annotate patrist.xml @ 0:f8847f5a5491 draft default tip

"planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
author nml
date Tue, 17 Dec 2019 09:53:52 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
1 <?xml version="1.0"?>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
2 <tool id="patrist" name="PATRIST" version="@VERSION@">
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
3 <description>extract patristic distance from a tree</description>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
4 <macros>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
5 <token name="@VERSION@">0.1.2</token>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
6 </macros>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
7 <requirements>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
8 <requirement type="package" version="3.8.0">python</requirement>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
9 <requirement type="package" version="1.74">biopython</requirement>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
10 </requirements>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
11 <version_command>python '$__tool_directory__/patrist.py'</version_command>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
12 <command detect_errors="aggressive">
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
13 <![CDATA[
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
14 python '$__tool_directory__/patrist.py'
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
15
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
16 #if '$minimize':
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
17 --minimize
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
18 #end if
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
19 #if '$keep_ties':
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
20 --keep_ties
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
21 #end if
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
22 --overwrite
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
23
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
24 '$tree' '$cutoff' '$outfile'
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
25 ]]>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
26 </command>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
27 <inputs>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
28 <param format="nhx" name="tree" type="data" multiple="false" label="Newick tree file" />
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
29 <param name="cutoff" type="float" value="0.5" label="Maximum patristic distance" />
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
30 <param name="minimize" type="boolean" truevalue="" falsevalue="" checked="false" label="Report no more than one nearest neighbour per tip" />
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
31 <param name="keep_ties" type="boolean" truevalue="" falsevalue="" checked="false" label="If more than one tip has the same patristic distance report all as nearest neighbours" />
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
32 </inputs>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
33 <outputs>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
34 <data name="outfile" format="csv" label="${tool.name} on ${on_string}:outfile.csv" />
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
35 </outputs>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
36 <tests>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
37 <test>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
38 <param name="tree" value="tree.nhx" />
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
39 <param name="cutoff" value="0.5" />
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
40 <output name="outfile" file="outfile.csv" ftype="csv" lines_diff="0" />
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
41 </test>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
42 </tests>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
43 <help>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
44 <![CDATA[
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
45
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
46 ===========
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
47 Description
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
48 ===========
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
49
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
50 .. class:: infomark
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
51
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
52 Patrist will rapidly extract patristic distances from a tree for clustering tips
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
53 below a user-defined threshold.
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
54
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
55 .. _Patrist: https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
56
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
57 -----
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
58 Input
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
59 -----
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
60
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
61 'tree', <input> file containing Newick tree string.
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
62
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
63 ----------
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
64 Parameters
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
65 ----------
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
66
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
67 'cutoff', Maximum patristic distance.
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
68 '--minimize', Report no more than one nearest neighbour per tip.
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
69 '--keep_ties', If more than one tip has the same patristic distance report all as nearest neighbours.
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
70
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
71 ------
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
72 Output
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
73 ------
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
74
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
75 'outfile', <output> file to write results in CSV format.' The script overwrites any file with the current file name in the output directory.
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
76
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
77 ]]>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
78 </help>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
79 <citations>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
80 </citations>
f8847f5a5491 "planemo upload for repository https://github.com/phac-nml/patrist commit f64cb2a8399f83d8c025c8efdc3c3eec72922a7d"
nml
parents:
diff changeset
81 </tool>