Mercurial > repos > iuc > newick_utils

annotate newick_display.xml @ 1:b4163d2f64ab draft default tip

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"planemo upload for repository https://github.com/tjunier/newick_utils commit 352b2b1efa8400e145f02adb34e36c4af4524e54"
author iuc
date Sun, 01 Dec 2019 17:33:02 -0500
parents fe4235285ee8
children
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1
b4163d2f64ab "planemo upload for repository https://github.com/tjunier/newick_utils commit 352b2b1efa8400e145f02adb34e36c4af4524e54"
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1 <tool id="newick_display" name="Newick Display" version="1.6+galaxy1">
0
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2 <description>visualize a phylogenetic tree</description>
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3 <edam_operations>
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4 <edam_operation>operation_0567</edam_operation>
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5 </edam_operations>
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6 <requirements>
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7 <requirement type="package" version="1.6">newick_utils</requirement>
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8 <requirement type="package" version="7.0.9_6">imagemagick</requirement>
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9 </requirements>
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10 <command detect_errors="aggressive"><![CDATA[
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11 nw_display
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12 #if $outformat != 'txt':
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13 -s
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14 #end if
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15 $scalebar
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16 -u '$legend'
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17 -I 'r'
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18 -i
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19 #if $condbranchsupport.branchsupport == "true":
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20 'fill:$condbranchsupport.supcolor;
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21 font-size:$condbranchsupport.supfontsize;
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22 transform:$condbranchsupport.suptransform;'
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23 #else:
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24 "visibility:hidden;"
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25 #end if
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26 -b
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27 #if $condbranchlength.branchlength == "true":
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28 'fill:$condbranchlength.lencolor;
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29 font-size:$condbranchlength.lenfontsize;
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30 transform:$condbranchlength.lentransform;'
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31 #else:
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32 "visibility:hidden;"
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33 #end if
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34
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35 -l 'font-family:$leafFont;font-size:$leafSize;'
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36 -d "stroke:grey;fill:none;stroke-width:2;stoke-linecap:round;"
fe4235285ee8 planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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37 -w $width
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38 $radial
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39
1
b4163d2f64ab "planemo upload for repository https://github.com/tjunier/newick_utils commit 352b2b1efa8400e145f02adb34e36c4af4524e54"
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40 '$fileNewick'
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41
1
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42 #if $outformat == 'png':
b4163d2f64ab "planemo upload for repository https://github.com/tjunier/newick_utils commit 352b2b1efa8400e145f02adb34e36c4af4524e54"
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43 | convert - 'png:$output'
b4163d2f64ab "planemo upload for repository https://github.com/tjunier/newick_utils commit 352b2b1efa8400e145f02adb34e36c4af4524e54"
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44 #else:
b4163d2f64ab "planemo upload for repository https://github.com/tjunier/newick_utils commit 352b2b1efa8400e145f02adb34e36c4af4524e54"
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45 > '$output'
b4163d2f64ab "planemo upload for repository https://github.com/tjunier/newick_utils commit 352b2b1efa8400e145f02adb34e36c4af4524e54"
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46 #end if
0
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47 ]]></command>
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48 <inputs>
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49 <param name="fileNewick" format="txt,newick,nw,nwk,nhx,mothur.tre" type="data" label="Newick file"/>
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50 <param name="scalebar" type="boolean" truevalue="" falsevalue="-S" checked="True" label="Display scale bar" />
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51 <param name="legend" type="text" value="" label="Unit name for the scale bar" />
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52 <param name="leafFont" type="text" value="sans-serif" label="Leaf font" />
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53 <param name="leafSize" type="text" value="10px" label="Leaf font-size" />
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54 <conditional name="condbranchsupport">
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55 <param name="branchsupport" type="select" label="Branch support">
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56 <option value="true">Display branch support</option>
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57 <option value="false" selected="true">Hide branch support</option>
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58 </param>
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59 <when value="true">
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60 <param name="supcolor" type="color" value="red" label="color" />
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61 <param name="supfontsize" type="text" value="10px" label="font-size" />
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62 <param name="suptransform" type="text" value="translateY(1.5em)" label="move" />
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63 </when>
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64 <when value="false" />
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65 </conditional>
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66 <conditional name="condbranchlength">
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67 <param name="branchlength" type="select" label="Branch length">
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68 <option value="true">Display branch length</option>
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69 <option value="false" selected="true">Hide branch length</option>
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70 </param>
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71 <when value="true">
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72 <param name="lencolor" type="color" value="blue" label="color" />
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73 <param name="lenfontsize" type="text" value="10px" label="font-size" />
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74 <param name="lentransform" type="text" value="translate(-1.5em,0em)" label="move" />
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75 </when>
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76 <when value="false" />
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77 </conditional>
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78 <param name="width" type="integer" value="800" label="Image width" help="in pixels for image output or in characters for text output" />
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79 <param name="radial" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Draw a radial tree" />
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80 <param name="outformat" type="select" label="Choose an output format">
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81 <option value="svg" selected="true">SVG</option>
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82 <option value="png">PNG</option>
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83 <option value="txt">Text</option>
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84 </param>
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85 </inputs>
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86 <outputs>
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87 <data name="output" format="svg" label="${tool.name} on ${on_string}: Tree Graph" >
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88 <change_format>
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89 <when input="outformat" value="png" format="png"/>
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90 <when input="outformat" value="txt" format="txt"/>
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91 </change_format>
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92 </data>
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93 </outputs>
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94 <tests>
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95 <test>
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96 <param name="fileNewick" value="tree.nwk"/>
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97 <param name="width" value="400"/>
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98 <param name="leafFont" value="courier"/>
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99 <output name="output" file="tree.svg" ftype="svg" lines_diff="2"/>
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100 </test>
fe4235285ee8 planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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101 <test><!-- test radial tree -->
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102 <param name="fileNewick" value="tree.nwk"/>
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103 <param name="radial" value="-r"/>
fe4235285ee8 planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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104 <param name="branchlength" value="true"/>
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105 <output name="output" file="tree2.svg" ftype="svg" lines_diff="2"/>
fe4235285ee8 planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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106 </test>
fe4235285ee8 planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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107 <test><!-- test with png output format -->
fe4235285ee8 planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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108 <param name="fileNewick" value="tree.nwk"/>
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109 <param name="radial" value="-r"/>
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110 <param name="branchlength" value="true"/>
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111 <param name="outformat" value="png"/>
fe4235285ee8 planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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112 <output name="output" file="tree.png" ftype="png" compare="sim_size" delta="15000"/>
fe4235285ee8 planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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113 </test>
1
b4163d2f64ab "planemo upload for repository https://github.com/tjunier/newick_utils commit 352b2b1efa8400e145f02adb34e36c4af4524e54"
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114 <test><!-- test with txt output format -->
0
fe4235285ee8 planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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115 <param name="fileNewick" value="tree.nwk"/>
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116 <param name="outformat" value="txt"/>
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117 <output name="output" file="tree.txt" ftype="txt"/>
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118 </test>
fe4235285ee8 planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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119 </tests>
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120 <help><![CDATA[
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121 **What it does**
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122
fe4235285ee8 planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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123 This tool outputs a graph representing the tree, either as text or
fe4235285ee8 planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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124 as a SVG or PNG image. Underscores in labels are replaced with spaces.
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125 Trees with no branch lengths are taken to be cladograms and are
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126 drawn with leaves aligned. Otherwise, the tree is assumed to be a
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127 phylogram: branch lengths are honored and a scale bar is drawn.
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128
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129 .. image:: $PATH_TO_IMAGES/example.png
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130 :alt: example newick tree graph
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131
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132 ]]></help>
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133 <citations>
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134 <citation type="doi">10.1186/1748-7188-3-7</citation>
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135 </citations>
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136 </tool>