<tool profile="16.07" id="mothur_make_fastq" name="Make.fastq" version="@WRAPPER_VERSION@.0">
    <description>Convert fasta and quality to fastq</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
@SHELL_OPTIONS@

## create symlinks to input datasets
ln -s '$fasta' fasta.dat &&
ln -s '$qfile' qfile.dat &&

echo 'make.fastq(
    fasta=fasta.dat,
    qfile=qfile.dat
    #if $chooseformat.use == "yes":
        ,format=${chooseformat.format}
    #end if
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="fasta" type="data" format="fasta" label="fasta - Fasta Sequence file"/>
        <param name="qfile" type="data" format="qual454,qualillumina,qualsolid,qual" label="qfile - Sequence Quality file"/>
        <conditional name="chooseformat">
            <param name="use" type="select" label="Choose quality format for your output sequences are" help="If none selected, this tool will keep the format of input qfile">
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="yes">
                <param name="format" type="select" optional="true" multiple="true">
                    <option value="sanger" selected="true">sanger</option>
                    <option value="illumina1.8+">Illumina 1.8+</option>
                    <option value="illumina">Illumina</option>
                </param>
            </when>
            <when value="no"/>
        </conditional>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="fastq" format="fasta" from_work_dir="fasta*.fastq" label="${tool.name} on ${on_string}: fastq">
            <change_format><!-- if set, chooseformat.format param should override qfile.ext format -->
                <when input="qfile.ext" value="qual454" format="fastqsanger"/>
                <when input="qfile.ext" value="qualillumina" format="fastqillumina"/>
                <when input="qfile.ext" value="qualsolid" format="fastqcssanger"/>
                <when input="chooseformat.format" value="sanger" format="fastqsanger"/>
                <when input="chooseformat.format" value="illumina1.8+" format="fastqsanger"/>
                <when input="chooseformat.format" value="illumina" format="fastqillumina"/>
            </change_format>
        </data>
    </outputs>
    <tests>
        <test><!-- test defaults -->
            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
            <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/>
            <output name="fastq" ftype="fastqsanger">
                <assert_contents>
                    <expand macro="test-fastq-format"/>
                    <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with quality score format conversion -->
            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
            <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/>
            <param name="use" value="yes"/>
            <param name="format" value="illumina"/>
            <output name="fastq" ftype="fastqillumina">
                <assert_contents>
                    <expand macro="test-fastq-format"/>
                    <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The make.fastq_ command reads a fasta file and quality file and creates a fastq.


.. _make.fastq: https://www.mothur.org/wiki/Make.fastq

    ]]></help>
    <expand macro="citations"/>
</tool>