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comparison mashtree-gt.xml @ 0:3a5ebae3386c

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planemo upload for repository https://toolrepo.galaxytrakr.org/view/jpayne/mashtree_gt/000000000000
author jpayne
date Tue, 21 May 2024 05:02:55 -0400
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-1:000000000000 0:3a5ebae3386c
1 <tool id="mashtree-gt" name="mashtree" version="1.4.6+galaxy0" python_template_version="3.5" profile="21.05">
2 <description>Create a tree using Mash distances.</description>
3 <requirements>
4 <requirement type="package" version="1.4.6">mashtree</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 #for $file in $input
8 ln -s ${file} ./${file.element_identifier}.fasta &&
9 #end for
10 mashtree --mindepth ${mindepth}
11 --genomesize ${genomesize}
12 --kmerlength ${kmerlength}
13 --sketch-size ${sketchsize}
14 --numcpus \${GALAXY_SLOTS:-4}
15 *.fasta
16 --outmatrix ${mashtree}
17 --seed 223
18 ]]></command>
19 <inputs>
20 <param label="Genome assembliy collection in FASTA format" name="input" type="data_collection" format="fasta" collection_type="list" />
21 <param label="Minimum depth. Use 0 for smart depth" type="integer" name="mindepth" value="0" />
22 <param label="Estimated genome size in bp" type="integer" name="genomesize" value="5000000" />
23 <param label="Kmer length" type="integer" name="kmerlength" value="21" />
24 <param label="Sketch size" type="integer" name="sketchsize" value="10000" />
25 </inputs>
26 <outputs>
27 <data name="mashtree" format="newick" />
28 </outputs>
29 <tests>
30 <test>
31 <param name="input">
32 <collection type="list">
33 <element ftype="fasta" name="SRR13160357" value="SRR13160357.fasta" />
34 <element ftype="fasta" name="SRR13160358" value="SRR13160358.fasta" />
35 <element ftype="fasta" name="SRR13160359" value="SRR13160359.fasta" />
36 <element ftype="fasta" name="SRR13160360" value="SRR13160360.fasta" />
37 <element ftype="fasta" name="SRR13167188" value="SRR13167188.fasta" />
38 </collection>
39 </param>
40 <param name="mindepth" value="0" />
41 <param name="genomesize" value="2500000" />
42 <param name="kmerlength" value="23" />
43 <param name="sketchsize" value="10000" />
44 <output name="mashtree" file="tree.dnd" />
45 </test>
46 </tests>
47 <help><![CDATA[
48 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.
49 ]]></help>
50 <citations>
51 <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>
52 <citation type="doi">https://doi.org/10.21105/joss.01762</citation>
53 </citations>
54 </tool>