Some bio.tools id not extracted

[bebatut]

For some tools, their bio.tools id were not extracted but are already in the wrapper.

Examples:

• MetaPhlAn: https://github.com/galaxyproject/tools-iuc/blob/main/tools/metaphlan/macros.xml
• ABRICATE: https://github.com/galaxyproject/tools-iuc/blob/main/tools/abricate/macros.xml

[bebatut]

The issue probably comes from there: https://github.com/bebatut/galaxy_tool_extractor/blob/c8737cc382ed9dd8a1dbb78bfaf3b7d1ae4f83ff/bin/extract_galaxy_tools.py#L215
As there are no standard names for a biotools element in macros files.

Example in ABRICATE:

    <xml name="xrefs">
      <xrefs>
        <xref type='bio.tools'>ABRicate</xref>
      </xrefs>
    </xml>

Possible solution: move get_biotools outside the for loop and apply it on root directly