Mercurial > repos > bebatut > format_metaphlan2_output
view format_metaphlan2_output.xml @ 1:1e74cb2c8e67 draft
"planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 2cc71b230101205641d7fafa822d4ab3d398066a"
author | bebatut |
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date | Mon, 14 Sep 2020 09:52:15 +0000 |
parents | 2bfa9b200600 |
children | 2c87f56bd53a |
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<tool id="format_metaphlan2_output" name="Format MetaPhlAn2" version="0.2.0"> <description>output to extract abundance at different taxonomic levels</description> <requirements> </requirements> <stdio> </stdio> <version_command></version_command> <command><![CDATA[ python $__tool_directory__/format_metaphlan2_output.py --metaphlan2_output $input_file --all_taxo_level_abundance_file $all_taxo_level_abundance_file --kingdom_abundance_file $kingdom_abundance_file --phylum_abundance_file $phylum_abundance_file --class_abundance_file $class_abundance_file --order_abundance_file $order_abundance_file --family_abundance_file $family_abundance_file --genus_abundance_file $genus_abundance_file --species_abundance_file $species_abundance_file --strains_abundance_file $strains_abundance_file ]]></command> <inputs> <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="Output file of MetaPhlAN with all taxonomic levels (from kingdom to strains, --metaphlan2_output)"/> </inputs> <outputs> <data name="all_taxo_level_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Abundances for all taxonomic levels" /> <data name="kingdom_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Kingdom abundances" /> <data name="phylum_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Phylum abundances" /> <data name="class_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Class abundances" /> <data name="order_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Order abundances" /> <data name="family_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Family abundances" /> <data name="genus_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Genus abundances" /> <data name="species_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Species abundances" /> <data name="strains_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Stain abundances" /> </outputs> <tests> <test> <param name="input_file" value="metaphlan2_output.txt"/> <output name="all_taxo_level_abundance_file" file="all_taxo_level_abundance.txt"/> <output name="kingdom_abundance_file" file="kingdom_abundance.txt"/> <output name="phylum_abundance_file" file="phylum_abundance.txt"/> <output name="class_abundance_file" file="class_abundance.txt"/> <output name="order_abundance_file" file="order_abundance.txt"/> <output name="family_abundance_file" file="family_abundance.txt"/> <output name="genus_abundance_file" file="genus_abundance.txt"/> <output name="species_abundance_file" file="species_abundance.txt"/> <output name="strains_abundance_file" file="strains_abundance.txt"/> </test> </tests> <help><![CDATA[ **What it does** This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains). 9 files are generated: one file per taxonomic levels with abundance for corresponding clades and one file combining all taxonomic levels and corresponding abundances. ]]></help> <citations> </citations> </tool>