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comparison mashtree-gt.xml @ 4:f2c1f3fa6e37 tip

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planemo upload for repository https://toolrepo.galaxytrakr.org/view/jpayne/mashtree_gt/000000000000
author jpayne
date Tue, 21 May 2024 09:04:14 -0400
parents 903a73fe724e
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3:903a73fe724e 4:f2c1f3fa6e37
11 --genomesize ${genomesize} 11 --genomesize ${genomesize}
12 --kmerlength ${kmerlength} 12 --kmerlength ${kmerlength}
13 --sketch-size ${sketchsize} 13 --sketch-size ${sketchsize}
14 --numcpus \${GALAXY_SLOTS:-4} 14 --numcpus \${GALAXY_SLOTS:-4}
15 *.fasta 15 *.fasta
16 --outmatrix ${mashtree} 16 --outmatrix ${matrix}
17 --seed 223 17 --seed 223
18 > ${mashtree}
18 ]]></command> 19 ]]></command>
19 <inputs> 20 <inputs>
20 <param label="Genome assembliy collection in FASTA format" name="input" type="data_collection" format="fasta" collection_type="list" /> 21 <param label="Genome assembliy collection in FASTA format" name="input" type="data_collection" format="fasta" collection_type="list" />
21 <param label="Minimum depth. Use 0 for smart depth" type="integer" name="mindepth" value="0" /> 22 <param label="Minimum depth. Use 0 for smart depth" type="integer" name="mindepth" value="0" />
22 <param label="Estimated genome size in bp" type="integer" name="genomesize" value="5000000" /> 23 <param label="Estimated genome size in bp" type="integer" name="genomesize" value="5000000" />
23 <param label="Kmer length" type="integer" name="kmerlength" value="21" /> 24 <param label="Kmer length" type="integer" name="kmerlength" value="21" />
24 <param label="Sketch size" type="integer" name="sketchsize" value="10000" /> 25 <param label="Sketch size" type="integer" name="sketchsize" value="10000" />
25 </inputs> 26 </inputs>
26 <outputs> 27 <outputs>
27 <data name="mashtree" format="newick" /> 28 <data name="mashtree" format="newick" label="${tool.name} on ${on_string} tree" />
29 <data name="matrix" format="tabular" label="${tool.name} on ${on_string} distance matrix" hidden="true" />
28 </outputs> 30 </outputs>
29 <tests> 31 <tests>
30 <test> 32 <test>
31 <param name="input"> 33 <param name="input">
32 <collection type="list"> 34 <collection type="list">
40 <param name="mindepth" value="0" /> 42 <param name="mindepth" value="0" />
41 <param name="genomesize" value="2500000" /> 43 <param name="genomesize" value="2500000" />
42 <param name="kmerlength" value="23" /> 44 <param name="kmerlength" value="23" />
43 <param name="sketchsize" value="10000" /> 45 <param name="sketchsize" value="10000" />
44 <output name="mashtree" file="tree.dnd" /> 46 <output name="mashtree" file="tree.dnd" />
47 <output name="matrix" file="matrix.tsv" />
45 </test> 48 </test>
46 </tests> 49 </tests>
47 <help><![CDATA[ 50 <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. 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.
49 ]]></help> 52 ]]></help>