<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" 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>