Mercurial > repos > padge > phykit

annotate phykit_alignment_tree_based.xml @ 1:1ac6ee298657 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
author padge
date Mon, 28 Mar 2022 16:30:53 +0000
parents 37b049bf729a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
1 <tool id="phykit_alignment_tree_based" name="PhyKit - Alignment- and tree-based functions" version="0.1.0" python_template_version="3.5">
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
2 <requirements>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
3 <requirement type="package" version="1.11.7">phykit</requirement>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
4 </requirements>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
5 <command detect_errors="exit_code"><![CDATA[
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
6 #if $tools.tool_selector == "treeness_over_rcv"
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
7 phykit treeness_over_rcv -a $tools.input1 -t $tools.input2 > $treeness_rcv;
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
8 #end if
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
9
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
10
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
11 ]]></command>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
12 <inputs>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
13 <conditional name="tools">
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
14 <param name="tool_selector" type="select" label="Select tool for processing the alignment(s)">
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
15 <option value="treeness_over_rcv">Calculate treeness/RCV for a given alignment and tree.</option>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
16 </param>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
17 <when value="treeness_over_rcv">
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
18 <param name="input1" type="data" format="fasta" multiple="false" label="Alignment file" optional="false" />
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
19 <param name="input2" type="data" format="newick" multiple="false" label="Tree file" optional="false" />
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
20 </when>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
21 </conditional>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
22 </inputs>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
23 <outputs>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
24 <data name="treeness_rcv" format="tabular" label="Three tab delimited values: col1: treeness/RCV col2: treeness col3: RCV" >
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
25 <filter>tools['tool_selector']=='treeness_over_rcv'</filter>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
26 </data>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
27 </outputs>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
28 <tests>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
29 <test>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
30 <param name="tool_selector" value="treeness_over_rcv" />
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
31 <param name="input1" value="simple.fa"/>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
32 <param name="input2" value="tree_simple.tre"/>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
33 <output name="treeness_rcv" file="test_treeness_over_rcv.txt"/>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
34 </test>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
35 </tests>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
36 <help><![CDATA[
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
37
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
38 Version: 1.11.3
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
39 Citation: Steenwyk et al. 2021, Bioinformatics. doi: 10.1093/bioinformatics/btab096
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
40 Documentation link: https://jlsteenwyk.com/PhyKIT/usage/index.html#alignment-and-tree-based-functions
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
41 Publication link: https://academic.oup.com/bioinformatics/article-abstract/37/16/2325/6131675
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
42
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
43 PhyKIT helps process and analyze multiple sequence alignments and phylogenies.
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
44
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
45 Generally, all functions are designed to help understand the contents of alignments
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
46 (e.g., gc content or the number of parsimony informative sites) and the shape
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
47 of trees (e.g., treeness, degree of violation of a molecular clock).
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
48
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
49
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
50 Alignment- and tree-based commands
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
51 ==================================
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
52 treeness_over_rcv (alias: toverr)
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
53 - calculates treeness/rcv, treeness, and rcv
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
54
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
55 ]]></help>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
56 <citations>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
57 <citation type="bibtex">
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
58 @misc{githubPhyKIT,
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
59 author = {LastTODO, FirstTODO},
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
60 year = {TODO},
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
61 title = {PhyKIT},
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
62 publisher = {GitHub},
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
63 journal = {GitHub repository},
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
64 url = {https://github.com/JLSteenwyk/PhyKIT},
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
65 }</citation>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
66 </citations>
37b049bf729a "planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
padge
parents:
diff changeset
67 </tool>