annotate mob_typer.xml @ 6:9424de64bfa8 draft

"planemo upload for repository https://github.com/phac-nml/mob-suite commit dc6eaf2675bf842ab7a52c3fdf16d01028cddc9a"

<tool id="mob_typer" name="MOB-Typer" version="2.0.5+galaxy0">
  <description>Get the plasmid type and mobility given its sequence</description>
  <requirements>
     <requirement type="package" version="2.0.5">mob_suite</requirement>
  </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}'
    ${host_range_detailed}
   --min_rep_evalue '$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_ori_evalue '$adv_param.min_ori_evalue_value'
   --min_mpf_evalue '$adv_param.min_mpf_evalue'
   --min_rep_ident '$adv_param.min_rep_ident'
   --min_mob_ident '$adv_param.min_mob_ident'
   --min_ori_ident '$adv_param.min_ori_ident'
   --min_mpf_ident '$adv_param.min_mpf_ident'
    --outdir 'outdir';
  ]]>
  </command>
  <inputs>
    <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
    <param name="host_range_detailed" type="boolean" truevalue="--host_range_detailed" falsevalue="" checked="true" label="Perform detailed host range analysis" />
    <section name="adv_param" title="Advanced parameters" expanded="False">
      <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn"/> 
      <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn"/> 
      <param name="min_con_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for contig blastn"/> 
      <param name="min_ori_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for oriT elements blastn"/>
      <param name="min_mpf_evalue" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for mpf elements blastn"/>
      <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer"  min="0" max="100" value="80"/>
      <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer"  min="0" max="100" value="80"/>
      <param name="min_ori_ident" label="Minimum sequence identity for oriT elements" type="integer"  min="0" max="100" value="90"/>
      <param name="min_mpf_ident" label="Minimum sequence identity for mpf elements" type="integer"  min="0" max="100" value="80"/>
    </section>
  </inputs>
  <outputs>
    <data name="plasmid_report" from_work_dir="outdir/mobtyper*_report.txt" label="${tool.name}: Plasmid report on ${input.element_identifier}"  format="tabular" />
    <data name="refseq_hostrange_phylogeny_tree" from_work_dir="outdir/*_refseqhostrange_phylogeny_tree.nwk" label="${tool.name} on ${input.element_identifier}: RefSeq Host Range Phylogeny Tree" format="newick">
      <filter>host_range_detailed</filter>
    </data>
    <data name="literature_hostrange_phylogeny_tree" from_work_dir="outdir/*_literaturehostrange_phylogeny_tree.nwk" label="${tool.name} on ${input.element_identifier}: Literature Host Range Phylogeny Tree" format="newick">
      <filter>host_range_detailed</filter>
    </data>
    <data name="refseq_hostrange_ascii_tree" from_work_dir="outdir/*_refseqhostrange_asci_tree.txt" label="${tool.name} on ${input.element_identifier}: RefSeq Host Range ASCII Tree" format="txt">
      <filter>host_range_detailed</filter>
    </data>
    <data name="literature_hostrange_ascii_tree" from_work_dir="outdir/*_literaturehostrange_asci_tree.txt" label="${tool.name} on ${input.element_identifier}: Literature Host Range ASCII Tree" format="txt">
      <filter>host_range_detailed</filter>
    </data>
    <data name="literature_report" from_work_dir="outdir/*_literature_report.txt" label="${tool.name} on ${input.element_identifier}: Literature Report" format="tabular">
      <filter>host_range_detailed</filter>
    </data>
    <data name="refseq_hostrange_report" from_work_dir="outdir/*_refseqhostrange_report.txt" label="${tool.name} on ${input.element_identifier}: RefSeq Host Range Report" format="tabular">
      <filter>host_range_detailed</filter>
    </data>
    <data name="refseq_hostrange_phylostats" from_work_dir="outdir/*_refseqhostrange_phylostats.txt" label="${tool.name} on ${input.element_identifier}: RefSeq Host Range Phylogeny Stats" format="tabular">
      <filter>host_range_detailed</filter>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="input" value="plasmid_476.fasta" ftype="fasta" />
      <param name="host_range_detailed" value="False" />
      <output name="plasmid_report">
        <assert_contents>
          <has_text text="000145__HE610900_00001"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="input" value="plasmid_476.fasta" ftype="fasta" />
      <param name="host_range_detailed" value="True" />
      <output name="refseq_hostrange_phylogeny_tree">
        <assert_contents>
          <has_text text="(624:1,984897:1)"/> 
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="input" value="plasmid_476.fasta" ftype="fasta" />
      <param name="host_range_detailed" value="True" />
      <output name="literature_hostrange_phylogeny_tree">
        <assert_contents>
          <has_text text="(90371:1,611:1,28144:1)"/> 
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="input" value="plasmid_476.fasta" ftype="fasta" />
      <param name="host_range_detailed" value="True" />
      <output name="refseq_hostrange_ascii_tree">
        <assert_contents>
          <has_text text="order, Enterobacterales"/>
          <has_text text="family, Enterobacteriaceae"/>
          <has_text text="genus, Shigella"/>
          <has_text text="species, Escherichia coli"/>
          <has_text text="genus, Serratia"/>
          <has_text text="species, Serratia marcescens"/>
          <has_text text="species, Klebsiella pneumoniae"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="input" value="plasmid_476.fasta" ftype="fasta" />
      <param name="host_range_detailed" value="True" />
      <output name="literature_hostrange_ascii_tree">
        <assert_contents>
          <has_text text="family, Enterobacteriaceae"/>
          <has_text text="species, Escherichia coli"/>
          <has_text text="species, Klebsiella pneumoniae"/>
          <has_text text="subspecies, Salmonella enterica subsp. enterica"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="input" value="plasmid_476.fasta" ftype="fasta" />
      <param name="host_range_detailed" value="True" />
      <output name="literature_report">
        <assert_contents>
          <has_text text="IncI1"/>
          <has_text text="R64"/>
          <has_text text="pHNRD174"/>
          <has_text text="pKHSB1"/>
          <has_text text="pCTXM1-MU2"/>
          <has_text_matching expression="family\tEnterobacteriaceae"/>
          <has_text_matching expression="order\tEnterobacteriales"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="input" value="plasmid_476.fasta" ftype="fasta" />
      <param name="host_range_detailed" value="True" />
      <output name="refseq_hostrange_report">
        <assert_contents>
          <has_text text="IncI1"/>
          <has_text text="Enterobacterales"/> 
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="input" value="plasmid_476.fasta" ftype="fasta" />
      <param name="host_range_detailed" value="True" />
      <output name="refseq_hostrange_phylostats">
        <assert_contents>
          <has_line_matching expression="rank\tsci_name\tdb_hits\tconvergance_rank\tconvergance_sci_name"/>
          <has_line_matching expression="family\tEnterobacteriaceae\t351"/>
          <has_line_matching expression="genus\tSalmonella\t113"/> 
        </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). 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>