<tool id="make-unique-id" name="BioPython Make Unique ID" version="1.0" profile="16.04">
    <description>Makes all record ids unique across all input data</description>
    <edam_topics>
        <edam_topic>topic_3345</edam_topic>
        <edam_topic>topic_3489</edam_topic>
        <edam_topic>topic_0091</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_3282</edam_operation>
    </edam_operations>
    <requirements>
        <requirement type="package" version="1.76">biopython</requirement>
    </requirements>
    <version_command><![CDATA[ python $__tool_directory__/make_unique_id.py -v ]]></version_command>
    <command detect_errors="aggressive"><![CDATA[
        python $__tool_directory__/make_unique_id.py ${inputs[0].ext}
        #for $input, $output in $zip($inputs, $outputs)
            $input $output
        #end for
    ]]></command>
    <inputs>
        <param name="inputs" type="data_collection" format="clustal,embl,fasta,fasta-2line,fastq-sanger,fastq,fastq-solexa,fastq-illumina,genbank,gb,imgt,nexus,phd,phylip,pir,seqxml,sff,stockholm,tab,qual" label="Input" />
    </inputs>
    <outputs>
        <collection name="outputs" type="list" structured_like="inputs" inherit_format="true" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="inputs" >
                <collection type="list">
                    <element name="test1" value="test-data/1.fastq" ftype="fastq" />
                    <element name="test2" value="test-data/1.fastq" ftype="fastq" />
                    <element name="test3" value="test-data/1.fastq" ftype="fastq" />
                </collection>
            </param>
            <output_collection name="outputs" type="list" count="3">
                <element name="test1" ftype="fastq" checksum="TODO" />
                <element name="test2" ftype="fastq" checksum="TODO" />
                <element name="test3" ftype="fastq" checksum="TODO" />
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
    Ensure record IDs are unique across datasets.
    Can read/write any formats supported by BioPython SeqIO.
    
    This is useful when aggregating data downstream and you want to ensure that there are no ID collisions.
    ]]></help>
    <citations>
        <citation type="doi">10.5281/zenodo.3364789</citation>
    </citations>
</tool>