Mercurial > repos > iuc > newick_utils
comparison newick_display.xml @ 0:fe4235285ee8 draft
planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
author | iuc |
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date | Mon, 01 Oct 2018 09:46:08 -0400 |
parents | |
children | b4163d2f64ab |
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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> |