<tool id="metaphlan2" name="MetaPhlAn2" version="2.5.0">

    <description>to profile the composition of microbial communities</description>

    <macros>
        <import>metaphlan2_macros.xml</import>
    </macros>

    <expand macro="requirements"/>
    <expand macro="stdio"/>

    <version_command>
<![CDATA[
metaphlan2.py -v
]]>
    </version_command>

    <command>
<![CDATA[
        (which bowtie2 || exit 200)

        &&

        #if $db.db_selector == "history"
            mkdir ref_db
            &&
            bowtie2-build $db.db_sequences ref_db/ref_db
            &&
            python $__tool_directory__/transform_json_to_pkl.py
                --json_input $db_metadata
                --pkl_output ref_db/metadata.pkl
            &&
        #end if

        metaphlan2.py
            $input_file
            -o $output_file
            --input_type ${input_file.datatype.file_ext}

            --bowtie2_exe `which bowtie2`

            #if $db.db_selector == "cached"
                #set $table = dict([(_[0], _[2]) for _ in $db.cached_db.input.options.tool_data_table.data])
                #set $db_choice = $db.cached_db.value
                --bowtie2db $table[$db_choice]
                --mpa_pkl $table[$db_choice]".pkl"
            #else
                --bowtie2db ref_db/ref_db
                --mpa_pkl ref_db/metadata.pkl
            #end if

            --no_map

            -t $analysis_type.analysis_type_select
            #if $analysis_type.analysis_type_select == "rel_ab"
                --tax_lev $analysis_type.taxonomic_level
            #else if $analysis_type.analysis_type_select == "marker_ab_table"
                --nreads $analysis_type.nreads
            #else if $analysis_type.analysis_type_select == "marker_pres_table"
                --pres_th $analysis_type.pres_th
            #end if

            --min_cu_len $min_cu_len
            --min_alignment_len $min_alignment_len

            $ignore_viruses
            $ignore_eukaryotes
            $ignore_bacteria
            $ignore_archaea

            --stat_q $stat_q
            -s $sam_output_file
]]>
    </command>

    <inputs>
        <param name="input_file" type="data" format="fastq,fasta,sam" label="Input file" help=""/>

        <conditional name="db">
            <param name="db_selector" type="select" label="Database with clade-specific marker genes" help="">
                <option value="cached" selected="true">Locally cached</option>
                <option value="history">From history</option>
            </param>

            <when value="cached">
                <param name="cached_db" label="Cached database with clade-specific marker genes" type="select" >
                <options from_data_table="metaphlan2_db" />
                </param>
            </when>
            <when value="history">
                <param name="db_sequences" type="data" format="fasta" label="Database with clade-specific marker genes from history" help="(--bowtie2db)"/>
                <param name="db_metadata" type="data" format="json" label="Metadata associate to the database with clade-specific marker genes from history" help="(--mpa_pkl)"/>
            </when>
        </conditional>

        <conditional name="analysis_type">
            <param name="analysis_type_select" type="select" label="Type of analysis to perform" help="(-t)">
              <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option>
              <option value="reads_map">Mapping from reads to clades (only reads hitting a marker)</option>
              <option value="clade_profiles">Normalized marker counts for clades with at least a non-null marker</option>
              <option value="marker_ab_table">Normalized marker counts (only when > 0.0 and normalized by metagenome size if --nreads is specified)</option>
              <option value="marker_counts">Non-normalized marker counts (use with extreme caution)</option>
              <option value="marker_pres_table">List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option>
            </param>

            <when value="rel_ab">
              <param name="taxonomic_level" type="select" label="Taxonomic level for the relative abundance output" help="(--tax_lev)">
                <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>
            </when>

            <when value="reads_map"/>
            <when value="clade_profiles"/>

            <when value="marker_ab_table">
                <param name="nreads" type="integer" value="0" label="Total number of reads in the original metagenome" help="It is used for normalizing the length-normalized counts with the metagenome size as well. No normalization applied if the value is not specified"/>
            </when>

            <when value="marker_counts"/>

            <when value="marker_pres_table">
                <param name="pres_th" type="integer" value="0" label=" Threshold for calling a marker present" help=""/>
            </when>
        </conditional>

        <param name="min_cu_len" type="integer" value="2000" label="Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances" help=""/>

        <param name="min_alignment_len" type="integer" value="0" label="Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded." help=""/>

        <param name="ignore_viruses" type='boolean' checked="true" truevalue='' falsevalue='--ignore_viruses' label="Profile viral organisms?" help="" />
        <param name="ignore_eukaryotes" type='boolean' checked="true" truevalue='' falsevalue='--ignore_eukaryotes' label="Profile eukaryotic organisms?" help="" />

        <param name="ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?" help="" />

        <param name="ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?" help="" />

        <param name="stat_q" type="float" value="0.1" label="Quantile value for the robust average" help=""/>
    </inputs>

    <outputs>
        <data format="tabular" name="output_file" label="${tool.name} on ${on_string}: Community profile" />
        <data format="sam" name="sam_output_file" label="${tool.name} on ${on_string}: SAM file" />
    </outputs>

    <tests>
        <test>
            <param name="input_file" value="input_sequences.fasta"/>
            <param name="db_selector" value="history" />
            <param name="db_metadata" value="marker_metadata.json" />
            <param name="db_sequences" value="marker_sequences.fasta" />
            <param name="analysis_type_select" value="rel_ab" />
            <param name="taxonomic_level" value="a" />
            <param name="min_cu_len" value="2000" />
            <param name="min_alignment_len" value="0" />
            <param name="ignore_viruses" value="" />
            <param name="ignore_eukaryotes" value="" />
            <param name="ignore_bacteria" value="" />
            <param name="ignore_archaea" value="" />
            <param name="stat_q" value="0.1" />
            <output name="output_file" file="community_profile.tabular"/>
        </test>
    </tests>

    <help><![CDATA[
**What it does**

MetaPhlAn is a computational tool to profile the structure and the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. For more information, check the `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_.

**Inputs**

Metaphlan2 takes as input a sequence file in fasta, fastq, a BowTie2 produced SAM file.

It is also possible to use a custom database with clade-specific marker genes. In this case, a fasta file with marker gene sequences is required and also a file containing metadata. This file is a json file with:

::

  {
    "taxonomy": {
            "taxonomy of genome1": genome1_length,
            "taxonomy of genome2": genome2_length,
            ...
        }
    "markers": {
            "marker1_name": {
                "clade": the clade that the marker belongs to,
                "ext": [list of external genomes where the marker appears],
                "len": length of the marker,
                "score": score of the marker,
                "taxon": the taxon of the marker
            }
            ...
        }
  }

The marker name correspond to the corresponding sequence name in the FastA file containing marker gene sequences.

**Outputs**

The main output file is a tab-separated file with the predicted taxon relative abundances.

    ]]></help>

    <citations>
        <citation type="doi">10.1038/nmeth.3589</citation>
    </citations>
</tool>