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1 <tool id="mashtree_gt" name="mashtree" version="1.4.6+galaxy0" python_template_version="3.5" profile="16.01">
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2 <description>Create a tree using Mash distances.</description>
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3 <requirements>
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4 <requirement type="package" version="1.4.6">mashtree</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 #for $file in $input
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8 ln -s ${file} ./${file.element_identifier}.fasta &&
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9 #end for
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10 mashtree --mindepth ${mindepth}
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11 --genomesize ${genomesize}
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12 --kmerlength ${kmerlength}
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13 --sketch-size ${sketchsize}
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14 --numcpus \${GALAXY_SLOTS:-4}
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15 *.fasta
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16 --outmatrix ${matrix}
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17 --seed 223
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18 > ${mashtree}
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19 ]]></command>
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20 <inputs>
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21 <param label="Genome assembliy collection in FASTA format" name="input" type="data_collection" format="fasta" collection_type="list" />
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22 <param label="Minimum depth. Use 0 for smart depth" type="integer" name="mindepth" value="0" />
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23 <param label="Estimated genome size in bp" type="integer" name="genomesize" value="5000000" />
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24 <param label="Kmer length" type="integer" name="kmerlength" value="21" />
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25 <param label="Sketch size" type="integer" name="sketchsize" value="10000" />
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26 </inputs>
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27 <outputs>
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28 <data name="mashtree" format="newick" label="${tool.name} on ${on_string} tree" />
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29 <data name="matrix" format="tabular" label="${tool.name} on ${on_string} distance matrix" hidden="true" />
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="input">
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34 <collection type="list">
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35 <element ftype="fasta" name="SRR13160357" value="SRR13160357.fasta" />
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36 <element ftype="fasta" name="SRR13160358" value="SRR13160358.fasta" />
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37 <element ftype="fasta" name="SRR13160359" value="SRR13160359.fasta" />
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38 <element ftype="fasta" name="SRR13160360" value="SRR13160360.fasta" />
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39 <element ftype="fasta" name="SRR13167188" value="SRR13167188.fasta" />
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40 </collection>
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41 </param>
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42 <param name="mindepth" value="0" />
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43 <param name="genomesize" value="2500000" />
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44 <param name="kmerlength" value="23" />
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45 <param name="sketchsize" value="10000" />
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46 <output name="mashtree" file="tree.dnd" />
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47 <output name="matrix" file="matrix.tsv" />
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48 </test>
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49 </tests>
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50 <help><![CDATA[
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51 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.
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52 ]]></help>
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53 <citations>
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54 <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>
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55 <citation type="doi">https://doi.org/10.21105/joss.01762</citation>
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56 </citations>
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57 </tool> |
