Mercurial > repos > iuc > newick_utils

annotate newick_display.xml @ 0:0db45bc4844f draft

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planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
author iuc
date Mon, 01 Oct 2018 09:45:49 -0400
parents
children 9298c1dbf31e
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0
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
iuc
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1 <tool id="newick_display" name="Newick Display" version="1.6">
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
iuc
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2 <description>visualize a phylogenetic tree</description>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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3 <edam_operations>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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4 <edam_operation>operation_0567</edam_operation>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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5 </edam_operations>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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6 <requirements>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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7 <requirement type="package" version="1.6">newick_utils</requirement>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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8 </requirements>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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9 <command detect_errors="aggressive"><![CDATA[
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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10 nw_display
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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11 #if $outformat != 'txt':
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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12 -s
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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13 #end if
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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14 $scalebar
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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15 -u '$legend'
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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16 -I 'r'
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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17 -i
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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18 #if $condbranchsupport.branchsupport == "true":
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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19 'fill:$condbranchsupport.supcolor;
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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20 font-size:$condbranchsupport.supfontsize;
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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21 transform:$condbranchsupport.suptransform;'
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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22 #else:
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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23 "visibility:hidden;"
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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24 #end if
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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25 -b
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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26 #if $condbranchlength.branchlength == "true":
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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27 'fill:$condbranchlength.lencolor;
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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28 font-size:$condbranchlength.lenfontsize;
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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29 transform:$condbranchlength.lentransform;'
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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30 #else:
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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31 "visibility:hidden;"
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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32 #end if
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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33
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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34 -l 'font-family:$leafFont;font-size:$leafSize;'
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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35 -d "stroke:grey;fill:none;stroke-width:2;stoke-linecap:round;"
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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36 -w $width
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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37 $radial
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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38
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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39 '$fileNewick' > output.svg
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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40
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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41 #if $outformat == 'png':
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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42 && convert output.svg output.png
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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43 && mv output.png '$output'
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
iuc
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44 #else:
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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45 && mv output.svg '$output'
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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46 #end if
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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47
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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48 ]]></command>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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49 <inputs>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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50 <param name="fileNewick" format="txt,newick,nw,nwk,nhx,mothur.tre" type="data" label="Newick file"/>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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51 <param name="scalebar" type="boolean" truevalue="" falsevalue="-S" checked="True" label="Display scale bar" />
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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52 <param name="legend" type="text" value="" label="Unit name for the scale bar" />
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
iuc
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53 <param name="leafFont" type="text" value="sans-serif" label="Leaf font" />
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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54 <param name="leafSize" type="text" value="10px" label="Leaf font-size" />
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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55 <conditional name="condbranchsupport">
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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56 <param name="branchsupport" type="select" label="Branch support">
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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57 <option value="true">Display branch support</option>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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58 <option value="false" selected="true">Hide branch support</option>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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59 </param>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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60 <when value="true">
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61 <param name="supcolor" type="color" value="red" label="color" />
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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62 <param name="supfontsize" type="text" value="10px" label="font-size" />
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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63 <param name="suptransform" type="text" value="translateY(1.5em)" label="move" />
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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64 </when>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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65 <when value="false" />
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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66 </conditional>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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67 <conditional name="condbranchlength">
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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68 <param name="branchlength" type="select" label="Branch length">
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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69 <option value="true">Display branch length</option>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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70 <option value="false" selected="true">Hide branch length</option>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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71 </param>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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72 <when value="true">
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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73 <param name="lencolor" type="color" value="blue" label="color" />
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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74 <param name="lenfontsize" type="text" value="10px" label="font-size" />
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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75 <param name="lentransform" type="text" value="translate(-1.5em,0em)" label="move" />
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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76 </when>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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77 <when value="false" />
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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78 </conditional>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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79 <param name="width" type="integer" value="800" label="Image width" help="in pixels for image output or in characters for text output" />
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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80 <param name="radial" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Draw a radial tree" />
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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81 <param name="outformat" type="select" label="Choose an output format">
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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82 <option value="svg" selected="true">SVG</option>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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83 <option value="png">PNG</option>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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84 <option value="txt">Text</option>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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85 </param>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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86 </inputs>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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87 <outputs>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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88 <data name="output" format="svg" label="${tool.name} on ${on_string}: Tree Graph" >
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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89 <change_format>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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90 <when input="outformat" value="png" format="png"/>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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91 <when input="outformat" value="txt" format="txt"/>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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92 </change_format>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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93 </data>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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94 </outputs>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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95 <tests>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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96 <test>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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97 <param name="fileNewick" value="tree.nwk"/>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
iuc
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98 <param name="width" value="400"/>
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99 <param name="leafFont" value="courier"/>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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100 <output name="output" file="tree.svg" ftype="svg" lines_diff="2"/>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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101 </test>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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102 <test><!-- test radial tree -->
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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103 <param name="fileNewick" value="tree.nwk"/>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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104 <param name="radial" value="-r"/>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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105 <param name="branchlength" value="true"/>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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106 <output name="output" file="tree2.svg" ftype="svg" lines_diff="2"/>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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107 </test>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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108 <test><!-- test with png output format -->
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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109 <param name="fileNewick" value="tree.nwk"/>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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110 <param name="radial" value="-r"/>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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111 <param name="branchlength" value="true"/>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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112 <param name="outformat" value="png"/>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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113 <output name="output" file="tree.png" ftype="png" compare="sim_size" delta="15000"/>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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114 </test>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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115 <test><!-- test with txt output format -->
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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116 <param name="fileNewick" value="tree.nwk"/>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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117 <param name="outformat" value="txt"/>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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118 <output name="output" file="tree.txt" ftype="txt"/>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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119 </test>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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120 </tests>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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121 <help><![CDATA[
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122 **What it does**
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123
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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124 This tool outputs a graph representing the tree, either as text or
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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125 as a SVG or PNG image. Underscores in labels are replaced with spaces.
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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126 Trees with no branch lengths are taken to be cladograms and are
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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127 drawn with leaves aligned. Otherwise, the tree is assumed to be a
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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128 phylogram: branch lengths are honored and a scale bar is drawn.
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129
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130 .. image:: $PATH_TO_IMAGES/example.png
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131 :alt: example newick tree graph
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132
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133 ]]></help>
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134 <citations>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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135 <citation type="doi">10.1186/1748-7188-3-7</citation>
0db45bc4844f planemo upload for repository https://github.com/tjunier/newick_utils commit e21a4f5dd923d549651f1a15c755e2de89cbd46d
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136 </citations>
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137 </tool>