<tool id="mob_hostrange" name="MOB-Hostrange" version="2.0.2+galaxy0">
    <description>
        Provides information on plasmid reproductive host range and transfer rate using both sequencing
        and experimental data from public databases (NCBI) and publications (PubMED).
    </description>
    <requirements>
        <requirement type="package" version="2.0.2">mob_suite</requirement>
    </requirements>   
    <command detect_errors="exit_code">
        <![CDATA[
            mob_hostrange
              ${exact_match}
              ${loose_match}
              ${host_range_detailed}
              #if str(${replicon_name}) != '':
                --replicon_name '${replicon_name}'
              #end if
              #if str(${relaxase_name}) != '':
                --relaxase_name '${relaxase_name}'
              #end if
              #if str(${relaxase_accession}) != '':
                --relaxase_accession '${relaxase_accession}'
              #end if
              #if str(${cluster_id}) != '':
                --cluster_id '${cluster_id}'
              #end if
              --inputseq '${inputseq}'
              --outdir '.'
        ]]>
    </command>
    <inputs>
        <param name="inputseq" type="data" format="fasta" label="Input plasmid" help="plasmid FASTA file"/>
        <param name="exact_match" type="boolean" truevalue="--exact_match" falsevalue="" checked="false"/>
        <param name="loose_match" type="boolean" truevalue="--loose_match" falsevalue="" checked="false"/>
        <param name="host_range_detailed" type="boolean" truevalue="--host_range_detailed" falsevalue="" checked="false"/>
        <param name="replicon_name" type="text" />
        <param name="relaxase_name" type="text" />
        <param name="relaxase_accession" type="text" />
        <param name="cluster_id" type="text" />
    </inputs>
    <outputs>
        <data name="hostrange_phylostats" label="${tool.name}: Phylostats report on ${input.name}" format="tabular">
            <discover_datasets pattern=".+hostrange_phylostats\.txt" visible="true" format="tabular" />
        </data>
        <data name="hostrange_report" label="${tool.name}: Hostrange report on ${input.name}" format="tabular">
            <discover_datasets pattern=".+hostrange_report\.txt" visible="true" format="tabular" />
        </data>
    </outputs>
    <tests>
        <test>
            <param name="inputseq" value="plasmid_476.fasta" ftype="fasta"/>
            <assert_stderr>
                <has_text text="RefSeq Plasmid database found no hits"/> 
            </assert_stderr>
        </test>
    </tests>
    <help>

        **Syntax**

        This tool provides information on plasmid reproductive host range and transfer rate using both sequencing and experimental data from public databases (NCBI) and publications (PubMED). The predicted host range represents a range of putative hosts where a given plasmid can stably replicate and be maintained by the host. The host range module makes no source attribution predictions of a plasmid.

        For more information please visit https://github.com/phac-nml/mob-suite/. 

        -----

        **Input:**

        A FASTA file with a single or multiple contigs (e.g. plasmid.fasta):


        **Output:**

        Tab-delimited reports listing predicted hostrange information. Refer to https://github.com/phac-nml/mob-suite#mob-hostrange-report-file-format for the description of each column.


    </help>
    <citations>
        <citation type="bibtex">
            @misc{githubmob-suite,
            author = {Robertson J, Nash J},
            title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
            publisher = {GitHub},
            journal = {GitHub repository},
            doi = {10.1099/mgen.0.000206},
            url = {https://github.com/phac-nml/mob-suite}
        }</citation>
    </citations>
</tool>