# HG changeset patch # User dcorreia # Date 1486390154 18000 # Node ID 715bbf2bbef54312c226632b1ef55ba66c9aee93 # Parent ceba45fbfcb86a0a9c76a19353942d54029507bb planemo upload commit e0ca504b3313992020acf8ab7aed0a261237766e-dirty diff -r ceba45fbfcb8 -r 715bbf2bbef5 newick_utilities/nwdisplay.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/newick_utilities/nwdisplay.xml Mon Feb 06 09:09:14 2017 -0500 @@ -0,0 +1,258 @@ + + Display a phylogenetic tree as SVG + + operation_0567 + + + newick_utilities + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +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 : rotate all labels by this amount (radians, default: 0) + [only SVG radial] + -A : rotate left-side labels by this amount (radians, + default: 0.0349 (=~ 2°)) [only SVG radial] + -b : CSS for branch length labels. [only SVG] + Default: 'font-size:small;font-family:sans'. + setting 'opacity:0' disables printing of branch lengths. + -c : 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: + + + is a valid CSS style specification (no spaces allowed) + e.g. 'font-size:small;font-family:italics;stroke:green'. + 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. + + 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). + , , and + 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 : 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 : CSS for inner node labels. [only SVG] + Default: 'font-size:small;font-family:sans'. + + setting 'visibility:hidden' disables printing of inner node labels. + -I 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 : 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 add this number of pixels to the horizontal position of + node labels. [SVG only] + + -o : 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 + "" 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 : 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 '/: string is used as unit name for scale bar (ignored + if no scale bar is drawn). + -U : 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: + + Clicking on a label will follow the link (if any). + -v : number of pixels between leaves (default: 40) [only SVG + orthogonal] + -w : graph should be no wider than , measured in + characters for text and pixels for SVG. Defaults: 80 (text), + 300 (SVG) + -W : 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 + +]]> + + + 10.1186/1748-7188-3-7 + + \ No newline at end of file diff -r ceba45fbfcb8 -r 715bbf2bbef5 newick_utilities/test-data/tree.nwk --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/newick_utilities/test-data/tree.nwk Mon Feb 06 09:09:14 2017 -0500 @@ -0,0 +1,1 @@ +((raccoon:19.19959,bear:6.80041):0.84600,((sea_lion:11.99700, seal:12.00300):7.52973,((monkey:100.85930,cat:47.14069):20.59201, weasel:18.87953):2.09460):3.87382,dog:25.46154); \ No newline at end of file diff -r ceba45fbfcb8 -r 715bbf2bbef5 newick_utilities/test-data/tree.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/newick_utilities/test-data/tree.svg Mon Feb 06 09:09:14 2017 -0500 @@ -0,0 +1,8 @@ + diff -r ceba45fbfcb8 -r 715bbf2bbef5 newick_utilities/test-data/tree2.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/newick_utilities/test-data/tree2.svg Mon Feb 06 09:09:14 2017 -0500 @@ -0,0 +1,8 @@ + diff -r ceba45fbfcb8 -r 715bbf2bbef5 newick_utilities/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/newick_utilities/tool_dependencies.xml Mon Feb 06 09:09:14 2017 -0500 @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff -r ceba45fbfcb8 -r 715bbf2bbef5 nwdisplay.xml --- a/nwdisplay.xml Tue Mar 15 10:52:31 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,255 +0,0 @@ - - Display a phylogenetic tree as SVG - - newick_utilities - - - 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -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 : rotate all labels by this amount (radians, default: 0) - [only SVG radial] - -A : rotate left-side labels by this amount (radians, - default: 0.0349 (=~ 2°)) [only SVG radial] - -b : CSS for branch length labels. [only SVG] - Default: 'font-size:small;font-family:sans'. - setting 'opacity:0' disables printing of branch lengths. - -c : 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: - + - is a valid CSS style specification (no spaces allowed) - e.g. 'font-size:small;font-family:italics;stroke:green'. - 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. - + 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). - , , and + 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 : 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 : CSS for inner node labels. [only SVG] - Default: 'font-size:small;font-family:sans'. - - setting 'visibility:hidden' disables printing of inner node labels. - -I 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 : 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 add this number of pixels to the horizontal position of - node labels. [SVG only] - - -o : 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 - "" 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 : 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 '/: string is used as unit name for scale bar (ignored - if no scale bar is drawn). - -U : 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: - - Clicking on a label will follow the link (if any). - -v : number of pixels between leaves (default: 40) [only SVG - orthogonal] - -w : graph should be no wider than , measured in - characters for text and pixels for SVG. Defaults: 80 (text), - 300 (SVG) - -W : 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 - -]]> - - - 10.1186/1748-7188-3-7 - - \ No newline at end of file diff -r ceba45fbfcb8 -r 715bbf2bbef5 test-data/tree.nwk --- a/test-data/tree.nwk Tue Mar 15 10:52:31 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -((raccoon:19.19959,bear:6.80041):0.84600,((sea_lion:11.99700, seal:12.00300):7.52973,((monkey:100.85930,cat:47.14069):20.59201, weasel:18.87953):2.09460):3.87382,dog:25.46154); \ No newline at end of file diff -r ceba45fbfcb8 -r 715bbf2bbef5 test-data/tree.svg --- a/test-data/tree.svg Tue Mar 15 10:52:31 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ - diff -r ceba45fbfcb8 -r 715bbf2bbef5 test-data/tree2.svg --- a/test-data/tree2.svg Tue Mar 15 10:52:31 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ - diff -r ceba45fbfcb8 -r 715bbf2bbef5 tool_dependencies.xml --- a/tool_dependencies.xml Tue Mar 15 10:52:31 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ - - - - - - \ No newline at end of file