<tool id="Sff_extractor" name="SFF converter" version="1.0.1">
    <description></description>
    <requirements>
        <requirement type="package" version="2.7">python</requirement>
    </requirements>
    <command>
#if   str($fastq_output) == "fastq_false"  #python  '$__tool_directory__/sff_extract.py' $clip --seq_file='$out_file3' --qual_file='$out_file4' --xml_file='$out_file2' '$input'
#elif str($fastq_output) == "fastq_true"   #python '$__tool_directory__/sff_extract.py' $clip --fastq --seq_file='$out_file1' --xml_file='$out_file2' '$input'
#end if#
    </command>
    <inputs>
        <param format="sff" name="input" type="data" label="Extract from this dataset"/>
        <param name="clip" type="select" label="Completely remove ends with low qual and/or adaptor sequence">
            <option value="">No</option>
            <option value="--clip">Yes</option>
        </param>
        <param name="fastq_output" type="boolean" truevalue="fastq_true" falsevalue="fastq_false" checked="False" label="Do you want FASTQ file instead of FASTA + FASTA quality file?" />
    </inputs>
    <outputs>
        <data format="fastqsanger" name="out_file1" >
            <filter>fastq_output is True</filter>
        </data>
        <data format="xml" name="out_file2">
        </data>  
        <data format="fasta" name="out_file3">
            <filter>fastq_output is False</filter>
        </data>
        <data format="qual" name="out_file4">
            <filter>fastq_output is False</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="2.sff"/>
            <param name="clip" value=""/>
            <param name="fastq_output" value="false"/>
            <output name="out_file2" file="sff_converter_xml_1.dat"/>
            <output name="out_file3" file="sff_converter_fasta.dat"/>
            <output name="out_file4" file="sff_converter_qual.dat"/>
        </test>
        <test>
            <param name="input" value="2.sff"/>
            <param name="clip" value=""/>
            <param name="fastq_output" value="true"/>
            <output name="out_file1" file="sff_converter_fastq.dat"/>
            <output name="out_file2" file="sff_converter_xml_2.dat"/>
        </test>
    </tests>
    <help>

**What it does**

This tool extracts data from the 454 Sequencer SFF format and creates three files containing the: 
Sequences (FASTA),
Qualities (QUAL) and 
Clippings (XML)

    </help>
</tool>