Set of improvements and fixes from Nicola Soranzo changeset: 9:c3dae016a3eb files: metaphlan.xml description: Update citation changeset: 8:f58b66b4e5fc files: metaphlan.xml description: Add select lists for -t and --tax_lev options Also some small fixes changeset: 7:94a2b29778b7 files: metaphlan_to_phyloxml.xml description: Clarify that only result of rel_ab analysis is accepted as input changeset: 6:b0eba028dee8 files: metaphlan.xml metaphlan_to_phyloxml.xml description: Fix whitespaces changeset: 5:4340075c8a93 files: tool_dependencies.xml description: Correct metaphlan clone URL to avoid a redirect changed metaphlan.xml changed metaphlan_to_phyloxml.xml changed tool_dependencies.xml

<tool id="meta_to_phylo" name="MetaPhlAn to PhyloXML" version="1.0.0">
  <description>converter</description>
  <command interpreter="python">metaphlan_to_phyloxml.py $input $output</command>
  <inputs>
    <param name="input" type="data" format="tabular" label="MetaPhlAn relative abundances"/>
  </inputs>
  <outputs>
    <data format="xml" name="output" label="${tool.name} on ${on_string}" /> 
  </outputs>
  <tests>
  </tests>
  <help>
This tool converts the results of metagonome profiling performed with MetaPhlAn from tabular to PhyloXML format. The tool accepts as input only the result of rel_ab analysis (profiling in terms of relative abundaces), not reads_map or clade_profiles analysis.
  </help>
</tool>