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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
author brinkmanlab
date Fri, 24 Jan 2020 17:35:19 -0500
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1 <tool id="extract-tree-order" name="BioPython Phylo Parse Newick Leaf Order" version="1.0" profile="16.04">
2 <description>Convert a newick tree to an ordered list of its leaves</description>
3 <edam_topics>
4 <edam_topic>topic_0084</edam_topic>
5 <edam_topic>topic_0091</edam_topic>
6 </edam_topics>
7 <edam_operations>
8 <edam_operation>operation_0326</edam_operation>
9 <edam_operation>operation_3434</edam_operation>
10 </edam_operations>
11 <requirements>
12 <requirement type="package" version="3.7">python</requirement>
13 <requirement type="package" version="1.73">biopython</requirement>
14 </requirements>
15 <command detect_errors="aggressive"><![CDATA[
16 python -c \$'from Bio import Phylo\nfor clade in Phylo.read("$input", "newick").get_terminals(order="preorder"): print(clade.name)' > '$output'
17 ]]></command>
18 <inputs>
19 <param name="input" type="data" format="newick" label="Input" />
20 </inputs>
21 <outputs>
22 <data name="output" format="txt" />
23 </outputs>
24 <tests>
25 <test expect_num_outputs="1">
26 <param name="input" value="test-data/test.newick" ftype="newick" />
27 <output name="output" file="test-data/output.txt" ftype="txt" />
28 </test>
29 </tests>
30 <help><![CDATA[
31 Convert a newick tree to an ordered list of its leaves as determined by BioPython.Phylo 'preorder'.
32
33 This is useful when tree order affects order of processing of the related data.
34
35 For example, you may want to do pairwise alignment of the sequences for adjacent leaves.
36
37 `('NC_008463':1.25269,('NC_002516':0.21042,'NC_018080':0.20913)0.940:0.00444,('NZ_CH482384':0.24749,('NC_011770':0.00035,('NZ_CP006982':0.00036,'NC_023066':0.00018)0.940:0.00019)1.000:0.18245)0.990:0.01335);`
38
39 returns
40
41 ```
42 NC_008463
43 NC_002516
44 NC_018080
45 NZ_CH482384
46 NC_011770
47 NZ_CP006982
48 NC_023066
49 ```
50 ]]></help>
51 <citations>
52 <citation type="doi">10.5281/zenodo.3364789</citation>
53 </citations>
54 </tool>