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comparison graphlan.xml @ 0:60757ca9092b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
author iuc
date Sat, 04 Mar 2017 10:26:21 -0500
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-1:000000000000 0:60757ca9092b
1 <tool id="graphlan" name="GraPhlAn" version="@WRAPPER_VERSION@.0">
2 <description>to produce graphical output of an input tree</description>
3 <macros>
4 <import>graphlan_macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <stdio>
8 <regex match="Warning"
9 source="stderr"
10 level="warning"
11 description="" />
12 </stdio>
13 <version_command>graphlan.py -v</version_command>
14 <command>
15 <![CDATA[
16 graphlan.py
17 --format '$image_format.format'
18 --size '$size'
19 #if $pad
20 --pad '$pad'
21 #end if
22 #if str($image_format.format) == "png" and $image_format.dpi
23 --dpi '$image_format.dpi'
24 #end if
25 '$input_tree'
26 #if str($image_format.format) == "png"
27 '$png_output_image'
28 #else if str($image_format.format) == "pdf"
29 '$pdf_output_image'
30 #else if str($image_format.format) == "ps"
31 '$ps_output_image'
32 #else if str($image_format.format) == "eps"
33 '$eps_output_image'
34 #else
35 '$svg_output_image'
36 #end if
37 ]]>
38 </command>
39 <inputs>
40 <param name="input_tree" type="data" format="txt,nhx,phyloxml" label="Input tree"/>
41 <conditional name="image_format">
42 <param argument='--format' type="select" label="Output format">
43 <option value="png" selected="true">PNG</option>
44 <option value="pdf">PDF</option>
45 <option value="ps">PS</option>
46 <option value="eps">EPS</option>
47 <option value="svg">SVG</option>
48 </param>
49 <when value="png">
50 <param argument="--dpi" type="integer" label="Dpi of the output image" optional="True"/>
51 </when>
52 <when value="pdf"/>
53 <when value="ps"/>
54 <when value="eps"/>
55 <when value="svg"/>
56 </conditional>
57 <param argument="--size" type="integer" value="7" label="Size of the output image"/>
58 <param argument="--pad" type="integer" label="Distance between the most external graphical element and the border of the image" optional="True"/>
59 </inputs>
60 <outputs>
61 <data format="png" name="png_output_image" label="${tool.name} on ${on_string}: PNG">
62 <filter>image_format['format']=="png"</filter>
63 </data>
64 <data format="pdf" name="pdf_output_image" label="${tool.name} on ${on_string}: PDF">
65 <filter>image_format['format']=="pdf"</filter>
66 </data>
67 <data format="ps" name="ps_output_image" label="${tool.name} on ${on_string}: PS">
68 <filter>image_format['format']=="ps"</filter>
69 </data>
70 <data format="eps" name="eps_output_image" label="${tool.name} on ${on_string}: EPS">
71 <filter>image_format['format']=="eps"</filter>
72 </data>
73 <data format="svg" name="svg_output_image" label="${tool.name} on ${on_string}: SVG">
74 <filter>image_format['format']=="svg"</filter>
75 </data>
76 </outputs>
77 <tests>
78 <test>
79 <param name="input_tree" value="intermediary_tree"/>
80 <param name="format" value="png"/>
81 <param name="dpi" value="100"/>
82 <param name="size" value="7"/>
83 <param name="pad" value="2"/>
84 <output name="png_output_image" file="png_image.png" />
85 </test>
86 </tests>
87 <help><![CDATA[
88 **What it does**
89
90 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.
91
92 For more information, check the `user manual <https://bitbucket.org/nsegata/graphlan/overview>`_.
93
94 ]]></help>
95 <expand macro="citations"/>
96 </tool>