view metaphlan2_macros.xml @ 0:f7353110d18c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8

<?xml version="1.0"?>
<macros>
    <token name="@WRAPPER_VERSION@">2.6.0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@WRAPPER_VERSION@">metaphlan2</requirement>
            <yield/>
        </requirements>
    </xml>
    <xml name="stdio">
        <stdio>
            <exit_code range="1:" level="fatal"   description="" />
            <regex match="ERROR"
                   source="stderr"
                   level="fatal"
                   description="" />
            <regex match="WARNING"
                   source="stderr"
                   level="warning"
                   description="" />
        </stdio>
    </xml>
    <xml name="citations">
      <citations>
          <citation type="doi">10.1038/nmeth.3589</citation>
      </citations>
    </xml>
    <xml name="tax_lev">
      <param argument="--tax_lev" type="select" label="Taxonomic level for the relative abundance output">
        <option value="a" selected="true">All taxonomic levels</option>
        <option value="k">Kingdoms (Bacteria and Archaea) only</option>
        <option value="p">Phyla only</option>
        <option value="c">Classes only</option>
        <option value="o">Orders only</option>
        <option value="f">Families only</option>
        <option value="g">Genera only</option>
        <option value="s">Species only</option>
      </param>
    </xml>
</macros>