<tool id="ncbi_acc_download" name="NCBI Accession Download" version="@TOOL_VERSION@_galaxy0">
    <description>Filters a fasta file using a list of sequence ids</description>
    <requirements>
      <requirement type="package" version="@TOOL_VERSION@">ncbi-acc-download</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        while read accession; do
        ncbi-acc-download
            --molecule '${molecule}'
            --format '${format}'
            '${accession}'
        done; < '${accessions}'
    ]]></command>
    <inputs>
        <param name="molecule" type="select" label="Molecule Type">
            <option value="nucleotide" selected="true">Nucleotide</option>
            <option value="protein">Protein</option>
        </param>
        <param name="format" type="select" label="File Format">
            <option value="fasta" selected="true">FASTA</option>
            <option value="genbank">GenBank</option>
            <option value="featuretable">Feature Table</option>
            <option value="gff3">GFF3</option>
	</param>
        <param name="accessions" type="data" format="tabular" />
    </inputs>
    <outputs>
        <collection name="output" type="list" format="fasta,genbank,feattable,gff3" label="Output files">
            <discover_datasets pattern="__name__" format="fasta,genbank,feattable,gff3" directory="." />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="molecule" value="nucleotide"/>
	    <param name="format" value="fasta"/>
            <param name="accessions" value="accessions_1.tsv"/>
            <output_collection name="output" type="list">
              <element file="CP011064.fa" ftype="fasta" />
	      <element file="CP021680.fa" ftype="fasta" />
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
    ]]></help>
    <citations>
    </citations>
</tool>