Mercurial > repos > ximgchess > neper

annotate neper_tessellation.xml @ 0:03bbcfd3d708 draft default tip

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"planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
author ximgchess
date Thu, 07 Jul 2022 12:31:10 +0000
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03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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1 <tool id="neper_tessellation" name="Neper Tessellation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="3.5">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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2 <description>generates polycrystals as tessellations</description>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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3 <macros>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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4 <import>macros.xml</import>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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5 <token name="@VERSION_SUFFIX@">0</token>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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6
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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7 <xml name="cells">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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8 <conditional name="cells">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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9 <param name="format" argument="-n" type="select" label="Specify cells by">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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10 <option value="number">number</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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11 <option value="from_morpho">from_morpho</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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12 <option value="expression"></option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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13 </param>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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14 <when value="number">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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15 <param name="number_of_cells" argument="-n" type="integer" value="10" min="1" label="the number of cells of the tessellation"/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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16 </when>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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17 <when value="from_morpho">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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18 </when>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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19 <when value="expression">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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20 </when>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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21 </conditional>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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22 </xml>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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23 <token name="@CELLS@">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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24 #if $cells.format == 'number'
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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25 -n $cells.number_of_cells
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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26 #elif $cells.format == 'from_morpho'
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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27 -n from_morpho
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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28 #end if
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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29 </token>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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30
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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31 <xml name="tessellation">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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32 <conditional name="tessellation">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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33 <param name="dim" argument="-dim" type="select" label="Dimensions">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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34 <option value="3" selected="true">3D</option>
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35 <option value="2">2D</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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36 </param>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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37 <when value="3">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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38 <conditional name="domain">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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39 <param name="shape" argument="-domain" type="select" label="Domain">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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40 <option value="cube">cube</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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41 <option value="cylinder">cylinder</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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42 <option value="sphere">sphere</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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43 </param>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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44 <when value="cube">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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45 <param name="size_x" type="float" value="1.0" min="0.0" label="size x"/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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46 <param name="size_y" type="float" value="1.0" min="0.0" label="size y"/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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47 <param name="size_z" type="float" value="1.0" min="0.0" label="size z"/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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48 </when>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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49 <when value="cylinder">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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50 <param name="height" type="float" value="1.0" min="0.0" label="height"/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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51 <param name="diameter" type="float" value="1.0" min="0.0" label="diameter"/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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52 </when>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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53 <when value="sphere">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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54 <param name="diameter" type="float" value="1.0" min="0.0" label="diameter"/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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55 </when>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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56 </conditional>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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57 </when>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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58 <when value="2">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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59 <conditional name="domain">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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60 <param name="shape" argument="-domain" type="select" label="Domain">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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61 <option value="square">square</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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62 <option value="circle">circle</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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63 </param>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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64 <when value="square">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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65 <param name="size_x" type="float" value="1.0" min="0.0" label="size x"/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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66 <param name="size_y" type="float" value="1.0" min="0.0" label="size y"/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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67 </when>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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68 <when value="circle">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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69 <param name="diameter" type="float" value="1.0" min="0.0" label="diameter"/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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70 </when>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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71 </conditional>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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72 </when>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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73 </conditional>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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74 </xml>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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75 <token name="@TESSELLATION@">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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76 -dim $tessellation.dim
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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77 #if $tessellation.domain.shape == 'cube'
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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78 -domain "${tessellation.domain.shape}($tessellation.domain.size_x,$tessellation.domain.size_y,$tessellation.domain.size_z)"
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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79 #elif $tessellation.domain.shape == 'cylinder'
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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80 -domain "${tessellation.domain.shape}($tessellation.domain.height,$tessellation.domain.diameter)"
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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81 #elif $tessellation.domain.shape == 'sphere'
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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82 -domain "${tessellation.domain.shape}($tessellation.domain.diameter)"
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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diff changeset
83 #elif $tessellation.domain.shape == 'square'
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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diff changeset
84 -domain "${tessellation.domain.shape}($tessellation.domain.size_x,$tessellation.domain.size_y)"
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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diff changeset
85 #elif $tessellation.domain.shape == 'circle'
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
parents:
diff changeset
86 -domain "${tessellation.domain.shape}($tessellation.domain.diameter)"
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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diff changeset
87 #end if
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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diff changeset
88 </token>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
parents:
diff changeset
89
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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diff changeset
90 <xml name="morpho">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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diff changeset
91 <conditional name="morpho">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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diff changeset
92 <param name="morpho_type" argument="-morpho" type="select" label="Morphology">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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diff changeset
93 <option value="voronoi" selected="true">voronoi</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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diff changeset
94 <option value="tesr">tesr file</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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diff changeset
95 <option value="gg">graingrowth</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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96 </param>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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diff changeset
97 <when value="voronoi">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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98 </when>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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diff changeset
99 <when value="tesr">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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100 <param name="tesr_file" type="data" format="neper.tesr" label="tesr file" help="Use -n from_morpho"/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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101 <param name="pts_region" type="select" optional="true" label="control points region">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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102 <option value="surf">surface voxels</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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103 <option value="all">all voxels</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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104 </param>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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105 <param name="pts_res" type="float" value="" min="1.0" optional="true" label="control points resolution" help="average number of control points along a direction of a grain"/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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106 </when>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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107 <when value="gg">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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108 </when>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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109 </conditional>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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110 </xml>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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111 <token name="@MORPHO@">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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112 #if $morpho.morpho_type == 'tesr'
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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113 -morpho "tesr:file($morpho.tesr_file)"
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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114 #set $pts = []
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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115 #if $morpho.pts_region
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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116 #silent $pts.append('region=' + str($morpho.pts_region))
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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117 #end if
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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118 #if $morpho.pts_res
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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119 #silent $pts.append('res=' + str($morpho.pts_res))
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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120 #end if
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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121 #if $pts
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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122 #set $args = ','.join($pts)
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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123 -morphooptiobj "tesr:pts($args)"
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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124 #end if
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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125 #end if
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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126 </token>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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127
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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128 <xml name="morphooptistop">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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129 <section name="morphooptistop" expanded="false" title="Set Optimization Stop Criteria">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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130 <param argument="-eps" type="float" value="" optional="true" label="Absolute error on objective function"/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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131 <param argument="-reps" type="float" value="" optional="true" label="Relative error on objective function"/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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132 <param argument="-xeps" type="float" value="" optional="true" label="Absolute error on components of the solution vector"/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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133 <param argument="-xreps" type="float" value="" optional="true" label="Relative error on components of the solution vector"/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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134 <param argument="-itermax" type="integer" value="" min="1" optional="true" label="After n iterations"/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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135 <param argument="-loopmax" type="integer" value="" min="1" optional="true" label="After n iteration loops"/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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136 <param argument="-time" type="float" value="" optional="true" label="After n seconds"/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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137 </section>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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138 </xml>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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139 <token name="@MORPHOOPTISTOP@">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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140 #set $stops = []
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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141 #if $morphooptistop.eps
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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142 #silent $stops.append('eps=' + str($morphooptistop.eps))
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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143 #end if
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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diff changeset
144 #if $morphooptistop.reps
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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145 #silent $stops.append('reps=' + str($morphooptistop.reps))
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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diff changeset
146 #end if
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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diff changeset
147 #if $morphooptistop.xeps
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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148 #silent $stops.append('xeps=' + str($morphooptistop.xeps))
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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diff changeset
149 #end if
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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150 #if $morphooptistop.xreps
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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diff changeset
151 #silent $stops.append('xreps=' + str($morphooptistop.xreps))
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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diff changeset
152 #end if
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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diff changeset
153 #if $morphooptistop.itermax
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
parents:
diff changeset
154 #silent $stops.append('itermax=' + str($morphooptistop.itermax))
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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diff changeset
155 #end if
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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diff changeset
156 #if $morphooptistop.loopmax
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
parents:
diff changeset
157 #silent $stops.append('loopmax=' + str($morphooptistop.loopmax))
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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diff changeset
158 #end if
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
parents:
diff changeset
159 #if $morphooptistop.time
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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diff changeset
160 #silent $stops.append('time=' + str($morphooptistop.time))
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
parents:
diff changeset
161 #end if
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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162 #if $stops
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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163 #set $stopargs = ','.join($stops)
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
ximgchess
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164 -morphooptistop "$stopargs"
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165 #end if
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166 </token>
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167
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168 <xml name="regularization">
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169 <conditional name="regularization">
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170 <param name="regularize" argument="-regularization" type="select" label="Regularize tessellation">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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171 <option value="0">No</option>
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172 <option value="1">Yes</option>
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173 </param>
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174 <when value="0"/>
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175 <when value="1">
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176 <param name="fmax" argument="-fmax" type="float" value="20.0" min="0.0" max="180.0" label="face flatness fault (in degrees)"
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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177 help="The flatness fault is the maxi- mum angle between the normals at two locations on a face."/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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178 <param name="mloop" argument="-mloop" type="integer" value="2" min="1" label="maximum number of regularization loops"/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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179 </when>
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180 </conditional>
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181 </xml>
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182 <token name="@REGULARIZATION@">
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183 -reg $regularization.regularize
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184 #if $regularization.regularize == '1'
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185 -fmax $regularization.fmax
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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186 -mloop $regularization.mloop
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187 #end if
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188 </token>
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189
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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190 <xml name="output_options">
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191 <section name="output_options" expanded="false" title="Output_options">
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192 <param name="tesrformat" argument="-tesrformat" type="select" optional="true" label="TESR format">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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193 <option value="ascii">ASCII</option>
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194 <option value="binary8">8-bit binary / unsigned char-type</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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195 <option value="binary16">16-bit binary / short-type little endian</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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196 <option value="binary16_big">16-bit binary / short-type big endian</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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197 <option value="binary32">32-bit binary / int-type little endian</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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198 <option value="binary32_big">32-bit binary / int-type big endian</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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199 </param>
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200 <param name="tesrsize" argument="-tesrsize" type="text" value="" optional="true" label="TESR size">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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201 <help><![CDATA[
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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202 Specify the number of points of a raster tessellation along a direction of the domain. In case of a domain of different lengths along the different directions, the argument stands for the geometrical average of the number of points along the different directions, so that the raster points are as close to cubic as possible. To specify different values along the x, y and z directions, combine the values with ‘:’. Default value: 20
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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203 ]]></help>
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204 <validator type="regex" message="integer sizes">[1-9]\d(:[1-9]\d+){,2}</validator>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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205 </param>
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206 <!-- macro for oridescriptor -->
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207 </section>
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208 </xml>
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209 <token name="@OUTPUT_OPTIONS@">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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210 #if 'tesr' in $format
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211 #if $output_options.tesrformat:
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212 -tesrformat '$output_options.tesrformat'
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213 #end if
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214 #if $output_options.tesrsize:
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215 -tesrsize '$output_options.tesrsize'
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216 #end if
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217 #end if
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218 </token>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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219 </macros>
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220 <expand macro="requirements" />
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221 <expand macro="version_command" />
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222 <command detect_errors="exit_code"><![CDATA[
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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223 neper -T
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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224 @CELLS@
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225 @TESSELLATION@
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226 @MORPHO@
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227 @MORPHOOPTISTOP@
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228 @TRANSFORM@
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229 @REGULARIZATION@
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230 @OUTPUT_OPTIONS@
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231 -format "$format"
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232 -o output
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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233 | grep -v '%$' | tee 'neper.log'
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234 ]]></command>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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235 <inputs>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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236 <expand macro="cells"/>
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237 <expand macro="tessellation"/>
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238 <expand macro="morpho"/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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239 <expand macro="morphooptistop"/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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240 <expand macro="transform"/>
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241 <expand macro="regularization"/>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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242 <expand macro="output_options"/>
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243 <param name="format" argument="-format" type="select" multiple="true" optional="false" label="Output format">
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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244 <option value="tess" selected="true">Neper scalar tessellation file (.tess)</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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245 <option value="tesr">Neper raster tessellation file (.tesr)</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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246 <option value="vtk">VTK raster file (.vtk)</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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247 <option value="geo">Gmsh geometry file (.geo)</option>
03bbcfd3d708 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/neper commit 9f77ab5ee7831c00b3a27e02ec8e59d95e6fb9cf"
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248 <option value="ply">Polygon File Format file (.ply)</option>
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249 </param>
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250 </inputs>
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251 <outputs>
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252 <data name="log" format="txt" label="${tool.name} on ${on_string} log" from_work_dir="neper.log"/>
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253 <data name="output_tess" format="neper.tess" label="${tool.name} on ${on_string} tess" from_work_dir="output.tess">
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254 <filter>'tess' in format</filter>
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255 </data>
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256 <data name="output_tesr" format="neper.tesr" label="${tool.name} on ${on_string} tesr" from_work_dir="output.tesr">
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257 <filter>'tesr' in format</filter>
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258 </data>
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259 <data name="output_vtk" format="vtkbinary" label="${tool.name} on ${on_string} vtk" from_work_dir="output.vtk">
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260 <filter>'vtk' in format</filter>
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261 </data>
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262 <data name="output_ply" format="plyascii" label="${tool.name} on ${on_string} ply" from_work_dir="output.ply">
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263 <filter>'ply' in format</filter>
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264 </data>
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265 <data name="output_geo" format="gmsh.geo" label="${tool.name} on ${on_string} geo" from_work_dir="output.geo">
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266 <filter>'geo' in format</filter>
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267 </data>
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268 </outputs>
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269 <tests>
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270 <!-- Test-1 neper -T -n 4 -->
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271 <test>
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272 <conditional name="cells">
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273 <param name="format" value="number"/>
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274 <param name="number_of_cells" value="4"/>
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275 </conditional>
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276 <output name="output_tess">
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277 <assert_contents>
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278 <has_text text="***tess" />
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279 <has_text_matching expression="[*][*]cell\n 4\n [*]id\n 1 2 3 4\n"/>
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280 </assert_contents>
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281 </output>
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282 </test>
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283 <!-- Test neper -T -n from_morpho -domain "cube(0.5,0.5,0.5)" -morpho "tesr:file(example_tesr.tesr)" -morphooptiobj "tesr:pts(region=surf,res=7)" -morphooptistop itermax=30 -reg 1 -->
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284 </tests>
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285 <help><![CDATA[
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286 **Neper Tessellation**
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287
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288 @NEPER_HELP@
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289
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290 Neper Tessellation Module *-T* generates polycrystals as tessellations. The two main capabilities are:
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291
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292 (i) the generation of tessellations from cell properties (e.g. a size distribution)
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293 (ii) the genera- tion of multiscale tessellations (i.e. including cell subdivisions).
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294
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295 These capabilities can also be used together. Tessellations are Laguerre (or Voronoi) tessellations and are therefore composed of convex cells. Once generated, the tessellations can be “regularized” by removing their smallest features (edges and faces), which then enables good-quality meshing with module -M. Periodicity conditions can be prescribed. Crystal orientations are pro- vided for the cells.
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296
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297 The output is a tessellation file written at a scalar (vectorial) or raster format. Scalar tessellations are intended to be passed to modules -M and -V while raster tessellations can be used by FFT solvers.
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298
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299 ]]></help>
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300 <expand macro="citations" />
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301 </tool>