<tool id="ectyper" name="ectyper" version="0.1">
    <requirements>
      <requirement type="package" version="0.1">ectyper</requirement>
      <requirement type="package" version="3.5">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
      #if $jobtype.select == "asm"
        ln -s $jobtype.draft ${draft.name}.fasta;  
      #else if $jobtype.select == "se"
        ln -s $jobtype.fastq1 ${fastq1.name}_1.fastq;  
      #else if $jobtype.select == "pe"
        ln -s $jobtype.fastq1 ${fastq1.name}.fastq;  
        ln -s $jobtype.fastq2 ${fastq2.name}.fastq;  
      #else if $jobtype.select == "cl"
        mkdir temp_data;
        #for $collection_file in $jobtype.collection_files
             cp $collection_file temp_data/.;
        #end for

      $__tool_directory__/ectyper  -i temp_data 
      -d $percent_identity
	    -l $percent_length
  	  -o "./"; cat ./output/output.csv > results.csv; 

      GALAXY_URL
      #end if


    #if $jobtype.select != "cl"
    	$__tool_directory__/ectyper 
      #if $jobtype.select == "asm"
        -i ${draft.name}.fasta
      #else if $jobtype.select == "se"
        -i ${fastq1.name}_1.fastq
      #else if $jobtype.select == "pe"
        -i ${fastq1.name}.fastq,${fastq2.name}.fastq
      #end if
      -d $percent_identity
	  -l $percent_length
  	  -o "./"; cat ./output/output.csv > results.csv;
    #end if 

    ]]></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</option>
          <option value="cl">Collection of Reads</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>
         <when value="cl">
              <param type="data_collection" name="collection_files" format="fastq" collection_type="list" label="FASTQS: Must be a Data Set list built from multiple fastq files" />
        </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 test or data set list of fastqs

**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>
     <citations>
        <citation type="bibtex">
        @misc{pope_dashnow_zobel_holt_raven_schultz_inouye_tomita_2014,
        title={SRST2: ecyper wraps a standalone serotyping module for Escherichia coli. Supports fasta and fastq file formats.},
        url={https://www.nml-lnm.gc.ca/},
        author={National Microbiology Laboratory },
       }</citation>
    </citations>
</tool>