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