<tool id="mob_typer" name="MOB-Typer" version="1.4.5">
  <description>Get the plasmid type and mobility given its sequence</description>
  <requirements>
     <requirement type="package" version="1.4.5">mob_suite</requirement>
  </requirements>   
  <command detect_errors="exit_code">
  <![CDATA[
    ln -s "${input}" "${input.name}";
    mob_typer  --num_threads \${GALAXY_SLOTS:-4} --infile "${input.name}" 
    #if str($adv_param.min_rep_evalue_condition.min_rep_evalue_param) == "True":
      --min_rep_evalue $adv_param.min_rep_evalue_condition.min_rep_evalue_value
    #end if 
    #if str($adv_param.min_mob_evalue_condition.min_mob_evalue_param) == "True":
      --min_mob_evalue $adv_param.min_mob_evalue_condition.min_mob_evalue_value
    #end if 
    #if str($adv_param.min_con_evalue_condition.min_con_evalue_param) == "True":
      --min_con_evalue $adv_param.min_con_evalue_condition.min_con_evalue_value
    #end if 
    #if str($adv_param.min_ori_evalue_condition.min_ori_evalue_param) == "True":
      --min_ori_evalue $adv_param.min_ori_evalue_condition.min_ori_evalue_value
    #end if 
    --outdir '.';
  ]]>
  </command>
  <inputs>
    <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
    <section name="adv_param" title="Advanced parameters" expanded="False">
      <conditional name="min_rep_evalue_condition">
        <param name="min_rep_evalue_param" label="Minimum evalue threshold for replicon blastn" type="select" value="False">
          <option value="False">No</option>
          <option value="True">Yes</option>
       </param>   
        <when value="True">
          <param name="min_rep_evalue_value" type="float" value="0.00001" min="0" max="1" label="e-value (default: 0.00001)"/> 
        </when>  
        <when value="False"/>
      </conditional>
      <conditional name="min_mob_evalue_condition">
        <param name="min_mob_evalue_param" label="Minimum evalue threshold for relaxase tblastn" type="select" value="False">
          <option value="False">No</option>
          <option value="True">Yes</option>
       </param>   
        <when value="True">
          <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="e-value (default: 0.00001)"/> 
        </when>  
        <when value="False"/>
      </conditional>
      <conditional name="min_con_evalue_condition">
        <param name="min_con_evalue_param" label="Minimum evalue threshold for contig blastn" type="select" value="False">
          <option value="False">No</option>
          <option value="True">Yes</option>
       </param>   
        <when value="True">
          <param name="min_con_evalue_value" type="float" value="0.00001" min="0" max="1" label="e-value (default: 0.00001)"/> 
        </when>  
        <when value="False"/>
      </conditional>
      <conditional name="min_ori_evalue_condition">
        <param name="min_ori_evalue_param" label="Minimum evalue threshold for oriT elements blastn" type="select" value="False">
          <option value="False">No</option>
          <option value="True">Yes</option>
       </param>   
        <when value="True">
          <param name="min_ori_evalue_value" type="float" value="0.00001" min="0" max="1" label="e-value (default: 0.00001)"/> 
        </when>  
        <when value="False"/>
      </conditional>
    </section>  
  </inputs>
  <outputs>
    <data name="outfile1" label="${tool.name}: Plasmid report on ${input.name}" format="tabular">
      <discover_datasets pattern=".+_report\.txt" visible="true" format="tabular" assign_primary_output="true"/>
    </data>  
  </outputs>
  <tests>
    <test>
        <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
        <assert_stdout>
            <has_text text="JN253636"/> 
         </assert_stdout>
    </test>
  </tests>
  <help>

**Syntax**

This tool provides *in-silico* predictions on plasmid typing including identification of replicon, relaxase and mate-pair formation protein types. MOB-typer also predicts mobility of a plasmid (Conjugative, Mobilizable, Non-mobilizable). Do not include multiple unrelated plasmids in the input FASTA file as they will be treated as a single 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 report listing identified plasmid(s) and their predicted mobility. Refer to https://github.com/phac-nml/mob-suite#mob-typer-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>