<tool id="legsta" name="legsta" version="@TOOL_VERSION@+galaxy1" profile="20.01">
    <description>Legionella pneumophila sequence based typing</description>

    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

    <command detect_errors="exit_code"><![CDATA[
        #import re
        #set safe_names=[]

        #for $i in $contigs
            #set safe_name=re.sub('[^\s\w\-.]', '_', str($i.element_identifier))
            $safe_names.append($safe_name)
            ln -s '$i' '$safe_name';
        #end for

        legsta

        $noheader
        $csv

        #for $safe_name in $safe_names
            '$safe_name'
        #end for

        > '$output'
    ]]></command>

    <inputs>
        <param type="data" name="contigs" format="genbank,embl,gff,gff3,fasta,fasta.gz,fastq,fastq.gz,clustal,stockholm" multiple="true" label="Contigs" help="One or more input files in FASTA, FASTQ, Genbank, EMBL, Clustal, Stockholm or GFF format." />
        <param name="noheader" type="boolean" argument="--noheader" truevalue="--noheader" falsevalue="" label="Remove table header" help="Removes the table header from the output (ie. FILE SBT flaA ...)" />
        <param name="csv" type="boolean" argument="--csv" truevalue="--csv" falsevalue="" label="CSV output" help="Prints the output in comma-separated value format instead of tab-separated value format." />
    </inputs>

    <outputs>
        <data name="output" format="tabular">
            <change_format>
                <when input="csv" value="--csv" format="csv" />
                <when input="csv" value="" format="tabular" />
            </change_format>
        </data>
    </outputs>

    <tests>
        <test>
            <param name="contigs" ftype="fasta" value="NC_006368.fna.bz2"/>
            <param name="csv" value="true"/>
            <output name="output">
                <assert_contents>
                    <has_text text="SBT,flaA,pilE,asd,mip,mompS,proA,neuA" />
                    <has_text text="NC_006368.fna.bz2,1,1,4,3,1,1,1,1" />
                </assert_contents>
            </output>
        </test>
    </tests>

    <help>
In silico sequence based typing (SBT) of Legionella pneumophila.

The purpose of the Legionella pneumophila SBT scheme is to provide a rapid and easily comparable method for the epidemiological typing of clinical and environmental isolates of Legionella pneumophila in outbreak investigations.
    </help>

    <citations>
        <citation type="bibtex">
@misc{githublegsta,
  author = {Seemann, Torsten and Da Silva, Anders Goncalves, and Buultjens, Andrew, and Kwong, Jason},
  title = {legsta},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/tseemann/legsta},
}</citation>
    </citations>
</tool>