Mercurial > repos > iuc > newick_utils

annotate newick_display.xml @ 2:f8e09a3bb21d draft default tip

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"planemo upload for repository https://github.com/tjunier/newick_utils commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 07:47:54 +0000
parents 9298c1dbf31e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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9298c1dbf31e "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>
2
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3 <xrefs>
f8e09a3bb21d "planemo upload for repository https://github.com/tjunier/newick_utils commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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4 <xref type="bio.tools">newick_utilities</xref>
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5 </xrefs>
0
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6 <edam_operations>
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7 <edam_operation>operation_0567</edam_operation>
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8 </edam_operations>
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9 <requirements>
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10 <requirement type="package" version="1.6">newick_utils</requirement>
1
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11 <requirement type="package" version="7.0.9_6">imagemagick</requirement>
0
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12 </requirements>
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13 <command detect_errors="aggressive"><![CDATA[
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14 nw_display
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15 #if $outformat != 'txt':
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16 -s
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17 #end if
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18 $scalebar
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19 -u '$legend'
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20 -I 'r'
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21 -i
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22 #if $condbranchsupport.branchsupport == "true":
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23 'fill:$condbranchsupport.supcolor;
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24 font-size:$condbranchsupport.supfontsize;
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25 transform:$condbranchsupport.suptransform;'
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26 #else:
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27 "visibility:hidden;"
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28 #end if
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29 -b
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30 #if $condbranchlength.branchlength == "true":
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31 'fill:$condbranchlength.lencolor;
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32 font-size:$condbranchlength.lenfontsize;
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33 transform:$condbranchlength.lentransform;'
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34 #else:
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35 "visibility:hidden;"
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36 #end if
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37
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38 -l 'font-family:$leafFont;font-size:$leafSize;'
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39 -d "stroke:grey;fill:none;stroke-width:2;stoke-linecap:round;"
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40 -w $width
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41 $radial
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42
1
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43 '$fileNewick'
0
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44
1
9298c1dbf31e "planemo upload for repository https://github.com/tjunier/newick_utils commit 352b2b1efa8400e145f02adb34e36c4af4524e54"
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45 #if $outformat == 'png':
9298c1dbf31e "planemo upload for repository https://github.com/tjunier/newick_utils commit 352b2b1efa8400e145f02adb34e36c4af4524e54"
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46 | convert - 'png:$output'
9298c1dbf31e "planemo upload for repository https://github.com/tjunier/newick_utils commit 352b2b1efa8400e145f02adb34e36c4af4524e54"
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47 #else:
9298c1dbf31e "planemo upload for repository https://github.com/tjunier/newick_utils commit 352b2b1efa8400e145f02adb34e36c4af4524e54"
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48 > '$output'
9298c1dbf31e "planemo upload for repository https://github.com/tjunier/newick_utils commit 352b2b1efa8400e145f02adb34e36c4af4524e54"
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49 #end if
0
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50 ]]></command>
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51 <inputs>
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52 <param name="fileNewick" format="txt,newick,nw,nwk,nhx,mothur.tre" type="data" label="Newick file"/>
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53 <param name="scalebar" type="boolean" truevalue="" falsevalue="-S" checked="True" label="Display scale bar" />
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54 <param name="legend" type="text" value="" label="Unit name for the scale bar" />
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55 <param name="leafFont" type="text" value="sans-serif" label="Leaf font" />
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56 <param name="leafSize" type="text" value="10px" label="Leaf font-size" />
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57 <conditional name="condbranchsupport">
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58 <param name="branchsupport" type="select" label="Branch support">
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59 <option value="true">Display branch support</option>
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60 <option value="false" selected="true">Hide branch support</option>
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61 </param>
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62 <when value="true">
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63 <param name="supcolor" type="color" value="red" label="color" />
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64 <param name="supfontsize" type="text" value="10px" label="font-size" />
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65 <param name="suptransform" type="text" value="translateY(1.5em)" label="move" />
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66 </when>
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67 <when value="false" />
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68 </conditional>
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69 <conditional name="condbranchlength">
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70 <param name="branchlength" type="select" label="Branch length">
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71 <option value="true">Display branch length</option>
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72 <option value="false" selected="true">Hide branch length</option>
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73 </param>
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74 <when value="true">
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75 <param name="lencolor" type="color" value="blue" label="color" />
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76 <param name="lenfontsize" type="text" value="10px" label="font-size" />
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77 <param name="lentransform" type="text" value="translate(-1.5em,0em)" label="move" />
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78 </when>
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79 <when value="false" />
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80 </conditional>
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81 <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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82 <param name="radial" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Draw a radial tree" />
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83 <param name="outformat" type="select" label="Choose an output format">
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84 <option value="svg" selected="true">SVG</option>
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85 <option value="png">PNG</option>
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86 <option value="txt">Text</option>
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87 </param>
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88 </inputs>
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89 <outputs>
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90 <data name="output" format="svg" label="${tool.name} on ${on_string}: Tree Graph" >
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91 <change_format>
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92 <when input="outformat" value="png" format="png"/>
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93 <when input="outformat" value="txt" format="txt"/>
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94 </change_format>
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95 </data>
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96 </outputs>
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97 <tests>
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98 <test>
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99 <param name="fileNewick" value="tree.nwk"/>
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100 <param name="width" value="400"/>
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101 <param name="leafFont" value="courier"/>
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102 <output name="output" file="tree.svg" ftype="svg" lines_diff="2"/>
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103 </test>
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104 <test><!-- test radial tree -->
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105 <param name="fileNewick" value="tree.nwk"/>
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106 <param name="radial" value="-r"/>
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107 <param name="branchlength" value="true"/>
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108 <output name="output" file="tree2.svg" ftype="svg" lines_diff="2"/>
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109 </test>
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110 <test><!-- test with png output format -->
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111 <param name="fileNewick" value="tree.nwk"/>
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112 <param name="radial" value="-r"/>
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113 <param name="branchlength" value="true"/>
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114 <param name="outformat" value="png"/>
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115 <output name="output" file="tree.png" ftype="png" compare="sim_size" delta="15000"/>
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116 </test>
1
9298c1dbf31e "planemo upload for repository https://github.com/tjunier/newick_utils commit 352b2b1efa8400e145f02adb34e36c4af4524e54"
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117 <test><!-- test with txt output format -->
0
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118 <param name="fileNewick" value="tree.nwk"/>
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119 <param name="outformat" value="txt"/>
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120 <output name="output" file="tree.txt" ftype="txt"/>
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121 </test>
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122 </tests>
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123 <help><![CDATA[
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124 **What it does**
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125
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126 This tool outputs a graph representing the tree, either as text or
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127 as a SVG or PNG image. Underscores in labels are replaced with spaces.
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128 Trees with no branch lengths are taken to be cladograms and are
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129 drawn with leaves aligned. Otherwise, the tree is assumed to be a
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130 phylogram: branch lengths are honored and a scale bar is drawn.
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131
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132 .. image:: $PATH_TO_IMAGES/example.png
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133 :alt: example newick tree graph
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134
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135 ]]></help>
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136 <citations>
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137 <citation type="doi">10.1186/1748-7188-3-7</citation>
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138 </citations>
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139 </tool>