<tool id="ectyper" name="ectyper" version="0.1">
    <requirements>
      <requirement type="package" version="0.1">ectyper</requirement>
      <requirement type="package" version="0.1.16">samtools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
      #if $jobtype.select == "asm"
        ln -s $jobtype.draft sample.fasta;  
      #else if $jobtype.select == "se"
        ln -s $jobtype.fastq1 sample_1.fastq;  
      #else if $jobtype.select == "pe"
        ln -s $jobtype.fastq1 sample_1.fastq;  
        ln -s $jobtype.fastq2 sample_2.fastq;  
      #end if

	  $__tool_directory__/ectyper 
      #if $jobtype.select == "asm"
        -i sample.fasta
      #else if $jobtype.select == "se"
        -i sample_1.fastq
      #else if $jobtype.select == "pe"
        -i sample_1.fastq
      #end if
      -d $percent_identity
	  -l $percent_length
  	  -o "./"; cat ./output/output.csv > results.csv; 

    ]]></command>
    <inputs>
      <conditional name="jobtype">
        <param name="select" type="select" label="Assembly or FASTQ Reads?">
          <option value="asm">Genome Assembly</option>
          <option value="se">Single-End Reads</option>
          <option value="pe">Paired-End Reads (only first fastq will be used)</option>
        </param>
        <when value="asm">
          <param name="draft" type="data" format="fasta" label="FASTA" />
        </when>
        <when value="se">
          <param name="fastq1" type="data" format="fastq" label="FASTQ" />
        </when>
        <when value="pe">
          <param name="fastq1" type="data" format="fastq" label="FASTQ" />
          <param name="fastq2" type="data" format="fastq" label="FASTQ" />
        </when>
      </conditional>

      <param name="percent_identity" type="integer" label="Percent identity required for an allele match [default 90]" value="90" />
      <param name="percent_length" type="integer" label="Percent length required for an allele match [default 50]" value="50" />
    
    </inputs>
    <outputs>
            <data format="csv" label="ectyper Results" name="${input.name}.ectperResults" from_work_dir="*.csv"/>
    </outputs>

    <help><![CDATA[
    
**Usage: ectyper**

**INPUT**

A fasta assembly or single or paired end reads

**PERCENTIDENTITY**

Percentage of identity wanted to use against the database. From 0 to 100, default is 90%.

**PERCENTLENGTH**

Percentage of length wanted to use against the database. From 0 to 100, default is 50%.

https://github.com/phac-nml/ecoli_serotyping

    ]]></help>
</tool>