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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
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-1:000000000000 0:c1bd0c560018
1 <tool id="qiime_make_phylogeny" name="Make phylogeny" version="1.9.1">
2
3 <description></description>
4
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8
9 <expand macro="requirements" />
10
11 <version_command><![CDATA[
12 make_phylogeny.py --version
13 ]]>
14 </version_command>
15
16 <stdio></stdio>
17
18 <command>
19 <![CDATA[
20 make_phylogeny.py
21 -i $input_fp
22 -o $result_fp
23 -t $tree_method
24 -l $log_fp
25 -r $root_method
26 ]]>
27 </command>
28
29 <inputs>
30 <param name="input_fp" type="data" format="fasta"
31 label="Input fasta alignment" help="(-i/--input_fp)"/>
32
33 <param name="tree_method" type="select"
34 label="Method for tree building" help="(-t/--tree_method)">
35 <option value="clustalw">ClustalW</option>
36 <option value="raxml_v730">raxml_v730</option>
37 <option value="muscle">muscle</option>
38 <option value="fasttree" selected="true">fasttree</option>
39 <option value="clearcut">clearcut</option>
40 </param>
41
42 <param name="root_method" type="select"
43 label="Method for choosing root of phylo tree" help="(-r/--root_method)">
44 <option value="midpoint">Midpoint</option>
45 <option value="tree_method_default" selected="true">Default method of tree method</option>
46 </param>
47
48 </inputs>
49
50 <outputs>
51 <data format="txt" name="result_fp"
52 label="${tool.name} on ${on_string}: Tree"/>
53 <data format="txt" name="log_fp"
54 label="${tool.name} on ${on_string}: Log"/>
55 </outputs>
56
57 <tests>
58 <test>
59 </test>
60 </tests>
61
62 <help><![CDATA[
63 **What it does**
64
65 This tool produces a tree from a multiple sequence alignment. Trees are constructed with a set of sequences representative of the OTUs
66
67 More information about this tool is available on
68 `QIIME documentation <http://qiime.org/scripts/make_phylogeny.html>`_.
69 ]]>
70 </help>
71
72 <citations>
73 <expand macro="citations" />
74 </citations>
75 </tool>