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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
author bebatut
date Wed, 20 Apr 2016 07:52:22 -0400
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1 <tool id="format_metaphlan2_output" name="Format MetaPhlAn2" version="0.1.0">
2 <description>output to extract abundance at different taxonomic levels</description>
3
4 <requirements>
5 </requirements>
6
7 <stdio>
8 </stdio>
9
10 <version_command></version_command>
11
12 <command><![CDATA[
13 python $__tool_directory__/format_metaphlan2_output.py
14 --metaphlan2_output $input_file
15 --all_taxo_level_abundance_file $all_taxo_level_abundance_file
16 --kingdom_abundance_file $kingdom_abundance_file
17 --phylum_abundance_file $phylum_abundance_file
18 --class_abundance_file $class_abundance_file
19 --order_abundance_file $order_abundance_file
20 --family_abundance_file $family_abundance_file
21 --genus_abundance_file $genus_abundance_file
22 --species_abundance_file $species_abundance_file
23 --strains_abundance_file $strains_abundance_file
24 ]]></command>
25
26 <inputs>
27 <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="Output file of MetaPhlAN with all taxonomic levels (from kingdom to strains, --metaphlan2_output)"/>
28 </inputs>
29
30 <outputs>
31 <data name="all_taxo_level_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Abundances for all taxonomic levels" />
32 <data name="kingdom_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Kingdom abundances" />
33 <data name="phylum_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Phylum abundances" />
34 <data name="class_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Class abundances" />
35 <data name="order_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Order abundances" />
36 <data name="family_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Family abundances" />
37 <data name="genus_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Genus abundances" />
38 <data name="species_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Species abundances" />
39 <data name="strains_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Stain abundances" />
40 </outputs>
41
42 <tests>
43 <test>
44 <param name="input_file" value="metaphlan2_output.txt"/>
45 <output name="all_taxo_level_abundance_file" file="all_taxo_level_abundance.txt"/>
46 <output name="kingdom_abundance_file" file="kingdom_abundance.txt"/>
47 <output name="phylum_abundance_file" file="phylum_abundance.txt"/>
48 <output name="class_abundance_file" file="class_abundance.txt"/>
49 <output name="order_abundance_file" file="order_abundance.txt"/>
50 <output name="family_abundance_file" file="family_abundance.txt"/>
51 <output name="genus_abundance_file" file="genus_abundance.txt"/>
52 <output name="species_abundance_file" file="species_abundance.txt"/>
53 <output name="strains_abundance_file" file="strains_abundance.txt"/>
54 </test>
55 </tests>
56
57 <help><![CDATA[
58 **What it does**
59
60 This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).
61
62 9 files are generated: one file per taxonomic levels with abundance for corresponding clades and one file combining all taxonomic levels and corresponding abundances.
63 ]]></help>
64
65 <citations>
66 </citations>
67 </tool>