Mercurial > repos > iuc > hyphy_annotate

comparison hyphy_annotate.xml @ 0:df56795c3d89 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
author iuc
date Tue, 20 Apr 2021 10:29:30 +0000
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children a88848771d2d
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1 <?xml version="1.0"?>
2 <tool id="hyphy_annotate" name="Annotate" version="@VERSION@">
3 <description>a newick tree with HyPhy</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 cp '$input_tree' input.nhx &&
10 cp '$compressed_msa' input.$compressed_msa.extension &&
11 cp '$__tool_directory__/scripts/annotator.bf' annotator.bf &&
12 hyphy annotator.bf
13 input.nhx '$root' input.$compressed_msa.extension '$label' labeled_tree.
14 @ERRORS@
15 ]]></command>
16 <inputs>
17 <param name="input_tree" type="data" format="nhx" label="Input tree" />
18 <param name="compressed_msa" type="data" format="fasta,fasta.gz" label="Multiple alignments" />
19 <param name="root" type="text" optional="false" value="REFERENCE" label="Root node" />
20 <param name="label" type="text" optional="false" value="Tree" label="Label for tree" />
21 </inputs>
22 <outputs>
23 <data name="labeled_tree_int" format="nhx" from_work_dir="labeled_tree.int.nwk" label="Labeled tree (int)" />
24 <data name="labeled_tree_clade" format="nhx" from_work_dir="labeled_tree.clade.nwk" label="Labeled tree (clade)" />
25 <data name="labeled_tree_full" format="nhx" from_work_dir="labeled_tree.full.nwk" label="Labeled tree (full)" />
26 </outputs>
27 <tests>
28 <test>
29 <param name="compressed_msa" ftype="fasta.gz" value="annotate-in1.fa.gz"/>
30 <param name="input_tree" ftype="nhx" value="annotate-in1.nhx"/>
31 <param name="multiple_hits" value="None" />
32 <param name="root" value="REFERENCE" />
33 <param name="label" value="Annotated" />
34 <param name="log" value="false" />
35 <output name="labeled_tree_int" file="annotate-out1-int.nhx" />
36 <output name="labeled_tree_full" file="annotate-out1-full.nhx" />
37 <output name="labeled_tree_clade" file="annotate-out1-clade.nhx" />
38 </test>
39 </tests>
40 <help><![CDATA[
41 HyPhy Annotate
42 ==============
43
44 Given a set of alignments and a newick tree, this tool produces an annotated tree with
45 the specified root node and label.
46 ]]></help>
47 <expand macro="citations">
48 <citation type="doi">10.1093/molbev/msv022</citation>
49 </expand>
50 </tool>