Mercurial > repos > iuc > graphlan

annotate graphlan.xml @ 0:8f62f666dcb6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
author iuc
date Sat, 04 Mar 2017 10:27:03 -0500
parents
children a490b70e46fc
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0
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
iuc
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1 <tool id="graphlan" name="GraPhlAn" version="@WRAPPER_VERSION@.0">
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
iuc
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2 <description>to produce graphical output of an input tree</description>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
iuc
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3 <macros>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
iuc
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4 <import>graphlan_macros.xml</import>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
iuc
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5 </macros>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
iuc
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6 <expand macro="requirements"/>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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7 <stdio>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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8 <regex match="Warning"
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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9 source="stderr"
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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10 level="warning"
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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11 description="" />
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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12 </stdio>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
iuc
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13 <version_command>graphlan.py -v</version_command>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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14 <command>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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15 <![CDATA[
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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16 graphlan.py
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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17 --format '$image_format.format'
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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18 --size '$size'
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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19 #if $pad
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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20 --pad '$pad'
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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21 #end if
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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22 #if str($image_format.format) == "png" and $image_format.dpi
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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23 --dpi '$image_format.dpi'
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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24 #end if
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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25 '$input_tree'
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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26 #if str($image_format.format) == "png"
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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27 '$png_output_image'
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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28 #else if str($image_format.format) == "pdf"
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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29 '$pdf_output_image'
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
iuc
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30 #else if str($image_format.format) == "ps"
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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31 '$ps_output_image'
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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32 #else if str($image_format.format) == "eps"
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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33 '$eps_output_image'
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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34 #else
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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35 '$svg_output_image'
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36 #end if
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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37 ]]>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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38 </command>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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39 <inputs>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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40 <param name="input_tree" type="data" format="txt,nhx,phyloxml" label="Input tree"/>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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41 <conditional name="image_format">
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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42 <param argument='--format' type="select" label="Output format">
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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43 <option value="png" selected="true">PNG</option>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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44 <option value="pdf">PDF</option>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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45 <option value="ps">PS</option>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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46 <option value="eps">EPS</option>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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47 <option value="svg">SVG</option>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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48 </param>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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49 <when value="png">
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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50 <param argument="--dpi" type="integer" label="Dpi of the output image" optional="True"/>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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51 </when>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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52 <when value="pdf"/>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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53 <when value="ps"/>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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54 <when value="eps"/>
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55 <when value="svg"/>
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56 </conditional>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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57 <param argument="--size" type="integer" value="7" label="Size of the output image"/>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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58 <param argument="--pad" type="integer" label="Distance between the most external graphical element and the border of the image" optional="True"/>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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59 </inputs>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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60 <outputs>
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61 <data format="png" name="png_output_image" label="${tool.name} on ${on_string}: PNG">
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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62 <filter>image_format['format']=="png"</filter>
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63 </data>
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64 <data format="pdf" name="pdf_output_image" label="${tool.name} on ${on_string}: PDF">
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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65 <filter>image_format['format']=="pdf"</filter>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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66 </data>
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67 <data format="ps" name="ps_output_image" label="${tool.name} on ${on_string}: PS">
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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68 <filter>image_format['format']=="ps"</filter>
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69 </data>
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70 <data format="eps" name="eps_output_image" label="${tool.name} on ${on_string}: EPS">
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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71 <filter>image_format['format']=="eps"</filter>
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72 </data>
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73 <data format="svg" name="svg_output_image" label="${tool.name} on ${on_string}: SVG">
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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74 <filter>image_format['format']=="svg"</filter>
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75 </data>
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76 </outputs>
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77 <tests>
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78 <test>
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79 <param name="input_tree" value="intermediary_tree"/>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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80 <param name="format" value="png"/>
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81 <param name="dpi" value="100"/>
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82 <param name="size" value="7"/>
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83 <param name="pad" value="2"/>
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84 <output name="png_output_image" file="png_image.png" />
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85 </test>
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86 </tests>
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87 <help><![CDATA[
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88 **What it does**
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89
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90 GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.
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91
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92 For more information, check the `user manual <https://bitbucket.org/nsegata/graphlan/overview>`_.
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93
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94 ]]></help>
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95 <expand macro="citations"/>
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96 </tool>