<tool id="cfsan_snp_pipeline_quast_select" name="CFSAN SNP Pipeline: Select best assembly"  version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>based on a combined QUAST table</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
#for $fasta_file in $input_collection_fasta
    ln -s $fasta_file $fasta_file.element_identifier &&
#end for
mv ./\$(python '$__tool_directory__/cfsan_snp_pipeline_quast_select.py' '$input_quast_tsv' '$criterion') '$output'
    ]]></command>
    <inputs>
        <param name="input_quast_tsv" type="data" format="tabular,tsv" label="Combined QUAST output tabular file"/>
        <param name="criterion" type="select" label="Select best assembly by">
            <option value="N50" selected="true">longest N50</option>
            <option value="Largest contig">longest single contig</option>
            <option value="# contigs">fewest contigs</option>
	    <option value="# contigs (>= 1000 bp)">fewest contigs of length 1kbp or longer</option>
            <option value="Total length">total assembly length</option>
	    <option value="Total length (>= 1000 bp)">total assembly length of contigs longer than 1kbp</option>
        </param>
        <param name="input_collection_fasta" type="data_collection" collection_type="list" format="fasta" label="Collection of FASTA assemblies"/>
    </inputs>
    <outputs>
        <data name="output" format="fasta" label="Best assembly by ${criterion}"/>
    </outputs>
    <tests>
        <test>
            <param name="input_quast_tsv" value="quast_report.tsv"/>
            <param name="input_collection_fasta" >
                <collection type="list">
                    <element name="SRR3168967" value="SRR3168967.fasta"/>
                </collection>
            </param>
            <param name="criterion" value="N50"/>
            <!-- the output is the same as the input here -->
            <output name="output" value="SRR3168967.fasta"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Selects the best assembly from a collection of assemblies and a combined QUAST report.
    ]]></help>
    <expand macro="citations"/>
</tool>