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comparison graphlan.xml @ 2:64e69b47b4ec draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit fe1ede437f1b0e414d84d75e6a607047d1678444-dirty
author bebatut
date Mon, 02 May 2016 05:44:20 -0400
parents 5cdaa98d9376
children
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1:5cdaa98d9376 2:64e69b47b4ec
1 <tool id="graphlan" name="GraPhlAn" version="1.0"> 1 <tool id="graphlan" name="GraPhlAn" version="0.9.7">
2 2
3 <description>to produce graphical output of an input tree</description> 3 <description>to produce graphical output of an input tree</description>
4 4
5 <requirements> 5 <macros>
6 <requirement type="package" version="1.66">biopython</requirement> 6 <import>graphlan_macros.xml</import>
7 <requirement type="package" version="1.4">matplotlib</requirement> 7 </macros>
8 <requirement type="package" version="1.0">graphlan</requirement> 8
9 </requirements> 9 <expand macro="requirements"/>
10 10
11 <stdio> 11 <stdio>
12 <regex match="Warning"
13 source="stderr"
14 level="warning"
15 description="" />
12 </stdio> 16 </stdio>
13 17
14 <version_command> 18 <version_command>
15 <![CDATA[ 19 <![CDATA[
16 graphlan.py -v 20 graphlan.py -v
47 #end if 51 #end if
48 ]]> 52 ]]>
49 </command> 53 </command>
50 54
51 <inputs> 55 <inputs>
52 <param name="input_tree" type="data" format="txt" label="Input tree in 56 <param name="input_tree" type="data" format="txt" label="Input tree" help="The tree must be in PhlyloXML, Newick or text format."/>
53 PhlyloXML format" help=""/>
54 57
55 <param name='format' type="select" label="Output format" 58 <param name='format' type="select" label="Output format" help="(--format)">
56 help="(--format)">
57 <option value="png" selected="true">PNG</option> 59 <option value="png" selected="true">PNG</option>
58 <option value="pdf">PDF</option> 60 <option value="pdf">PDF</option>
59 <option value="ps">PS</option> 61 <option value="ps">PS</option>
60 <option value="eps">EPS</option> 62 <option value="eps">EPS</option>
61 <option value="svg">SVG</option> 63 <option value="svg">SVG</option>
95 </data> 97 </data>
96 </outputs> 98 </outputs>
97 99
98 <tests> 100 <tests>
99 <test> 101 <test>
100 <param name="input_tree" value="output_modified_tree.txt"/> 102 <param name="input_tree" value="intermediary_tree.txt"/>
101 <param name='format' value="png"/> 103 <param name="format" value="png"/>
102 <param name="dpi" value="100"/> 104 <param name="dpi" value="100"/>
103 <param name="size" value="7"/> 105 <param name="size" value="7"/>
104 <param name="pad" value="2"/> 106 <param name="pad" value="2"/>
105 <output name="png_output_image" value="output_image.png" /> 107 <output name="png_output_image" file="png_image.png" />
106 </test> 108 </test>
107 </tests> 109 </tests>
108 110
109 <help><![CDATA[ 111 <help><![CDATA[
110
111 **What it does** 112 **What it does**
112 113
113 GraPhlAn is a software tool for producing high-quality circular 114 GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.
114 representations of taxonomic and phylogenetic trees. GraPhlAn focuses on
115 concise, integrative, informative, and publication-ready representations of
116 phylogenetically- and taxonomically-driven investigation.
117 115
118 For more information, check the `user manual <https://bitbucket.org/nsegata/graphlan/overview>`_. 116 For more information, check the `user manual <https://bitbucket.org/nsegata/graphlan/overview>`_.
119 117
120 ]]></help> 118 ]]></help>
121 119