<tool id="fastq_to_fasta_python" name="FASTQ to FASTA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>converter</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <edam_topics>
        <edam_topic>topic_0622</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_3434</edam_operation>
    </edam_operations>
    <expand macro="requirements"/>
    <command><![CDATA[
gx-fastq-to-fasta '$input_file' '$output_file' '${input_file.extension[len('fastq'):]}'
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ file to convert" />
    </inputs>
    <outputs>
        <data name="output_file" format="fasta" />
    </outputs>
    <tests>
        <!-- basic test -->
        <test>
            <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
            <output name="output_file" file="fastq_to_fasta_python_1.out" />
        </test>
        <!-- basic test -->
        <test>
            <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger.gz" ftype="fastqsanger.gz" />
            <output name="output_file" file="fastq_to_fasta_python_1.out" />
        </test>
        <!-- color space test -->
        <test>
            <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" />
            <output name="output_file" file="fastq_to_fasta_python_2.out" />
        </test>
        <!-- test of ignoring invalid score values: this input has ascii characters falling outside of illumina range, but they should not matter -->
        <test>
            <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqillumina" />
            <output name="output_file" file="fastq_to_fasta_python_1.out" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

This tool converts FASTQ sequencing reads to FASTA sequences.
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btq281</citation>
    </citations>
</tool>