<tool id="mob_typer" name="MOB-Typer" version="@VERSION@+galaxy0">
  <description>Get the plasmid type and mobility given its sequence</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="bio_tools"/>
  <expand macro="requirements"/>
  <version_command>mob_typer --version</version_command>
  <command detect_errors="exit_code">
  <![CDATA[
    ln -s '${input}' '${input.name}' &&
    mob_typer  --num_threads \${GALAXY_SLOTS:-4} --infile '${input.name}'


   #if $adv_param.multi
    --multi
   #end if 

   --min_rep_evalue '$adv_param.min_rep_evalue_value'
   --min_mob_evalue '$adv_param.min_mob_evalue_value'
   --min_con_evalue '$adv_param.min_con_evalue_value'
   --min_length '$adv_param.min_length'
   --min_rep_ident '$adv_param.min_rep_ident'
   --min_mob_ident '$adv_param.min_mob_ident'

   --min_con_ident '$adv_param.min_con_ident'
   --min_rep_cov '$adv_param.min_rep_cov'
   --min_mob_cov '$adv_param.min_mob_cov'
   --min_con_cov '$adv_param.min_con_cov'
   --min_overlap '$adv_param.min_overlap'
   
   #if $adv_param.plasmid_db
   --plasmid_db '$adv_param.plasmid_db'
   #end if


   #if $adv_param.plasmid_mash_db
   --plasmid_mash_db '$adv_param.plasmid_mash_db'
   #end if

   #if $adv_param.plasmid_meta
   --plasmid_meta '$adv_param.plasmid_meta'
   #end if

   #if $adv_param.repetitive_mask
   --repetitive_mask '$adv_param.repetitive_mask'
   #end if

   #if $adv_param.plasmid_mob
   --plasmid_mob '$adv_param.plasmid_mob'
   #end if
   
   #if $adv_param.plasmid_mpf
   --plasmid_mpf '$adv_param.plasmid_mpf'
   #end if

   #if $adv_param.plasmid_orit
   --plasmid_orit '$adv_param.plasmid_orit'
   #end if

   #if $adv_param.debug
   --debug
   #end if
   
   #if $adv_param.biomarker_report_file
   --biomarker_report_file biomarker_report.txt
   #end if
   

   --out_file plasmid_report.txt;

  ]]>
  </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">
      <param name="multi" type="boolean" truevalue="true" falsevalue="" checked="false" label="Treat each input sequence as an independent plasmid?" help="Treat each sequence in the FASTA file as a separate input (--multi)" />
      <param name="biomarker_report_file" type="boolean" truevalue="true" falsevalue="" checked="false" label="Output BLAST biomarker report?" help="The report will report all biomarkers identified in a given query plasmid (--biomarker_report_file)" />

      <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn" help="(--min_rep_evalue)"/> 
      <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn" help="(--min_mob_evalue)"/> 
      <param name="min_con_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for contig blastn" help="(--min_con_evalue)"/> 
      <param name="min_length" type="integer" value="1000" label="Minimum length of contigs to classify (bp)" help="(--min_length)"/> 
      <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer"  min="0" max="100" value="80" help="(--min_rep_ident)"/>
      <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer"  min="0" max="100" value="80" help="(--min_mob_ident)"/>
      <param name="min_con_ident" label="Minimum sequence identity for contigs" type="integer"  min="0" max="100" value="80" help="(--min_con_ident)"/>
      <param name="min_rep_cov" label="Minimum percentage coverage of replicon query by input assembly" type="integer"  min="0" max="100" value="80" help="(--min_rep_ident)"/>
      <param name="min_mob_cov" label="Minimum percentage coverage of relaxase query by input assembly" type="integer"  min="0" max="100" value="80" help="(--min_mob_cov)"/>
      <param name="min_con_cov" label="Minimum percentage coverage of assembly contig by the plasmid reference database to be considered" type="integer"  min="0" max="100" value="70" help="(--min_con_cov)"/>
      <param name="min_overlap" label="Minimum overlap of fragments (bp)" type="integer"  min="0" max="100" value="10" help="(--min_overlap)"/>
      <param name="debug" type="boolean" truevalue="true" falsevalue="" checked="false" label="Provide debug information?" help="(--debug)"/>
      <param name="plasmid_db" optional="true" type="data" format="fasta" label="Reference Database of complete plasmids" help="(--plasmid_db)"/>
      <param name="plasmid_mash_db" optional="true" type="data" format="binary" label="Custom MASH database of plasmids" help="Custom MASH plasmid reference database (--plasmid_mash_db)"/>
      <param name="plasmid_meta" type="data" optional="true" format="text" label="Plasmid cluster metadata file" help="MOB-cluster plasmid cluster formatted metadata file matched to the reference plasmid database (--plasmid_meta)"/>
      <param name="plasmid_replicons" type="data" optional="true" format="fasta" label="FASTA file with plasmid replicons" help="FASTA of plasmid replicons custom database (--plasmid_replicons)"/>
      <param name="repetitive_mask" type="data" optional="true" format="fasta" label="FASTA of known repetitive elements" help="FASTA of known repetitive elements custom database (--repetitive_mask)"/>
      <param name="plasmid_mob" type="data" optional="true" format="fasta" label="FASTA of plasmid relaxases" help="FASTA of plasmid relaxases custom database (--plasmid_mob)"/>
      <param name="plasmid_mpf" type="data" optional="true" format="fasta" label="FASTA of known plasmid mate-pair proteins" help="FASTA of known plasmid mate-pair proteins custom database (--plasmid_mpf)"/>
      <param name="plasmid_orit" type="data" optional="true" format="fasta" label="FASTA of known plasmid oriT dna sequences" help="FASTA of known plasmid oriT DNA sequences custom database (--plasmid_orit)"/>
    </section>
  </inputs>
  <outputs>
    <data name="plasmid_report" from_work_dir="plasmid_report.txt" label="${tool.name}: Plasmid report on ${input.element_identifier}"  format="tabular" />
    <data name="biomarker_report" from_work_dir="biomarker_report.txt" label="${tool.name}: Biomarker report on ${input.element_identifier}"  format="tabular" />
  </outputs>
  <tests>
    <test>
      <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
      <output name="plasmid_report">
        <assert_contents>
          <has_text text="KJ484639"/>
          <has_text text="MOBP"/>
          <has_text text="NC_019097"/>
          <has_text text="conjugative"/>
          <has_text text="AA474"/>
          <has_text text="AI614"/>
          <has_text_matching expression="family\tEnterobacteriaceae"/>
        </assert_contents>
      </output>
    </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) and potential host range. 

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 and host range and optionally a biomarker report (if selected). Refer to https://github.com/phac-nml/mob-suite#mob-typer-report-file-format for the description of each column.

**Note:** Do not include multiple unrelated plasmids in the input FASTA file as they will be treated as a single plasmid or turn on the **--multi** parameter (i.e. *Treat each input sequence as an independent plasmid?*).
  </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>