -v
25 ]]> 15 ]]>
32 -k $krona 22 -k $krona
33 ]]> 23 ]]>
34 </command> 24 </command>
35 25
36 <inputs> 26 <inputs>
37 <param name="input_file" type="data" format="tabular,txt" label="Input 27 <param name="input_file" type="data" format="tabular,txt" label="Input file (MetaPhlAN2 output)" help="(--profile)"/>
38 file (MetaPhlAN2 output)" help="(--profile)"/>
39 </inputs> 28 </inputs>
40 29
41 <outputs> 30 <outputs>
42 <data format="tabular" name="krona" 31 <data format="tabular" name="krona" label="${tool.name} on ${on_string}: Krona file" />
43 label="${tool.name} on ${on_string}: Krona file" />
44 </outputs> 32 </outputs>
45 33
46 <tests> 34 <tests>
47 <test> 35 <test>
48 <param name="input_file" value="metaphlan2_profiled_metagenome.txt"/> 36 <param name="input_file" value="metaphlan2_profiled_metagenome.txt"/>