Integrate MetaPhlAn2 as an external tool

Tool desciption

Add "MetaPhlAn2" item to the "External Tools" tab of the "UGENE Application Settings". The description should be the following:

MetaPhlAn2 (METAgenomic PHyLogenetic ANalysis) is a tool for profiling the composition of microbial communities (bacteria, archaea, eukaryotes, and viruses) from whole-metagenome shotgun sequencing data.

Also, add "Version" and "Binary path" info, as in other external tools (see, for example, "kraken" executable).

Tool dependencies: "python", "Bowtie2"

"MetaPhlAn2" has dependencies: "python", python module "numpy", and "bowtie2-align". If at least one of the tools is not available, show the standard message:

External tool 'conservation_plot' cannot be validated as it depends on other tools, some of which are not valid. The list of tools is the following: the_list_of_tools

(Note that original MetaPhlAn2 requires also "bowtie2-build", the tool is used to build index from reference DB. However, we'll provide the DB as a Bowtie index already, so "bowtie2-build" dependency is not required.)

Absence of util script

If "utils/read_fastx.py" script is not present, the tool should be marked as invalid. Show an error message in the tool description field (use standard red color, make the text bold):

MetaPhlAn2 script "utils/read_fastx.py" is not present!

Test plan

See tests "Metagenomics > MetaPhlAn > External tool".