Mercurial > repos > brinkmanlab > extract_tree_order
comparison extract_tree_order.xml @ 0:e9f04f5172e4 draft
"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 |
parents | |
children | ddf5427278ee |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:e9f04f5172e4 |
---|---|
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> |