<tool id="ectyper" name="ectyper" version="1.0.0">
  <description>ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats.</description>
  <requirements>
     <requirement type="package" version="1.0.0">ectyper</requirement>
  </requirements>
  <command detect_errors="exit_code">
  <![CDATA[
  #set $genomes = ''
  #if hasattr($input, '__iter__')
    #for $i in $input
        ln -s "${i}" "${i.element_identifier}" &&
        #if len($genomes) > 0
          #set $genomes = $genomes + ',' + str($i.element_identifier)
        #else
          #set $genomes = str($i.element_identifier)
        #end if      
    #end for
  #else
    ln -s "${input}" "${input.element_identifier}" &&
    #set $genomes = $input.element_identifier
  #end if

  #if $adv_param.mash_input
    ln -s "${adv_param.mash_input}" mash_sketch.msh &&
  #end if


  #if $adv_param.db_input
    ln -s "${adv_param.db_input}" custom_db.json &&
  #end if


  ectyper  --cores \${GALAXY_SLOTS:-4} 
  --input "${genomes}" 
  -opid '$adv_param.opid'
  -opcov '$adv_param.opcov'
  -hpid '$adv_param.hpid'
  -hpcov '$adv_param.hpcov'

  #if $adv_param.verifyEcoli
    --verify
  #end if

  #if $adv_param.mash_input
    --refseq mash_sketch.msh
  #end if

  #if $adv_param.db_input
    --dbpath custom_db.json
  #end if

  --output '.'
  ]]>
  </command>
  <inputs>
    <param name="input" type="data"  format="fastq,fasta" label="Genome(s) input(s)" help="FASTA or FASTQ file(s)"/>
    <section name="adv_param" title="Advanced parameters" expanded="False">
      <param name="opid" label="O antigen minimum %identity" type="integer" value="90" min="1" max="100"/>
      <param name="opcov" label="O antigen minimum %coverage" type="integer" value="90" min="1" max="100"/>
      <param name="hpid" label="H antigen minimum %identity" type="integer" value="95" min="1" max="100"/>
      <param name="hpcov" label="H antigen minimum %coverage" type="integer" value="50" min="1" max="100"/>
      <param name="verifyEcoli" type="boolean" checked="true" label="Enable E. coli species verification"/>
      <param name="blastresults" type="boolean" checked="false"  label="Include BLAST allele alignment results tab-delim file in the outputs?" />
      <param name="logging" type="boolean" checked="false"  label="Include log file in the run outputs?" />
      <param name="mash_input" type="data" optional="true" format="binary" label="Mash genome sketches (Optional)" help="Optionally provide custom MASH genome sketch to help with species identification (otherwise default RefSeq sketch is used)"/>
      <param name="db_input" type="data" optional="true" format="json" label="Custom database of alleles (Optional)" help="Optionally provide custom database of alleles in JSON format"/>
    </section>
  </inputs>
  <outputs>
    <data name="output_result" format="tabular" from_work_dir="output.tsv" label="${tool.name} serotype report on ${input.element_identifier}"> </data>
    <data name="output_log" format="txt" from_work_dir="ectyper.log" label="${tool.name} log file on ${input.element_identifier}">
        <filter>adv_param['logging']==True</filter>
    </data>
    <data name="output_blast" format="tabular" from_work_dir="blast_output_alleles.txt"  label="${tool.name} BLAST results file on ${input.element_identifier}">
         <filter>adv_param['blastresults']==True</filter>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="input" value="Escherichia2.fastq"/>
      <assert_stderr>
            <has_text text="O22"/> 
            <has_text text="H8"/> 
      </assert_stderr>
      <output name="output_result" ftype="tabular" >
          <assert_contents>
              <has_text_matching expression="O22"/>
         </assert_contents>
      </output>
    </test>
  </tests>

  <help>
**Syntax**


This tool identifies the serotype of both assembled or assembly-free Escherichia coli genome samples based on a set of the key O and H antigen determinant genes including *wzm/wzt* or *wzx/wzy* and *fliC/flkA/flmA*.
Unique to the tool, species identification module allows for non-E.coli genomes identification including other Escherichia genus species.
This version improves antigen call rates on "difficult samples" by use of an adaptive threshold. This is especially useful when antigen genes are truncated or poorly covered by raw reads.
If no antigen call is being predicted by the tool, try to lower %coverage parameter first. For more information on the new Quality Control module and running parameter details please visit https://github.com/phac-nml/ecoli_serotyping.


-----

**Input:**

Accepts a variety of inputs including both single and/or multiple FASTQ and/or FASTA file(s). Inputs might contain pure raw reads, but for more accurate results, draft assemblies are recommended.


The default MASH RefSeq genome sketch (https://gembox.cbcb.umd.edu/mash/refseq.genomes.k21s1000.msh) containing approximately 91K genomes is included and automatically updated every 6 months.



**Output:**

Tab-delimited report listing identified O and H antigens together with corresponding the highest-scoring alleles and normalized BLAST score defined as (%identity x %coverage) / 1e4.
If *verifyEcoli* parameter is enabled, final report will contain allele quality control information on results for reporting purposes. PASS (REPORTABLE) QC flag means that O and H antigen calls are of sufficient to unambiguously resolve them from all other antigens.

-----

**Parameters (Optional):**
  - **Enable E. coli species verification:** for species verification in case samples are of non-E.coli origin
  - **Include BLAST allele alignment results tab-delim file in the outputs?** Get reference allele sequences and detailed BLAST output
  - **Include log file in the run outputs?:** Get optional logs of the ectyper run for a more detailed results assessment and troubleshooting

  </help>
<citations>
    <citation type="bibtex">
  @misc{githubectyper,
  author = {Laing Chad},
  title = {ECtyper - serotyping module for Escherichia coli},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/phac-nml/ecoli_serotyping}
    }</citation>
</citations>
</tool>