<tool id="chewbbaca_prepexternalschema" name="chewBBACA PrepExternalSchema" version="2.1.0+galaxy0">
    <description>Adapt an external schema to be used with chewBBACA.</description>
    <requirements>
        <requirement type="package" version="2.1.0">chewbbaca</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        mkdir input_files &&
        #for $f in str( $input_fasta ).split(','):
          #set $filename = os.path.basename( str($f) ).replace(".dat", "")
          ln -s ${f} input_files/${filename}.fasta
        #end for
        chewBBACA.py PrepExternalSchema
          --cpu \${GALAXY_SLOTS:-1}
          -i 'input_files'
          --bsr '${bsr}'
          --len '${len}'
          -o schema
          && tar -czf schema.tgz schema
        ]]>
    </command>
    <inputs>
        <param name="input_fasta" format="fasta" type="data" multiple="true" label="Schema files (fasta)" />
        <param name="bsr" type="float" value="0.6" optional="true" label="BSR score" />
        <param name="min_len" type="integer" min="1" value="100" max="100000" optional="true" label="Minimum length" />
    </inputs>
    <outputs>
        <data name="schema_zipped" format="zip" label="${tool.name}: on ${on_string}: Schema (zipped)" from_work_dir="schema.tgz"/>
        <data name="invalid_alleles" format="txt" label="${tool.name}: on ${on_string}: Invalid Alleles" from_work_dir="schema_invalid_alleles.txt"/>
        <data name="invalid_alleles" format="txt" label="${tool.name}: on ${on_string}: Invalid Genes" from_work_dir="schema_invalid_genes.txt"/>
        <data name="summary_stats" format="txt" label="${tool.name}: on ${on_string}: Summary Stats" from_work_dir="schema_summary_stats.txt"/>
    </outputs>
    <tests>
        
    </tests>
    <help><![CDATA[
    ]]>
    </help>
   <expand macro="citations"/>
</tool>