jpayne@0: <tool id="quast-select" name="Select Best" version="0.1.0" profile="16.10">
jpayne@0:     <description>assembly based on a combined QUAST table</description>
jpayne@0:     <requirements>
jpayne@0:         <requirement type="package">python</requirement>
jpayne@0:     </requirements>
jpayne@0:     <command detect_errors="exit_code"><![CDATA[
jpayne@0:         #for $asm in $coll
jpayne@0:         ln -s $asm ./$asm.element_identifier &&
jpayne@0:         #end for
jpayne@0:         cp ./\$(python $__tool_directory__/quast_select.py $table $criterion) $output
jpayne@0:     ]]></command>
jpayne@0:     <inputs>
jpayne@0:         <param type="data" format="tsv" name="table" label="Combined QUAST output (from table_union)"/>
jpayne@0:         <param type="select" label="Select best assembly by..." name="criterion">
jpayne@0:             <option value="N50">Longest N50</option>
jpayne@0:             <option value="Largest contig">Longest single contig</option>
jpayne@0:             <option value="# contigs">Fewest contigs</option>
jpayne@0:             <option value="# contigs (>= 1000 bp)">Fewest contigs of length 1kbp or longer</option>
jpayne@0:             <option value="Total length">Total assembly length</option>
jpayne@0:             <option value="Total length (>= 1000 bp)">Total assembly length of contigs longer than 1kbp</option>
jpayne@0:         </param>
jpayne@0:         <param type="data_collection" collection_type="list" format="fasta" name="coll" label="Collection of FASTA assemblies" />
jpayne@0:     </inputs>
jpayne@0:     <outputs>
jpayne@0:         <data format="fasta" name="output" label="Best assembly by ${criterion}" />
jpayne@0:     </outputs>
jpayne@0:     <tests>
jpayne@0:         <test>
jpayne@0:             <param name="table" value="combined_table.tsv" />
jpayne@0:             <param name="coll" >
jpayne@0:                 <collection type="list">
jpayne@0:                     <element name="sample1" value="sample1.fasta" />
jpayne@0:                     <element name="sample2" value="sample2.fasta" />
jpayne@0:                     <element name="sample3" value="sample3.fasta" />
jpayne@0:                     <element name="sample4" value="sample4.fasta" />
jpayne@0:                 </collection>
jpayne@0:             </param>
jpayne@0:             <param name="criterion" value="N50"/>
jpayne@0:             <output name="output" value="sample1.fasta" />
jpayne@0:         </test>
jpayne@0:     </tests>
jpayne@0:     <help><![CDATA[
jpayne@0:         Pick the best assembly from a collection of assemblies and a combined QUAST report.
jpayne@0:     ]]></help>
jpayne@0: </tool>