Mercurial > repos > bebatut > combine_metaphlan2_humann2
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43"
author | bgruening |
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date | Wed, 19 Oct 2022 14:44:00 +0000 |
parents | e25efca0a49c |
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<tool id="combine_metaphlan2_humann2" name="Combine MetaPhlAn2 and HUMAnN2 outputs" version="0.2.0"> <description>to relate genus/species abundances and gene families/pathways abundances</description> <requirements> </requirements> <stdio> <exit_code range="1:" /> <exit_code range=":-1" /> </stdio> <version_command></version_command> <command><![CDATA[ python $__tool_directory__/combine_metaphlan2_humann2.py --metaphlan2_fp '$metaphlan2_file' --humann2_fp '$humann2_file' --type '$type' #if str($type) == 'gene_families' --output_fp '$gene_families_output_file' #else --output_fp '$pathway_output_file' #end if ]]></command> <inputs> <param name="metaphlan2_file" format="txt,tabular" type="data" label="Input file corresponding to MetaPhlAn2 output" help="The MetaPhlAn2 output file contains relative abundance of clades at different taxonomic levels (--metaphlan2_file)"/> <param name="humann2_file" format="txt,tabular" type="data" label="Input file corresponding to HUMAnN2 output" help="The HUMAnN2 output file contains relative abundance of gene families or pathways with corresponding taxonomic stratification (--humann2_file)"/> <param name='type' type="select" label="Type of characteristics in HUMAnN2 file" help="(--type)"> <option value="gene_families" selected="true">Gene families</option> <option value="pathways">Pathways</option> </param> </inputs> <outputs> <data name="gene_families_output_file" format="tabular" label="${tool.name} on ${on_string}: Gene family abundances related to genus/species abundances" > <filter>type=="gene_families"</filter> </data> <data name="pathway_output_file" format="tabular" label="${tool.name} on ${on_string}: Pathway abundances related to genus/species abundances" > <filter>type=="pathways"</filter> </data> </outputs> <tests> <test> <param name="metaphlan2_file" value="metaphlan2_input.txt"/> <param name="humann2_file" value="humann2_gene_families_input.tabular"/> <param name='type' value="gene_families"/> <output name="gene_families_output_file"> <assert_contents> <has_n_columns n="8"/> <has_n_lines n="29434"/> <has_text text="Staphylococcus_epidermidis"/> <has_text text="Putative transposon Tn552 DNA invertase bin3"/> <has_size value="3467947"/> </assert_contents> </output> </test> <test> <param name="metaphlan2_file" value="metaphlan2_input.txt"/> <param name="humann2_file" value="humann2_pathways_input.tabular"/> <param name='type' value="pathways"/> <output name="pathway_output_file"> <assert_contents> <has_n_columns n="8"/> <has_n_lines n="1533"/> <has_text text="Rhodobacter_sphaeroides"/> <has_text text="superpathway of acetyl CoA biosynthesis"/> <has_size value="186363"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ **What it does** This tool combine MetaPhlAn2 outputs and HUMANnN2 outputs. For each gene families/pathways and the corresponding taxonomic stratification, you get relative abundance of this gene family/pathway and the relative abundance of corresponding species and genus. ]]></help> <citations> </citations> </tool>