<tool id="metaphlan" name="MetaPhlAn" version="1.0">
<requirements>
<requirement type="package">metaphlan</requirement>
<requirement type="package" version="2.2.25+">blast</requirement>
</requirements>
  <description>Metagenomic Phylogenetic Analysis</description>
  <command>
      metaphlan.py
      #if str($source.type) == "fasta":
          ${source.fasta_input}
      #else:
          ${source.blast_input}
      #end if
      ${metaphlan_out}
      --nproc 4
      #if str($source.type) == "fasta":
      --blastout metagenome.outfmt6.txt
      --evalue ${source.evalue}
      #end if
      --lib_dir ${GALAXY_DATA_INDEX_DIR}/shared/metaphlan
      --min_cu_len ${min_cu_len}
      --min_nreads ${min_nreads}
  </command>
  <inputs>

    <conditional name="source">
        <param name="type" type="select" label="Input Type">
            <option value="fasta">multi-fasta file containing metagenomic reads</option>
            <option value="blast">NCBI BLAST output file</option>
        </param>
      <when value="fasta">
        <param format="fasta" name="fasta_input" type="data" label="from"/>
        <param name="evalue" type="float" size="15" value="0.00001" label="evalue threshold for the blasting" />
      </when>
      <when value="blast">
        <param format="tabular" name="blast_input" type="data" label="from"/>
      </when>
    </conditional>

    <param name="tax_lev" type="select" label="Taxonomic Level" help="The taxonomic level for the relative abundance output">
        <option value="a">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>
    <param name="min_cu_len" type="integer" value="10000" help="min_cu_len" label="Minimum total nucleotide length for the unique markers for estimating the abundance without considering children clade abundances" />
    <param name="min_nreads" type="integer" value="5" help="min_nreads" label="minimum total reads assigned to a clade for estimating the abundance without considering children clade abundances" />
  </inputs>
  <outputs>
    <data format="tabular" name="metaphlan_out" label="MetaPhlAn on ${on_string}" />
    <data format="tabular" name="blast_out" from_work_dir="metagenome.outfmt6.txt" label="MetaPhlAn BLAST on ${on_string}">
        <filter>source['type'] == "fasta"</filter>
    </data>
  </outputs>
  <tests>
  </tests>
  <help>

**What it does**
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. MetaPhlAn relies on unique clade-specific marker genes identified from reference genomes, allowing orders of magnitude speedups and unambiguous taxonomic assignments.

MetaPhlAn main features are:

More than 100x computational speedup compared to Blast-based approaches or other available methods with species level resolution
Higher accuracy in estimating the true composition of microbial communities in terms of organismal relative abundance
Unambiguous read-to-taxa assignments as conserved inter-clade sequences are removed from the reference sequence data

---------

**Inputs**

The input file can be a multi-fasta file containing metagenomic reads OR a NCBI BLAST output file (-outfmt 6 format) of the metagenomic read fasta file against the metaflan database.

**outputs**

The output is a tab-separated output file of the predicted taxon relative abundances.
If the input is a multi-fasta file then the output from the BLAST operation is also provided as an additional output.

---------

**Settings**::

  --tax_lev TAXONOMIC_LEVEL
                        The taxonomic level for the relative abundance 
                        output:
                        'a' : all taxonomic levels
                        'k' : kingdoms (Bacteria and Archaea) only
                        'p' : phyla only
                        'c' : classes only
                        'o' : orders only
                        'f' : families only
                        'g' : genera only
                        's' : species only
                        [default 'a']
  --evalue              evalue threshold for the blasting
                        [default 1e-6]
  --min_cu_len          minimum total nucleotide lenght for the unique
                        markers for estimating the abundance without
                        considering children clade abundances
                        [default 10000]
  --min_nreads          minimum total reads assigned to a clade for
                        estimating the abundance without considering
                        children clade abundances
                        [default 5]

-----

**Citation**

If you find MetaPhlAn useful in your research, please cite our paper:
Nicola Segata, Levi Waldron, Annalisa Ballarini, Vagheesh Narasimhan, Olivier Jousson, Curtis Huttenhower.
"Fast and accurate metagenomic profiling of microbial community composition using unique clade-specific marker genes"
***in review***

    </help>
</tool>