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"planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/neper commit f244346f2a64254d571245db7a768fed41f6d660"
author ximgchess
date Sat, 13 Nov 2021 14:27:58 +0000
parents 82edf8dea5db
children
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82edf8dea5db "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/neper commit fd705c5d17e50a45fb6833d269aa23387391687a"
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1 <macros>
82edf8dea5db "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/neper commit fd705c5d17e50a45fb6833d269aa23387391687a"
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2 <token name="@TOOL_VERSION@">4.1.2</token>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="@TOOL_VERSION@">neper</requirement>
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6 <requirement type="package" version="4.8.4">gmsh</requirement>
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7 <requirement type="package" version="3.7.0.8">povray</requirement>
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8 <yield/>
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9 </requirements>
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10 </xml>
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11 <xml name="citations">
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12 <citations>
82edf8dea5db "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/neper commit fd705c5d17e50a45fb6833d269aa23387391687a"
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13 <citation type="doi">10.1016/j.cma.2011.01.002</citation>
82edf8dea5db "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/neper commit fd705c5d17e50a45fb6833d269aa23387391687a"
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14 <citation type="doi">10.1016/j.cma.2017.10.029</citation>
82edf8dea5db "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/neper commit fd705c5d17e50a45fb6833d269aa23387391687a"
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15 <citation type="doi">10.1107/S1600576718009019</citation>
82edf8dea5db "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/neper commit fd705c5d17e50a45fb6833d269aa23387391687a"
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16 <yield />
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17 </citations>
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18 </xml>
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19 <xml name="version_command">
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20 <version_command>neper --version</version_command>
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21 </xml>
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22
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23 <xml name="optional_yn" token_arg="-x" token_label="Show" token_help="">
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24 <param argument="@ARG@" type="select" optional="true" label="@LABEL@" help="@HELP@">
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25 <option value="0">No</option>
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26 <option value="1">Yes</option>
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27 </param>
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28 </xml>
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29
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30 <xml name="coords2d" token_label="Set" token_x="1.0" token_y="1.0">
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31 <param name="x" type="float" value="@X@" label="@LABEL@ x"/>
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32 <param name="y" type="float" value="@Y@" label="@LABEL@ y"/>
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33 </xml>
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34 <xml name="coords3d" token_label="Set" token_x="1.0" token_y="1.0" token_z="1.0">
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35 <param name="x" type="float" value="@X@" label="@LABEL@ x"/>
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36 <param name="y" type="float" value="@Y@" label="@LABEL@ y"/>
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37 <param name="z" type="float" value="@Z@" label="@LABEL@ z"/>
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38 </xml>
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39
82edf8dea5db "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/neper commit fd705c5d17e50a45fb6833d269aa23387391687a"
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40 <xml name="size2d" token_label="Set" token_xl="x" token_yl="y" token_x="1" token_y="1">
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41 <param name="x" type="integer" value="@X@" min="0" label="@LABEL@ @XL@"/>
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42 <param name="y" type="integer" value="@Y@" min="0" label="@LABEL@ @YL@"/>
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43 </xml>
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44 <xml name="size3d" token_label="Set" token_xl="x" token_yl="y" token_zl="z" token_x="1" token_y="1" token_z="1">
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45 <param name="x" type="integer" value="@X@" min="0" label="@LABEL@ @XL@"/>
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46 <param name="y" type="integer" value="@Y@" min="0" label="@LABEL@ @YL@"/>
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47 <param name="z" type="integer" value="@Z@" min="0" label="@LABEL@ @ZL@"/>
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48 </xml>
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49
82edf8dea5db "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/neper commit fd705c5d17e50a45fb6833d269aa23387391687a"
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50 <xml name="tx2d" token_label="Set" token_xl="x" token_yl="y" token_x="1" token_y="1">
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51 <param name="x" type="float" value="@X@" label="@LABEL@ @XL@"/>
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52 <param name="y" type="float" value="@Y@" label="@LABEL@ @YL@"/>
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53 <yield/>
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54 </xml>
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55 <xml name="tx3d" token_label="Set" token_xl="x" token_yl="y" token_zl="z" token_x="1" token_y="1" token_z="1">
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56 <expand macro="tx2d" label="@LABEL@" xl="@XL@" yl="@YL@" x="@X@" y="@Y@">
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57 <param name="z" type="float" value="@Z@" label="@LABEL@ @ZL@"/>
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58 </expand>
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59 </xml>
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60 <xml name="tx4d" token_label="Set" token_xl="x" token_yl="y" token_zl="z" token_al="a" token_x="1" token_y="1" token_z="1" token_a="1">
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61 <expand macro="tx3d" label="@LABEL@" xl="@XL@" yl="@YL@" zl="@ZL@" x="@X@" y="@Y@" z="@Z@">
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62 <param name="a" type="float" value="@A@" label="@LABEL@ @AL@"/>
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63 </expand>
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64 </xml>
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65 <xml name="set_ny" token_name="scale" token_label="Scale">
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66 <conditional name="@NAME@">
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67 <param name="set_@NAME@" type="select" label="@LABEL@">
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68 <option value="no">No</option>
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69 <option value="yes">Yes</option>
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70 </param>
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71 <when value="no"/>
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72 <when value="yes">
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73 <yield/>
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74 </when>
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75 </conditional>
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76 </xml>
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77 <xml name="set_nv" token_name="option" token_label="Option">
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78 <conditional name="@NAME@">
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79 <param name="set_@NAME@" type="select" label="@LABEL@">
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80 <option value="no">No</option>
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81 <option value="by_value">by value </option>
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82 </param>
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83 <when value="no"/>
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84 <when value="by_value">
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85 <yield/>
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86 </when>
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87 </conditional>
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88 </xml>
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89 <xml name="set_nve" token_name="option" token_label="Option">
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90 <conditional name="@NAME@">
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91 <param name="set_@NAME@" type="select" label="@LABEL@">
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92 <option value="no">No</option>
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93 <option value="by_value">by value </option>
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94 <option value="by_expr">by expression</option>
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95 </param>
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96 <when value="no"/>
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97 <when value="by_value">
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98 <yield/>
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99 </when>
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100 <when value="by_expr">
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101 <yield/>
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102 </when>
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103 </conditional>
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104 </xml>
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105
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106 <xml name="transform">
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107 <section name="transform" expanded="false" title="Set Transforms">
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108 <expand macro="set_ny" name="scale" label="Set scale">
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109 <expand macro="tx3d" label="scale" lx="x factor" ly="y factor" lz="z factor"/>
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110 </expand>
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111 <expand macro="set_ny" name="rotate" label="Set rotate">
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112 <expand macro="tx4d" label="rotate" lx="x axis" ly="y axis" lz="z axis" la="angle"/>
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113 </expand>
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114 <expand macro="set_ny" name="translate" label="Set translate">
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115 <expand macro="tx3d" label="translate" lx="x distance" ly="y distance" lz="z distance"/>
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116 </expand>
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117 </section>
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118 </xml>
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119 <token name="@TRANSFORM@">
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120 #set $transforms = []
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121 #if $transform.scale.set_scale == 'yes'
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122 #silent $transforms.append('scale(' + str($transform.scale.x) + ',' + str($transform.scale.y) + ',' + str($transform.scale.z) + ')')
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123 #end if
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124 #if $transform.rotate.set_rotate == 'yes'
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125 #silent $transforms.append('rotate(' + str($transform.rotate.x) + ',' + str($transform.rotate.y) + ',' + str($transform.rotate.z) + ',' + str($transform.rotate.a) + ')')
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126 #end if
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127 #if $transform.translate.set_translate == 'yes'
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128 #silent $transforms.append('translate(' + str($transform.translate.x) + ',' + str($transform.translate.y) + ',' + str($transform.translate.z) + ')')
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129 #end if
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130 #if $transforms
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131 #set $txargs = ','.join($transforms)
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132 -transform "$txargs"
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133 #end if
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134 </token>
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135
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136 <token name="@NEPER_HELP@">
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137 Neper_ is a software package for polycrystal generation and meshing. The polycrystals can be 2D or 3D.
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138 See the neper user manual for a complete description: https://neper.info/docs/neper.pdf
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139
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140 *Only a small number of the neper options are currently implemented in this galaxy tool.
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141 If there is an option you need, please create an issue at:* https://github.com/ximg-chess/galaxytools/issues
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142
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143
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144 .. _Neper: https://github.com/rquey/neper
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145
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146 </token>
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147 </macros>