jpayne@3: <tool id="mashtree_gt" name="mashtree" version="1.4.6+galaxy0" python_template_version="3.5" profile="16.01">
jpayne@0:     <description>Create a tree using Mash distances.</description>
jpayne@0:     <requirements>
jpayne@0:         <requirement type="package" version="1.4.6">mashtree</requirement>
jpayne@0:     </requirements>
jpayne@0:     <command detect_errors="exit_code"><![CDATA[
jpayne@0:         #for $file in $input
jpayne@0:             ln -s ${file} ./${file.element_identifier}.fasta &&
jpayne@0:         #end for
jpayne@0:         mashtree --mindepth ${mindepth} 
jpayne@0:                  --genomesize ${genomesize} 
jpayne@0:                  --kmerlength ${kmerlength} 
jpayne@0:                  --sketch-size ${sketchsize} 
jpayne@0:                  --numcpus \${GALAXY_SLOTS:-4} 
jpayne@0:                  *.fasta
jpayne@0:                  --outmatrix ${mashtree}
jpayne@0:                  --seed 223
jpayne@0:     ]]></command>
jpayne@0:     <inputs>
jpayne@0:         <param label="Genome assembliy collection in FASTA format" name="input" type="data_collection" format="fasta" collection_type="list" />
jpayne@0:         <param label="Minimum depth. Use 0 for smart depth" type="integer" name="mindepth" value="0" />
jpayne@0:         <param label="Estimated genome size in bp" type="integer" name="genomesize" value="5000000" />
jpayne@0:         <param label="Kmer length" type="integer" name="kmerlength" value="21" />
jpayne@0:         <param label="Sketch size" type="integer" name="sketchsize" value="10000" />
jpayne@0:     </inputs>
jpayne@0:     <outputs>
jpayne@0:         <data name="mashtree" format="newick" />
jpayne@0:     </outputs>
jpayne@0:     <tests>
jpayne@0:         <test>
jpayne@0:             <param name="input">
jpayne@0:                 <collection type="list">
jpayne@0:                     <element ftype="fasta" name="SRR13160357" value="SRR13160357.fasta" />
jpayne@0:                     <element ftype="fasta" name="SRR13160358" value="SRR13160358.fasta" />
jpayne@0:                     <element ftype="fasta" name="SRR13160359" value="SRR13160359.fasta" />
jpayne@0:                     <element ftype="fasta" name="SRR13160360" value="SRR13160360.fasta" />
jpayne@0:                     <element ftype="fasta" name="SRR13167188" value="SRR13167188.fasta" />
jpayne@0:                 </collection>
jpayne@0:             </param>
jpayne@0:             <param name="mindepth" value="0" />
jpayne@0:             <param name="genomesize" value="2500000" />
jpayne@0:             <param name="kmerlength" value="23" />
jpayne@0:             <param name="sketchsize" value="10000" />
jpayne@0:             <output name="mashtree" file="tree.dnd" />
jpayne@0:         </test>
jpayne@0:     </tests>
jpayne@0:     <help><![CDATA[
jpayne@0:         Create a tree using Mash distances. The tree is created using the Mash distance matrix. The tree is created using the neighbor-joining algorithm. The tree is written in Newick format.
jpayne@0:     ]]></help>
jpayne@0:     <citations>
jpayne@0:         <citation type="bibtex">Katz, L. S., Griswold, T., Morrison, S., Caravas, J., Zhang, S., den Bakker, H.C., Deng, X., and Carleton, H. A., (2019). Mashtree: a rapid comparison of whole genome sequence files. Journal of Open Source Software, 4(44), 1762</citation>
jpayne@0:         <citation type="doi">https://doi.org/10.21105/joss.01762</citation>
jpayne@0:     </citations>
jpayne@0: </tool>