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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit 7aadbbdef6da644837f62ea428cb859eeff34f04-dirty
author bebatut
date Thu, 26 May 2016 09:38:11 -0400
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-1:000000000000 0:83baf73b0e79
1 <tool id="graphlan" name="GraPhlAn" version="0.9.7">
2
3 <description>to produce graphical output of an input tree</description>
4
5 <macros>
6 <import>graphlan_macros.xml</import>
7 </macros>
8
9 <expand macro="requirements"/>
10
11 <stdio>
12 <regex match="Warning"
13 source="stderr"
14 level="warning"
15 description="" />
16 </stdio>
17
18 <version_command>
19 <![CDATA[
20 graphlan.py -v
21 ]]>
22 </version_command>
23
24 <command>
25 <![CDATA[
26 graphlan.py
27 --format $format
28
29 #if $dpi
30 --dpi $dpi
31 #end if
32
33 --size $size
34
35 #if $pad
36 --pad $pad
37 #end if
38
39 $input_tree
40
41 #if str($format) == "png"
42 $png_output_image
43 #else if str($format) == "pdf"
44 $pdf_output_image
45 #else if str($format) == "ps"
46 $ps_output_image
47 #else if str($format) == "eps"
48 $eps_output_image
49 #else
50 $svg_output_image
51 #end if
52 ]]>
53 </command>
54
55 <inputs>
56 <param name="input_tree" type="data" format="txt" label="Input tree" help="The tree must be in PhlyloXML, Newick or text format."/>
57
58 <param name='format' type="select" label="Output format" help="(--format)">
59 <option value="png" selected="true">PNG</option>
60 <option value="pdf">PDF</option>
61 <option value="ps">PS</option>
62 <option value="eps">EPS</option>
63 <option value="svg">SVG</option>
64 </param>
65
66 <param name="dpi" type="integer" label="Dpi of the output image
67 (Optional)" help="For non vectorial formats (--dpi)" optional="True"/>
68
69 <param name="size" type="integer" value="7" label="Size of the output image
70 (in inches)" help="(--size)"/>
71
72 <param name="pad" type="integer" label="Distance between the most external
73 graphical element and the border of the image (Optional)"
74 help="(--pad)" optional="True"/>
75 </inputs>
76
77 <outputs>
78 <data format="png" name="png_output_image"
79 label="${tool.name} on ${on_string}: Image">
80 <filter>format=="png"</filter>
81 </data>
82 <data format="pdf" name="pdf_output_image"
83 label="${tool.name} on ${on_string}: Image">
84 <filter>format=="pdf"</filter>
85 </data>
86 <data format="ps" name="ps_output_image"
87 label="${tool.name} on ${on_string}: Image">
88 <filter>format=="ps"</filter>
89 </data>
90 <data format="eps" name="eps_output_image"
91 label="${tool.name} on ${on_string}: Image">
92 <filter>format=="eps"</filter>
93 </data>
94 <data format="svg" name="svg_output_image"
95 label="${tool.name} on ${on_string}: Image">
96 <filter>format=="svg"</filter>
97 </data>
98 </outputs>
99
100 <tests>
101 <test>
102 <param name="input_tree" value="intermediary_tree.txt"/>
103 <param name="format" value="png"/>
104 <param name="dpi" value="100"/>
105 <param name="size" value="7"/>
106 <param name="pad" value="2"/>
107 <output name="png_output_image" file="png_image.png" />
108 </test>
109 </tests>
110
111 <help><![CDATA[
112 **What it does**
113
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.
115
116 For more information, check the `user manual <https://bitbucket.org/nsegata/graphlan/overview>`_.
117
118 ]]></help>
119
120 <citations>
121 </citations>
122 </tool>