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comparison make_phylogeny.xml @ 0:e82369a926e3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
author iuc
date Thu, 18 May 2017 09:34:15 -0400
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children 9e5b2251a6a5
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-1:000000000000 0:e82369a926e3
1 <tool id="qiime_make_phylogeny" name="Make phylogeny" version="@WRAPPER_VERSION@.0">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements">
7 <requirement type="package" version="8.2.9">raxml</requirement>
8 <requirement type="package" version="2.1">clustalw</requirement>
9 <requirement type="package" version="3.8.1551">muscle</requirement>
10 <requirement type="package" version="1.0.9">clearcut</requirement>
11 </expand>
12 <version_command>make_phylogeny.py --version</version_command>
13 <command detect_errors="aggressive"><![CDATA[
14 make_phylogeny.py
15 --input_fp '$input_fp'
16 --result_fp '$result_fp'
17 --tree_method '$tree_method'
18 --log_fp '$log_fp'
19 --root_method '$root_method'
20 ]]></command>
21 <inputs>
22 <param argument="--input_fp" type="data" format="fasta" label="Input fasta alignment"/>
23 <param argument="--tree_method" type="select" label="Method for tree building">
24 <option value="clustalw">ClustalW</option>
25 <option value="raxml_v730">raxml_v730</option>
26 <option value="muscle">muscle</option>
27 <option value="fasttree" selected="true">fasttree</option>
28 <option value="clearcut">clearcut</option>
29 </param>
30 <param argument="--root_method" type="select" label="Method for choosing root of phylo tree">
31 <option value="midpoint">Midpoint</option>
32 <option value="tree_method_default" selected="true">Default method of tree method</option>
33 </param>
34 </inputs>
35 <outputs>
36 <data name="result_fp" format="nhx" label="${tool.name} on ${on_string}: Tree"/>
37 <data name="log_fp" format="txt" label="${tool.name} on ${on_string}: Log"/>
38 </outputs>
39 <tests>
40 <test>
41 <param name="input_fp" value="make_phylogeny/aligned.fasta"/>
42 <param name="tree_method" value="fasttree"/>
43 <param name="root_method" value="tree_method_default" />
44 <output name="result_fp" file="make_phylogeny/fasttree_tree_method_default.tre"/>
45 <output name="log_fp">
46 <assert_contents>
47 <has_text text="Method:fasttree"/>
48 <has_text text="CogentTreeBuilder parameters:"/>
49 </assert_contents>
50 </output>
51 </test>
52 <test>
53 <param name="input_fp" value="make_phylogeny/aligned.fasta"/>
54 <param name="tree_method" value="raxml_v730"/>
55 <param name="root_method" value="tree_method_default" />
56 <output name="result_fp" ftype="nhx" >
57 <assert_contents>
58 <has_text text="seq_20"/>
59 <has_text text="seq_46"/>
60 <has_text text="seq_11"/>
61 </assert_contents>
62 </output>
63 <output name="log_fp">
64 <assert_contents>
65 <has_text text="Method:raxml_v730"/>
66 <has_text text="CogentTreeBuilder parameters:"/>
67 </assert_contents>
68 </output>
69 </test>
70 <test>
71 <param name="input_fp" value="make_phylogeny/aligned.fasta"/>
72 <param name="tree_method" value="muscle"/>
73 <param name="root_method" value="tree_method_default" />
74 <output name="result_fp" file="make_phylogeny/muscle.tre"/>
75 <output name="log_fp">
76 <assert_contents>
77 <has_text text="Method:muscle"/>
78 <has_text text="CogentTreeBuilder parameters:"/>
79 </assert_contents>
80 </output>
81 </test>
82 <test>
83 <param name="input_fp" value="make_phylogeny/aligned.fasta"/>
84 <param name="tree_method" value="clustalw"/>
85 <param name="root_method" value="tree_method_default" />
86 <output name="result_fp" file="make_phylogeny/clustalw.tre"/>
87 <output name="log_fp">
88 <assert_contents>
89 <has_text text="Method:clustalw"/>
90 <has_text text="CogentTreeBuilder parameters:"/>
91 </assert_contents>
92 </output>
93 </test>
94 <test>
95 <param name="input_fp" value="make_phylogeny/aligned.fasta"/>
96 <param name="tree_method" value="clearcut"/>
97 <param name="root_method" value="tree_method_default" />
98 <output name="result_fp" ftype="nhx" >
99 <assert_contents>
100 <has_text text="seq_20"/>
101 <has_text text="seq_46"/>
102 <has_text text="seq_11"/>
103 </assert_contents>
104 </output>
105 <output name="log_fp">
106 <assert_contents>
107 <has_text text="Method:clearcut"/>
108 <has_text text="CogentTreeBuilder parameters:"/>
109 </assert_contents>
110 </output>
111 </test>
112 <test>
113 <param name="input_fp" value="make_phylogeny/aligned.fasta"/>
114 <param name="tree_method" value="fasttree"/>
115 <param name="root_method" value="midpoint" />
116 <output name="result_fp" file="make_phylogeny/fasttree_midpoint.tre"/>
117 <output name="log_fp">
118 <assert_contents>
119 <has_text text="Method:fasttree"/>
120 <has_text text="CogentTreeBuilder parameters:"/>
121 </assert_contents>
122 </output>
123 </test>
124 </tests>
125 <help><![CDATA[
126 **What it does**
127
128 This tool produces a tree from a multiple sequence alignment. Trees are constructed with a set of sequences representative of the OTUs
129
130 More information about this tool is available on
131 `QIIME documentation <http://qiime.org/scripts/make_phylogeny.html>`_.
132 ]]></help>
133 <citations>
134 <expand macro="citations"/>
135 </citations>
136 </tool>