<tool id="meningotype" name="Meningotype" version="@TOOL_VERSION@+galaxy0" profile="21.05">
    <description>assign sequence type to Neisseria meningitidis genome assemblies</description>
    <macros>
        <token name="@TOOL_VERSION@">0.8.5</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">meningotype</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">meningotype</requirement>
        <!-- coreutils dep added because of a bug in the meningotype 0.8.5 container - it doesn't have `file` -->
        <requirement type="package" version="9.0">coreutils</requirement>
    </requirements>
    <version_command>meningotype --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
        #if $db_source == 'network'
            python3 '$__tool_directory__/update_db.py' &&
        #end if
        #if $input.source == "single"
            #set $input_data = "'" + $input.fasta.element_identifier.replace(' uncompressed', '') + "'"
            ln -s '$input.fasta' $input_data &&
        #else
            #set $input_data = ""
            #for $el in $input.fastas
                #set $name = $el.element_identifier.replace(' uncompressed', '')
                ln -s '$el' '$name' &&

                #set $input_data = $input_data + " '" + $name + "'"
            #end for
        #end if
        meningotype 
        #if $db_source == "network"
            --db ./db
        #end if
            $input_data
            --cpus \${GALAXY_SLOTS:-1}
            #if "mlst" in $typing
                --mlst
            #end if
            #if "finetype" in $typing
                --finetype
            #end if
            #if "porb" in $typing
                --porB
            #end if
            #if "bast" in $typing
                --bast
            #end if
            #if $write_allele_sequences
                --printseq allele_sequences
            #end if
            #if not $include_header
                | python3 '$__tool_directory__/strip_header.py'
            #end if
            >'$output_tsv' &&
            python3 '$__tool_directory__/check_output.py' '$output_tsv'
    ]]></command>
    <inputs>
        <conditional name="input">
            <param type="select" name="source" label="Input type">
                <option value="collection" selected="true">Dataset collection</option>
                <option value="single">Single dataset</option>
            </param>
            <when value="collection">
                <param name="fastas" type="data_collection" format="fasta" collection_type="list" label="N. meningtidis genomes in FASTA format" />
            </when>
            <when value="single">
                <param type="data" format="fasta" name="fasta" label="Input FASTA" help="N. meningitidis genome in FASTA format" />
            </when>
        </conditional>
        <param type="select" name="db_source" label="Database source">
            <!-- the latest version of the DBs are stored on PubMLST.  -->
            <option value="network" selected="true">Network</option>
            <option value="builtin">Built-in</option>
        </param>
        <param type="select" multiple="true" name="typing" label="Typing to perform">
            <option value="mlst" selected="true">MLST</option>
            <option value="finetype" selected="true">porA and fetA fine typing</option>
            <option value="bast" selected="true">Bexsero antigen sequence typing (BAST)</option>
            <option value="porb" selected="true">porB (NEIS2020) sequence typing</option>
        </param>
        <param type="boolean" name="include_header" checked="false" label="Include header in output" />
        <param type="boolean" name="write_allele_sequences" checked="false" label="Output sequences of porA, fetA, portB and BAST alleles" />
    </inputs>
    <outputs>
        <data format="tabular" name="output_tsv" label="Meningotype on ${on_string}">
            <actions>
                <action name="column_names" type="metadata" default="Sample_ID,Serogroup,ctrA,MLST,porA,fetA,porB,fHbp,NHBA,NadA,BAST" />
            </actions>
        </data>
        <collection  format="fasta" type="list" name="output_allele_sequences" label="Meningotype allele sequences on ${on_string}">
            <discover_datasets pattern="__name_and_ext__" directory="allele_sequences" />
            <filter>write_allele_sequences</filter>
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="1"> <!-- test1: basic functionality -->
            <conditional name="input">
               <param name="source" value="single" /> 
               <param name="fasta" value="input.fasta.gz" ftype="fasta.gz"/>
            </conditional>
            <param name="db_source" value="builtin" />
            <param name="typing" value="mlst,finetype,bast,porb" />
            <output name="output_tsv">
                <assert_contents>
                    <has_n_columns n="11" />
                    <has_text text="9367" />
                    <has_text text="21-15,16" />
                    <has_text text="F1-7" />
                    <has_text text="NEIS2020_506" />
                    <has_text text="27" />
                    <has_text text="798" />
                    <has_text text="0" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1"> <!-- test2: test with header included -->
            <conditional name="input">
                <param name="source" value="single" /> 
                <param name="fasta" value="input.fasta.gz" ftype="fasta.gz"/>
            </conditional>
            <param name="db_source" value="builtin" />
            <param name="typing" value="mlst,finetype,bast,porb" />
            <param name="include_header" value="true" /> 
            <output name="output_tsv">
                <assert_contents>
                    <has_n_columns n="11" />
                    <has_text text="SAMPLE_ID" /> <!-- the header -->
                    <has_text text="9367" />
                    <has_text text="21-15,16" />
                    <has_text text="F1-7" />
                    <has_text text="NEIS2020_506" />
                    <has_text text="27" />
                    <has_text text="798" />
                    <has_text text="0" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="2"> <!-- test 3: test allele sequence output -->
            <conditional name="input">
                <param name="source" value="single" /> 
                <param name="fasta" value="input.fasta.gz" ftype="fasta.gz"/>
            </conditional>
            <param name="db_source" value="builtin" />
            <param name="typing" value="mlst,finetype,bast,porb" />
            <param name="write_allele_sequences" value="true" />
            <output name="output_tsv">
                <assert_contents>
                    <has_n_columns n="11" />
                    <has_text text="9367" />
                    <has_text text="21-15,16" />
                    <has_text text="F1-7" />
                    <has_text text="NEIS2020_506" />
                    <has_text text="27" />
                    <has_text text="798" />
                    <has_text text="0" />
                </assert_contents>
            </output>
            <output_collection name="output_allele_sequences">
                <element name="NHBA_seqs" file="NHBA_seqs.fasta" ftype="fasta" />
                <element name="NadA_seqs" file="NadA_seqs.fasta" ftype="fasta" />
                <element name="fHbp_seqs" file="fHbp_seqs.fasta" ftype="fasta" />
                <element name="fetA_seqs" file="fetA_seqs.fasta" ftype="fasta" />
                <element name="porA_seqs" file="porA_seqs.fasta" ftype="fasta" />
                <element name="porB_seqs" file="porB_seqs.fasta" ftype="fasta" />
            </output_collection>
        </test>
        <test expect_num_outputs="1"> <!-- test4: test input collection -->
            <conditional name="input">
               <param name="source" value="collection" />
               <param name="fastas">
                    <collection type="list">
                        <element name="input1" value="input.fasta.gz" ftype="fasta.gz" />
                        <element name="input2" value="input2.fasta.gz" ftype="fasta.gz" />
                    </collection>
               </param>
            </conditional>
            <param name="db_source" value="builtin" />
            <param name="typing" value="mlst,finetype,bast,porb" />
            <output name="output_tsv">
                <assert_contents>
                    <has_n_columns n="11" />
                    <has_n_lines n="2" />
                    <has_text text="9367" />
                    <has_text text="21-15,16" />
                    <has_text text="F1-7" />
                    <has_text text="NEIS2020_506" />
                    <has_text text="27" />
                    <has_text text="798" />
                    <has_text text="0" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        meningotype_: In silico typing of Neisseria meningitidis contigs

        * Serotyping

        * MLST

        * Finetyping (porA, fetA, porB)

        * Bexsero antigen sequence typing (BAST) (fHbp, NHBA, NadA, PorA)

        The databases used in the tool are sourced from PubMLST_. The default behaviour is to download updated
        copies of the databases before running the tool. While this can be ineffecient for e.g. typing a single
        isolate, the databases built-in to the tool are not the most recent versions.

        If many isolates are being typed, they can be provided as a dataset collection. The output of the tool
        will contain one line of data for each isolate.

        By default the header line is not included in the tool output (to make concatenation of results easier).

        If output of matched alleles is requested, FASTA files are produced for each matching allele, with information
        on which dataset was matched in the FASTA header.

        .. _meningotype: https://github.com/MDU-PHL/meningotype
        .. _PubMLST: https://pubmlst.org/
    ]]></help>
    <citations>
        <citation type="bibtex">
            <![CDATA[
            @misc{Kwong2018,
                author = {Kwong, J.C. and Gonçalves da Silva, A. and Stinear, T. P. and Howden, B. P. and Seemann, T.},
                title = {meningotype: in silico typing for Neisseria meningitidis.},
                year = {2018},
                publisher = {GitHub},
                journal = {GitHub repository},
                howpublished = {\url{https://github.com/MDU-PHL/meningotype}},
                commit = {aece5c9851c7ffc8357306a33a369307dddb726f}
              }
            ]]>
        </citation>
    </citations>
</tool>