Mercurial > repos > brinkmanlab > extract_tree_order
annotate 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 |
rev | line source |
---|---|
0
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
1 <tool id="extract-tree-order" name="BioPython Phylo Parse Newick Leaf Order" version="1.0" profile="16.04"> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
2 <description>Convert a newick tree to an ordered list of its leaves</description> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
3 <edam_topics> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
4 <edam_topic>topic_0084</edam_topic> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
5 <edam_topic>topic_0091</edam_topic> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
6 </edam_topics> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
7 <edam_operations> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
8 <edam_operation>operation_0326</edam_operation> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
9 <edam_operation>operation_3434</edam_operation> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
10 </edam_operations> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
11 <requirements> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
12 <requirement type="package" version="3.7">python</requirement> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
13 <requirement type="package" version="1.73">biopython</requirement> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
14 </requirements> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
15 <command detect_errors="aggressive"><![CDATA[ |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
16 python -c \$'from Bio import Phylo\nfor clade in Phylo.read("$input", "newick").get_terminals(order="preorder"): print(clade.name)' > '$output' |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
17 ]]></command> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
18 <inputs> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
19 <param name="input" type="data" format="newick" label="Input" /> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
20 </inputs> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
21 <outputs> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
22 <data name="output" format="txt" /> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
23 </outputs> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
24 <tests> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
25 <test expect_num_outputs="1"> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
26 <param name="input" value="test-data/test.newick" ftype="newick" /> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
27 <output name="output" file="test-data/output.txt" ftype="txt" /> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
28 </test> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
29 </tests> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
30 <help><![CDATA[ |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
31 Convert a newick tree to an ordered list of its leaves as determined by BioPython.Phylo 'preorder'. |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
32 |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
33 This is useful when tree order affects order of processing of the related data. |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
34 |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
35 For example, you may want to do pairwise alignment of the sequences for adjacent leaves. |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
36 |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
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);` |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
38 |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
39 returns |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
40 |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
41 ``` |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
42 NC_008463 |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
43 NC_002516 |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
44 NC_018080 |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
45 NZ_CH482384 |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
46 NC_011770 |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
47 NZ_CP006982 |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
48 NC_023066 |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
49 ``` |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
50 ]]></help> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
51 <citations> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
52 <citation type="doi">10.5281/zenodo.3364789</citation> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
53 </citations> |
e9f04f5172e4
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff
changeset
|
54 </tool> |