<tool id="mitokmer_v1" name="mitokmer 1" version="1.0">
    <description>Eukaryotic abundance prediction by mitochondrial content</description>
    <requirements>
      <requirement type="package" version="2.7">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

        rm $__tool_directory__/R*.fastq;
        #if $reads.reads_select == "paired"
        #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
        #set $forward = $reads.forward
        #set $reverse = $reads.reverse
        #else
        #set $name = $reads.allreads.name.split('.')[0].replace(' ','_')
        #set $forward = $reads.allreads
        #set $reverse = $reads.allreads
        #end if
        echo $name;
        echo "-=-=-";
        #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz')
        #set $fwd = "R1.fastq.gz"
        #set $rev = "R2.fastq.gz"
        #else if $forward.is_of_type('fastq', 'fastqsanger')
        #set $fwd = "R1.fastq"
        #set $rev = "R2.fastq"
        #else if $forward.is_of_type('fasta.gz')
        #set $fwd = "R1.fasta.gz"
        #set $rev = "R2.fasta.gz"
        #else
        #set $fwd = "R1.fasta"
        #set $rev = "R2.fasta"
        #end if
        ln -s $forward $__tool_directory__/$fwd;
        ln -s $reverse $__tool_directory__/$rev;
        #if $reads.reads_select == "single"
        #set $rev = "none"
        #end if
        python $__tool_directory__/kmer_read_m3.py
        -w $__tool_directory__
        -d $__tool_directory__/output
        -i $__tool_directory__/$fwd $__tool_directory__/$rev;
        echo "run cat";
        rm $__tool_directory__/results*;
        cat $__tool_directory__/output/mitokmer_result.csv > $__tool_directory__/results.csv;
    ]]></command>
    <inputs>

        <conditional name="reads">
            <param name="reads_select" type="select" label="One FASTQ dataset from your history, or two datasets from your history">
                <option value="single">One FASTQ dataset from your history</option>
                <option value="paired">Two FASTQ datasets from your history</option>
            </param>
            <when value="single">
                <param label="all reads" type="data" name="allreads" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz"/>
            </when>
            <when value="paired">
                <param label="Forward reads" type="data" name="forward" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
                <param label="Reverse reads" type="data" name="reverse" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
            </when>
        </conditional>

    </inputs>
    <outputs>
      <data format="tabular" label="mitokmer Results" name="results" from_work_dir="results.csv"/>
    </outputs>
    <tests>
        <test>
         <param name="reads_select" value="single" />
         <param name="allreads" value="1a.fasta" format="fasta"/>
         <output name="output1" file="output/mitokmer_result.csv"/>
        </test>
    </tests>

    <help><![CDATA[

**Usage: mitokmer.py**

    ]]></help>
    <citations>
       <citation type="bibtex">
        meh
       }</citation>
    </citations>

</tool>