<tool id="ectyper" name="ectyper" version="0.8.1">
  <description>ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats.</description>
  <requirements>
     <requirement type="package" version="0.8.1">ectyper</requirement>
  </requirements>
  <command detect_errors="exit_code">
  <![CDATA[
  #set $genomes = ''
  #if hasattr($input, '__iter__')
    #for $i in $input
        ln -s "${i}" "${i.name}" &&
        #if len($genomes) > 0
          #set $genomes = $genomes + ',' + str($i.name)
        #else
          #set $genomes = str($i.name)
        #end if      
    #end for
  #else
    ln -s "${input}" "${input.name}" &&
    #set $genomes = $input.name
  #end if
 
  ectyper  --cores \${GALAXY_SLOTS:-4} 
  --input "${genomes}" 
  --percentIdentity '$adv_param.min_percentIdentity'
  --percentLength '$adv_param.percentLength'
  #if $adv_param.verifyEcoli
    --verify
  #end if
  #if $adv_param.alleleSequence
    --sequence
  #end if
  --output '.'
  ]]>
  </command>
  <inputs>
    <param name="input" type="data"  format="fastq,fasta" label="Input(s)" help="FASTA or FASTQ file(s) with contig(s)"/>
    <section name="adv_param" title="Advanced parameters" expanded="False">
      <param name="min_percentIdentity" type="integer" value="90" min="1" max="100"/>
      <param name="percentLength" type="integer" value="50" min="1" max="100"/>
      <param name="verifyEcoli" type="boolean" checked="true" label="Enable E. coli species verification"/>
      <param name="alleleSequence" type="boolean" checked="false" label="Print the allele sequences as the final columns of the output?"/> 
      <param name="logging" type="boolean" checked="false"  label="Include log file in the run outputs?" />
    </section>  
  </inputs>
  <outputs>
    <data name="output_result" format="tabular" from_work_dir="output.tsv" label="${tool.name} serotype report"> </data> 
    <data name="output_log" format="text" from_work_dir="ectyper.log" label="${tool.name} log file"> 
        <filter>adv_param['logging']==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 Escherichia coli genome sequences based on a set of *wzm/wzt*, *wzx/wzy* and *fliC/flkA/flmA* alleles corresponding to O and H antigens, respectively. 

For more information please visit https://github.com/phac-nml/ecoli_serotyping. 

-----

**Input:**

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


**Output:**

Tab-delimited report listing identified O and H antigens together with corresponding highest scoring alleles and normalized BLAST score defined as (%identity x query coverage length) / 10000

-----

**Parameters (Optional):**

  - **Print the allele sequences as the final columns of the output?** Turn ON/OFF addition of the actual O and H antigen allelic sequences in the report
  - **Enable E. coli species verification:** Turn ON/OFF for more rigorous species verification (recommended)
  - **Include log file in the run outputs?:** Turn ON/OFF optional output of the ectyper log file for a more detailed results assessment

  </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>