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Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
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1 <tool id="make_phylogeny" name="make_phylogeny" version="1.2.0">
2 <description>Make Phylogeny</description>
3 <requirements>
4 <requirement type="binary">make_phylogeny.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 make_phylogeny.py
9 --input_fp=$input_fp
10 --tree_method=$tree_method
11 --root_method=$root_method
12 --result_fp=$result_fp
13 --log_fp=$log_fp
14 </command>
15 <inputs>
16 <param name="input_fp" type="data" format="align" label="input_fp"
17 help="Path to read input alignment [REQUIRED]"/>
18 <param name="tree_method" type="select" label="tree_method"
19 help="Method for tree building. Valid choices are: clearcut, clustalw, raxml, fasttree_v1, fasttree, muscle [default: fasttree]">
20 <option value="clearcut">clearcut</option>
21 <option value="clustalw">clustalw</option>
22 <option value="raxml">raxml</option>
23 <option value="fasttree_v1">fasttree_v1</option>
24 <option value="fasttree" selected="true">fasttree</option>
25 <option value="muscle">muscle</option>
26 </param>
27 <param name="root_method" type="select" label="root_method"
28 help="method for choosing root of phylo tree Valid choices are: midpoint, tree_method_default [default: tree_method_default]">
29 <option value="tree_method_default" selected="true">tree_method_default</option>
30 <option value="midpoint">midpoint</option>
31 </param>
32 </inputs>
33 <outputs>
34 <data format="txt" name="log_fp" label="${tool.name} on ${on_string}: log" />
35 <data format="tre" name="result_fp" label="${tool.name} on ${on_string}: tree" />
36 </outputs>
37 <tests>
38 </tests>
39 <help>
40
41 </help>
42 </tool>
43