diff nwdisplay.xml @ 0:5c11638687d0 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nwdisplay.xml	Tue Mar 15 10:53:34 2016 -0400
@@ -0,0 +1,255 @@
+<tool id="nwdisplay" name="Newick Display" version="1">
+    <description>Display a phylogenetic tree as SVG</description>
+    <requirements>
+        <requirement type="package" version="1.6">newick_utilities</requirement>
+    </requirements>
+    <command>
+			nw_display
+			-s 
+			$scalebar
+			-u "$legend"
+			-I 'r'
+			-i
+			#if $condbranchsupport.branchsupport == "true":
+			   "fill:$condbranchsupport.supcolor;
+			    font-size:$condbranchsupport.supfontsize;
+			    transform:$condbranchsupport.suptransform;"
+			#else:
+			     "visibility:hidden;"
+			#end if
+			-b
+			#if $condbranchlength.branchlength == "true":
+               "fill:$condbranchlength.lencolor;
+                font-size:$condbranchlength.lenfontsize;
+                transform:$condbranchlength.lentransform;"
+            #else:
+                 "visibility:hidden;"
+            #end if			
+			
+			-l "font-family:$leafPolice;font-size:$leafSize;"
+			-d "stroke:grey;fill:none;stroke-width:2;stoke-linecap:round;"
+			-w  $width
+			$radial
+			
+		    $fileNewick > $output
+		
+    </command>
+	<inputs>
+		<param name="fileNewick" format="txt,nw,nwk,nhx" type="data" label="Newick file" />
+		<param name="scalebar" type="boolean" truevalue="" falsevalue="-S"	checked="True" label="Display scale bar" />
+		<param name="legend" type="text" value="" label="Unit name scale" />
+		<param name="leafPolice" type="text" value="sans-serif" label="Leaf police" />
+		<param name="leafSize" type="text" value="10px" label="Leaf font-size" />
+		<conditional name="condbranchsupport">
+			<param name="branchsupport" type="select" label="Branch support">
+			    <option value="true">Display branch support</option>
+                <option value="false" selected="true">Hide branch support</option>
+            </param>
+			<when value="true">
+				<param name="supcolor" type="text" value="red" label="color" />
+				<param name="supfontsize" type="text" value="10px" label="font-size" />
+				<param name="suptransform" type="text" value="translateY(1.5em)" label="move" />
+			</when>
+			<when value="false" />
+		</conditional>
+		<conditional name="condbranchlength">
+			<param name="branchlength" type="select" label="Branch length">
+				<option value="true">Display branch length</option>
+				<option value="false" selected="true">Hide branch length</option>
+			</param>
+			<when value="true">
+				<param name="lencolor" type="text" value="blue" label="color" />
+				<param name="lenfontsize" type="text" value="10px" label="font-size" />
+				<param name="lentransform" type="text" value="translate(-1.5em,0em)" label="move" />
+			</when>
+			<when value="false" />
+		</conditional>
+		<param name="width" type="integer" value="800"	label="SVG Tree width (px)" />
+		<param name="radial" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Draw a radial tree" />
+	</inputs>
+	<outputs>
+		<data name="output" format="svg" label="${fileNewick.name}.svg" />
+	</outputs>
+	<tests>
+		<test>
+		    <param name="fileNewick" value="tree.nwk"/>
+		    <param name="width" value="400"/>
+		    <param name="leafPolice" value="courier"/>
+            <output name="output" file="tree.svg" lines_diff="2"/>
+		</test>
+		<test>
+            <param name="fileNewick" value="tree.nwk"/>
+            <param name="radial" value="-r"/>
+            <param name="branchlength" value="true"/>
+            <output name="output" file="tree2.svg" lines_diff="2"/>
+        </test>
+	</tests>
+    <help>
+<![CDATA[
+**Displays a tree as a graph, as text or SVG.**
+
+
+Synopsis
+--------
+
+nw_display [options] <tree filename|->
+
+Input
+-----
+
+Argument is the name of the file containing one or more trees,
+or '-' (in which case the tree is read on stdin).
+
+Output
+------
+
+Outputs a graph representing the tree, either as text (default) or
+as SVG (option -s). Underscores in labels are replaced with spaces.
+Trees with no branch lengths are taken to be cladograms and are
+drawn with leaves aligned. Otherwise, the tree is assumed to be a
+phylogram: branch lengths are honored and a scale bar is drawn.
+
+SVG graphics can be converted to other formats with converters
+such as Inkscape (e.g. to PDF) or ImageMagick (e.g. to PNG or JPEG).
+Inkscape is available from www.inkscape.org and ImageMagick from
+www.imagemagick.org.
+
+Options
+-------
+
+    -a <number>: rotate all labels by this amount (radians, default: 0)
+       [only SVG radial]
+    -A <number>: rotate left-side labels by this amount (radians,
+       default: 0.0349 (=~ 2°)) [only SVG radial]
+    -b <string>: CSS for branch length labels. [only SVG]
+       Default: 'font-size:small;font-family:sans'.
+       setting 'opacity:0' disables printing of branch lengths.
+    -c <filename>: use specified file as CSS map [only SVG]. A CSS map
+       is a text file which specifies a style (CSS) for a clade.
+       Each line has the following structure:
+       <CSS> <flag> <label>+
+       <CSS> is a valid CSS style specification (no spaces allowed)
+       e.g. 'font-size:small;font-family:italics;stroke:green'.
+       <flag> is either 'Individual' or 'Clade' (case is not important, can
+       be abbreviated down to 'I' or 'C'). If set to 'Clade', the style is
+       applied to the clade defined by the labels. If 'Individual', the
+       style is applied to each node individually.
+       <label>+ is a nonempty, whitespace-separated list of Newick labels
+       (spaces are allowed IFF the label is enclosed in ''). If a label
+       matches more than one node, all matching nodes are used.
+       Default: no CSS map, whole tree is black (unless specified otherwise
+       via option -d).
+       <CSS>, <flag>, and <labels>+ are separated by whitespace.
+       The following specifies red stroke for a clade defined by A, B and C;
+       and 2-pixel wide, blue stroke for individual nodes D, E, and F:
+       stroke:red           Clade   A B C
+       stroke:blue;stroke-width:2   I   D E F
+       If no colormap is specified, the default is (but see option -d):
+       stroke:black;fill:none;stroke-width:1;stroke-linecap:round
+    -d <string>: CSS for 'plain' tree nodes (i.e., unless overridden by -c)
+       [only SVG]
+       Default: stroke:black;fill:none;stroke-width:1;stroke-linecap:round
+
+    -h: prints this message and exits
+
+    -i <string>: CSS for inner node labels. [only SVG]
+       Default: 'font-size:small;font-family:sans'.
+
+       setting 'visibility:hidden' disables printing of inner node labels.
+    -I <char> sets the position of the inner node label. Valid options are
+       'l' (near the leaves), 'm' (middle) or 'r' (near the root). Default
+       is 'l'.
+
+    -l <string>: CSS for leaf node labels. [only SVG]
+       Default: 'font-size:medium;font-family:sans'.
+       setting 'visibility:hidden' disables printing of leaf node labels.
+       Note: if you change this, you will probably need to adjust the
+       space allocated to leaf labels - see option -W.
+    -n <number> add this number of pixels to the horizontal position of
+       node labels. [SVG only]
+
+    -o <filename>: use specified file as ornament map. Works like the CSS
+       map (see option -c), except that it specifies arbitrary SVG snippets
+       instead of CSS styles. For example, the following
+       "<circle style='fill:red' r='5'>" Clade A B C
+       will draw a red circle of radius 5 at the root of the clade defined
+       by nodes A, B, and C. Keyword 'Individual' is also accepted and
+       works like for CSS.
+
+    -R <integer>: use that many pixels for the root [only SVG]
+
+    -r: draw a radial tree (default: orthogonal) [only SVG]
+
+    -s: output graph as SVG (default: ASCII graphics). All output is on
+       stdout, so if there is more than one tree, stdout will be a
+       concatenation of SVG documents. These can be split into individual
+       files with the csplit(1) command:
+
+       $ nw_display -s many_trees.nw > multiple_svg
+       $ csplit -zs -f tree\_ -b '%02d.svg' multiple_svg '/<?xml/' {*}
+
+       will generate as many SVG files as there are Newick trees in
+       many_trees.nw. The files will be named tree_01.svg, tree_02.svg, etc.
+
+    -S: suppress scale bar (ignored for cladograms)
+
+    -t: set the zero of the scale at the maximum depth instead of the root.
+       This is useful when the branch lengths are in time units: zero marks
+       the present, and the scale shows the age of the ancestral nodes.
+    -u <string>: string is used as unit name for scale bar (ignored
+       if no scale bar is drawn).
+    -U <URL_filename>: use specified URL map [only SVG]. A URL map
+       is a text file which specifies a URL for a label.
+       Each line has the following structure:
+       <label> <URL>
+       Clicking on a label will follow the link (if any).
+    -v <number>: number of pixels between leaves (default: 40) [only SVG
+       orthogonal]
+    -w <number>: graph should be no wider than <number>, measured in
+       characters for text and pixels for SVG. Defaults: 80 (text),
+       300 (SVG)
+    -W <number>: use this as an estimate of the width of a leaf label
+       character (in pixels) [only SVG]. This affects the space left for
+       the tree nodes. Default: 5.0 You will probably need this if you
+       change the leaf label font properties (option -l), especially size.
+       You will probably need trial and error to find the right value.
+
+LibXML
+......
+
+If LibXML is being used, the handling of ornaments (-o) is more elaborate.
+See the tutorial, section 2.2 (displaying) for details.
+This executable uses LibXML2.
+
+Examples
+--------
+
+# display tree as ASCII::
+
+$ nw_display data/catarrhini
+
+# display tree as SVG, using a color map::
+
+$ nw_display -s -c data/color.map data/catarrhini
+
+# ditto, convert to other graphics formats::
+
+$ nw_display -s -c data/color.map data/catarrhini > catarrhini.svg
+$ convert catarrhini.svg catarrhini.png # PNG, with ImageMagick
+$ convert catarrhini.svg catarrhini.jpeg    # JPEG, with ImageMagick
+$ inkscape -z -f catarrhini.svg -A catarrhini.pdf # PDF, with Inkscape
+
+# the same; no branch lengths::
+
+$ nw_display -s -b 'visibility:hidden' -c data/color.map data/catarrhini
+
+# radial tree, leaf labels in italics::
+
+$ nw_display -s -r -l 'font-style:italics' data/catarrhini
+
+]]>
+</help>
+ <citations>
+        <citation type="doi">10.1186/1748-7188-3-7</citation> 
+ </citations>
+</tool>
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