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comparison graphlan_annotate.xml @ 0:c5746c07ca5e draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
author bebatut
date Mon, 01 Feb 2016 07:45:14 -0500
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1 <tool id="graphlan_annotate" name="Modify an input tree for GraPhlAn" version="0.1.0">
2
3 <description></description>
4
5 <requirements>
6 <requirement type="package" version="1.66">biopython</requirement>
7 <requirement type="package" version="1.4">matplotlib</requirement>
8 <requirement type="package" version="1.0">graphlan</requirement>
9 </requirements>
10
11 <stdio>
12 </stdio>
13
14 <version_command>
15 <![CDATA[
16 python \${GRAPHLAN_DIR}/graphlan_annotate.py -v
17 ]]>
18 </version_command>
19
20 <command>
21 <![CDATA[
22 python \${GRAPHLAN_DIR}/graphlan_annotate.py
23 #if $annot
24 --annot $annot
25 #end if
26
27 $input_tree
28 $output_tree
29 ]]>
30 </command>
31
32 <inputs>
33 <param name="input_tree" type="data" format="txt" label="Input tree"
34 help="Newick, Nexus, PhyloXML or plain text"/>
35
36 <param name="annot" type="data" format="txt" label="Annotation file
37 (Optional)" help="(--annot)" optional="True"/>
38 </inputs>
39
40 <outputs>
41 <data format="text" name="output_tree"
42 label="${tool.name} on ${on_string}: Tree in PhyloXML" />
43 </outputs>
44
45 <tests>
46 <test>
47 </test>
48 </tests>
49
50 <help><![CDATA[
51
52 **What it does**
53
54 GraPhlAn is a software tool for producing high-quality circular
55 representations of taxonomic and phylogenetic trees. GraPhlAn focuses on
56 concise, integrative, informative, and publication-ready representations of
57 phylogenetically- and taxonomically-driven investigation.
58
59 `graphlan_annotate` modifies any input tree (in any of the three standard format)
60 adding additional information regarding structural or graphical aspects of the tree
61 (like colors and style of the taxa, labels, shadows, heatmaps, ...).
62
63 For more information, check the `user manual <https://bitbucket.org/nsegata/graphlan/overview>`_.
64
65 ]]></help>
66
67 <citations>
68 </citations>
69 </tool>