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comparison newick_display.xml @ 0:0db45bc4844f draft

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planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
author iuc
date Mon, 01 Oct 2018 09:45:49 -0400
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children 9298c1dbf31e
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-1:000000000000 0:0db45bc4844f
1 <tool id="newick_display" name="Newick Display" version="1.6">
2 <description>visualize a phylogenetic tree</description>
3 <edam_operations>
4 <edam_operation>operation_0567</edam_operation>
5 </edam_operations>
6 <requirements>
7 <requirement type="package" version="1.6">newick_utils</requirement>
8 </requirements>
9 <command detect_errors="aggressive"><![CDATA[
10 nw_display
11 #if $outformat != 'txt':
12 -s
13 #end if
14 $scalebar
15 -u '$legend'
16 -I 'r'
17 -i
18 #if $condbranchsupport.branchsupport == "true":
19 'fill:$condbranchsupport.supcolor;
20 font-size:$condbranchsupport.supfontsize;
21 transform:$condbranchsupport.suptransform;'
22 #else:
23 "visibility:hidden;"
24 #end if
25 -b
26 #if $condbranchlength.branchlength == "true":
27 'fill:$condbranchlength.lencolor;
28 font-size:$condbranchlength.lenfontsize;
29 transform:$condbranchlength.lentransform;'
30 #else:
31 "visibility:hidden;"
32 #end if
33
34 -l 'font-family:$leafFont;font-size:$leafSize;'
35 -d "stroke:grey;fill:none;stroke-width:2;stoke-linecap:round;"
36 -w $width
37 $radial
38
39 '$fileNewick' > output.svg
40
41 #if $outformat == 'png':
42 && convert output.svg output.png
43 && mv output.png '$output'
44 #else:
45 && mv output.svg '$output'
46 #end if
47
48 ]]></command>
49 <inputs>
50 <param name="fileNewick" format="txt,newick,nw,nwk,nhx,mothur.tre" type="data" label="Newick file"/>
51 <param name="scalebar" type="boolean" truevalue="" falsevalue="-S" checked="True" label="Display scale bar" />
52 <param name="legend" type="text" value="" label="Unit name for the scale bar" />
53 <param name="leafFont" type="text" value="sans-serif" label="Leaf font" />
54 <param name="leafSize" type="text" value="10px" label="Leaf font-size" />
55 <conditional name="condbranchsupport">
56 <param name="branchsupport" type="select" label="Branch support">
57 <option value="true">Display branch support</option>
58 <option value="false" selected="true">Hide branch support</option>
59 </param>
60 <when value="true">
61 <param name="supcolor" type="color" value="red" label="color" />
62 <param name="supfontsize" type="text" value="10px" label="font-size" />
63 <param name="suptransform" type="text" value="translateY(1.5em)" label="move" />
64 </when>
65 <when value="false" />
66 </conditional>
67 <conditional name="condbranchlength">
68 <param name="branchlength" type="select" label="Branch length">
69 <option value="true">Display branch length</option>
70 <option value="false" selected="true">Hide branch length</option>
71 </param>
72 <when value="true">
73 <param name="lencolor" type="color" value="blue" label="color" />
74 <param name="lenfontsize" type="text" value="10px" label="font-size" />
75 <param name="lentransform" type="text" value="translate(-1.5em,0em)" label="move" />
76 </when>
77 <when value="false" />
78 </conditional>
79 <param name="width" type="integer" value="800" label="Image width" help="in pixels for image output or in characters for text output" />
80 <param name="radial" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Draw a radial tree" />
81 <param name="outformat" type="select" label="Choose an output format">
82 <option value="svg" selected="true">SVG</option>
83 <option value="png">PNG</option>
84 <option value="txt">Text</option>
85 </param>
86 </inputs>
87 <outputs>
88 <data name="output" format="svg" label="${tool.name} on ${on_string}: Tree Graph" >
89 <change_format>
90 <when input="outformat" value="png" format="png"/>
91 <when input="outformat" value="txt" format="txt"/>
92 </change_format>
93 </data>
94 </outputs>
95 <tests>
96 <test>
97 <param name="fileNewick" value="tree.nwk"/>
98 <param name="width" value="400"/>
99 <param name="leafFont" value="courier"/>
100 <output name="output" file="tree.svg" ftype="svg" lines_diff="2"/>
101 </test>
102 <test><!-- test radial tree -->
103 <param name="fileNewick" value="tree.nwk"/>
104 <param name="radial" value="-r"/>
105 <param name="branchlength" value="true"/>
106 <output name="output" file="tree2.svg" ftype="svg" lines_diff="2"/>
107 </test>
108 <test><!-- test with png output format -->
109 <param name="fileNewick" value="tree.nwk"/>
110 <param name="radial" value="-r"/>
111 <param name="branchlength" value="true"/>
112 <param name="outformat" value="png"/>
113 <output name="output" file="tree.png" ftype="png" compare="sim_size" delta="15000"/>
114 </test>
115 <test><!-- test with txt output format -->
116 <param name="fileNewick" value="tree.nwk"/>
117 <param name="outformat" value="txt"/>
118 <output name="output" file="tree.txt" ftype="txt"/>
119 </test>
120 </tests>
121 <help><![CDATA[
122 **What it does**
123
124 This tool outputs a graph representing the tree, either as text or
125 as a SVG or PNG image. Underscores in labels are replaced with spaces.
126 Trees with no branch lengths are taken to be cladograms and are
127 drawn with leaves aligned. Otherwise, the tree is assumed to be a
128 phylogram: branch lengths are honored and a scale bar is drawn.
129
130 .. image:: $PATH_TO_IMAGES/example.png
131 :alt: example newick tree graph
132
133 ]]></help>
134 <citations>
135 <citation type="doi">10.1186/1748-7188-3-7</citation>
136 </citations>
137 </tool>