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annotate macros.xml @ 2:f0db3e3b9d99 draft

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"planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 447defcd2ae30127f163e6a3adec52926f4a6c9c"
author ximgchess
date Mon, 07 Dec 2020 22:32:14 +0000
parents a0be4e3aa66d
children 54513f5fc836
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1 <macros>
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2 <token name="@TOOL_VERSION@">0.8.0</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@">hexrd</requirement>
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6 <yield/>
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7 </requirements>
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8 </xml>
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9 <xml name="citations">
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10 <citations>
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11 <citation type="doi">10.1016/j.matchar.2020.110366</citation>
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12 <yield />
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13 </citations>
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14 </xml>
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15
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16 <token name="@CMD_IMPORTS@">
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17 #import re
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18 #import yaml
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19
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20 #set global $img_panel_dict = dict()
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21 #if $detector.panel_assignment == 'panel_table'
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22 #set $fh = open(str($detector.image_panel_table),'r')
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23 #for $line in $fh:
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24 #set $fields = $line.strip().split('\t')
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25 #silent $img_panel_dict[$fields[0]] = $fields[1]
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26 #end for
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27 #end if
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28 #set global $panels = $yaml.safe_load(open(str($instrument),'r'))['detectors'].keys()
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29 #def identifier_or_name($input1)
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30 #if hasattr($input1, 'element_identifier')
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31 #return $input1.element_identifier
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32 #elif hasattr($input1, 'name')
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33 #return $input1.name
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34 #else
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35 #return str($input1)
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36 #end if
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37 #end def
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38 #def clean($name1)
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39 #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](npz|hexrd|yml|dat|out)$','', $name1.split()[-1]))
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40 #return $name_clean
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41 #end def
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42 #def ln_name($ds,$ext)
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43 #set $lname = "%s.%s" % ($clean($identifier_or_name($ds)),$ext)
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44 #return $lname
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45 #end def
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46 #def get_panel($img_input):
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47 #set $img_name = $identifier_or_name($img_input)
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48 #if $img_panel_dict and $img_name in $img_panel_dict:
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49 #return $img_panel_dict[$img_name]
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50 #end if
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51 #for $p in $panels:
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52 #if $p in $img_name:
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53 #return $p
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54 #end if
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55 #end for
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56 #return $img_name
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57 #end def
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58 </token>
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59
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60 <xml name="common_config" token_multiple_inputs="true" >
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61 <param name="inputs" type="data" format="hexrd.npz" multiple="true" label="Image series frame-cache"/>
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62 <conditional name="detector">
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63 <param name="panel_assignment" type="select" label="Assign detector panel to images">
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64 <option value="infer_from_name" selected="true">Infer the panel from the image name</option>
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65 <option value="panel_table">Input a table with image panels assignments</option>
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66 </param>
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67 <when value="infer_from_name"/>
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68 <when value="panel_table">
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69 <param name="image_panel_table" type="data" format="tabular" label="Image panel assignment table">
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70 <help>A 2-column table:image dataset name detector panel name</help>
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71 </param>
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72 </when>
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73 </conditional>
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74 <param name="instrument" type="data" format="hexrd.yml" label="instrument"/>
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75 <param name="material" type="data" format="material.hexrd" label="material"/>
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76 <param name="active_material" type="text" value="" label="active material name">
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77 <validator type="empty_field" />
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78 </param>
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79 </xml>
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80
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81 <token name="@CMD_LINKS@"><![CDATA[@CMD_IMPORTS@
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82 mkdir -p imageseries &&
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83 ln -s '$material' $ln_name($material,'hexrd') &&
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84 ln -s '$instrument' $ln_name($instrument,'yml') &&
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85 #for $input in $inputs
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86 ln -s '$input' imageseries/$ln_name($input,'npz') &&
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87 #end for
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88 ]]>
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89 </token>
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90 <token name="@FIT_GRAIN_LINKS@"><![CDATA[@CMD_LINKS@
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91 ln -s '$ome_map' $ln_name($ome_map,'npz') &&
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92 ln -s '$accepted_orientations' $ln_name($accepted_orientations,'dat') &&
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93 ##mkdir -p analysis &&
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94 ##cp '$grains_estimate' analysis/$ln_name($grains_estimate,'out') &&
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95 ]]>
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96 </token>
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97
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98 <token name="@CONVERT2TAB@"><![CDATA[for i in `find analysis -name '[gs]*.out'`; do sed -i.bak "s/[ ][ ][ ]*/\$(printf '\t')/g" \${i}; done]]></token>
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99
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100 <token name="@COMMON_YML@"><![CDATA[@CMD_IMPORTS@
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101 analysis_name: analysis
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102
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103 multiprocessing: -1
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104
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105 material:
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106 definitions: $ln_name($material,'hexrd')
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107 active: $active_material
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108
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109 instrument: $ln_name($instrument,'yml')
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110
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111 image_series:
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112 format: frame-cache
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113 data:
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114 #for $input in $inputs
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115 - file: imageseries/$ln_name($input,'npz')
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116 args: {}
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117 panel: $get_panel($input) # must match detector key
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118 #end for
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119
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120 ]]></token>
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121
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122 <xml name="find_orientations_config">
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123 <expand macro="common_config" token_multiple_inputs="true" />
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124 <section name="orientation_maps" title="Orientation Maps" expanded="true">
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125 <param name="threshold" type="integer" value="25" min="1" label="threshold"/>
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126 <param name="bin_frames" type="integer" value="1" label="bin frames"/>
2
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127 <!-- active_hkls should be able to be optional="true" -->
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128 <param name="active_hkls" type="text" value="" label="active hkl planes">
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129 <help>commas separated list of planes, e.g.: 0,1,2,3,4,5</help>
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130 <validator type="regex" message="plane indeces separated by commas">^\d(,\d)*$</validator>
0
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131 </param>
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132 </section>
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133 <param name="on_map_threshold" type="integer" value="1" min="1" label="on-map threshold used in the scoring"/>
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134 <section name="search_options" title="Search Options" expanded="true">
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135 <conditional name="search">
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136 <param name="search_type" type="select" label="Specify Search">
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137 <option value="seed_search" selected="true">use seed search</option>
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138 <option value="use_quaternion_grid">use quaternion grid</option>
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139 </param>
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140 <when value="seed_search">
2
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141 <!-- hkl_seeds should be able to be optional="true" -->
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142 <param name="hkl_seeds" type="text" value="" label="hkl seeds">
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143 <help>commas separated list of planes, e.g.: 0,1,2 (subset of active hkl planes)</help>
0
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144 <validator type="regex" message="">^\d(,\d)*$</validator>
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145 </param>
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146 <param name="fiber_step" type="float" value="0.5" min="0" max="10" label="fiber step"/>
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147 <conditional name="params">
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148 <param name="method" type="select" label="Method">
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149 <option value="label" selected="true">label</option>
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150 <option value="blob_dog">blob_dog</option>
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151 <option value="blob_log">blob_log</option>
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152 </param>
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153 <when value="label">
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154 <param name="filter_radius" type="integer" value="1" min="1" label="label filter radius"/>
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155 <param name="threshold" type="integer" value="1" min="1" label="label threshold"/>
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156 </when>
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157 <when value="blob_dog">
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158 <param name="min_sigma" type="float" value="0.5" min="0" max="10" label="blob_dog min_sigma"/>
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159 <param name="max_sigma" type="float" value="5.0" min="0" max="10" label="blob_dog max_sigma"/>
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160 <param name="sigma_ratio" type="float" value="1.6" min="0" max="10" label="blob_dog sigma_ratio"/>
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161 <param name="threshold" type="float" value="0.01" min="0" max="1.0" label="blob_dog threshold"/>
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162 <param name="overlap" type="float" value="0.1" min="0" max="1.0" label="blob_dog overlap"/>
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163 </when>
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164 <when value="blob_log">
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165 <param name="min_sigma" type="float" value="0.5" min="0" max="10" label="blob_log min_sigma"/>
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166 <param name="max_sigma" type="float" value="5.0" min="0" max="10" label="blob_log max_sigma"/>
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167 <param name="num_sigma" type="integer" value="10" min="0" max="20" label="blob_log num_sigma"/>
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168 <param name="threshold" type="float" value="0.01" min="0" max="1.0" label="blob_log threshold"/>
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169 <param name="overlap" type="float" value="0.1" min="0" max="1.0" label="blob_log overlap"/>
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170 </when>
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171 </conditional>
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172 </when>
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173 <when value="use_quaternion_grid">
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174 <param name="quaternion_grid" type="data" format="hexrd.npz" label="quaterion grid file"/>
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175 </when>
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176 </conditional>
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177 </section>
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178 <section name="omega" title="Omega" expanded="true">
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179 <param name="omega_tolerance" type="float" value="1.0" min="0" max="10.0" label="omega tolerance"/>
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180 </section>
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181 <section name="eta" title="eta" expanded="true">
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182 <param name="eta_tolerance" type="float" value="1.0" min="0" max="10.0" label="eta tolerance"/>
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183 <param name="eta_mask" type="float" value="5.0" min="0" max="10.0" label="eta mask"/>
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184 </section>
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185 <section name="clustering" title="Clustering" expanded="true">
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186 <param name="clustering_algorithm" type="select" label="Clustering algorithm">
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187 <option value="dbscan" selected="true">dbscan</option>
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188 <option value="sph-dbscan">sph-dbscan</option>
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189 <option value="ort-dbscan">ort-dbscan</option>
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190 <option value="fclusterdata">fclusterdata (won't work for large problems)</option>
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191 </param>
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192 <param name="clustering_radius" type="float" value="1.0" min="0" max="10" label="clustering radius"/>
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193 <param name="clustering_completeness" type="float" value="0.85" min="0" max="1" label="clustering completeness threshold"/>
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194 </section>
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195 <!--
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196 -->
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197 </xml>
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198
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199 <token name="@FIND_ORIENTATIONS_YML@"><![CDATA[@COMMON_YML@
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200
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201 #set active_hkls = 'all'
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202 #if $orientation_maps.active_hkls:
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203 #set active_hkls = '[' + str($orientation_maps.active_hkls) + ']'
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204 #end if
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205 find_orientations:
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206 orientation_maps:
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207 # A file name must be specified. If it doesn't exist, one will be created
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208 file: null
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209
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210 threshold: $orientation_maps.threshold
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211 bin_frames: $orientation_maps.bin_frames # defaults to 1
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212
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213 # "all", or a list of hkl orders used to find orientations
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214 # defaults to all orders listed in the material definition
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215 active_hkls: $active_hkls
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216
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217 # either search full quaternion grid, or seed search based on sparse
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218 # orientation maps. For input search space:
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219 #
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220 # use_quaternion_grid: some/file/name
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221 #
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222 # otherwise defaults to seeded search
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223 #if $search_options.search.search_type == 'use_quaternion_grid'
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224 use_quaternion_grid:
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225 #elif $search_options.search.search_type == 'seed_search'
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226 #set hkl_seeds = '[' + str($search_options.search.hkl_seeds) + ']'
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227 seed_search: # this section is ignored if use_quaternion_grid is defined
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228 hkl_seeds: $hkl_seeds # hkls ids to use, must be defined for seeded search
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229 fiber_step: $search_options.search.fiber_step # degrees, defaults to ome tolerance
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230 # Method selection:
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231 # Now 3 choices: label (the original), 'blob_dog', and 'blob_log'
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232 # Each has its own parameter names, examples below.
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233 #
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234 method:
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235 #if $search_options.search.params.method == 'label'
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236 label:
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237 filter_radius: $search_options.search.params.filter_radius
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238 threshold: $search_options.search.params.threshold
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239 #elif $search_options.search.params.method == 'blob_dog'
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240 blob_dog:
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241 min_sigma: $search_options.search.params.min_sigma
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242 max_sigma: $search_options.search.params.max_sigma
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243 sigma_ratio: $search_options.search.params.sigma_ratio
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244 threshold: $search_options.search.params.threshold
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245 overlap: $search_options.search.params.overlap
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246 #elif $search_options.search.params.method == 'blob_log'
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247 blob_log:
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248 min_sigma: $search_options.search.params.min_sigma
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249 max_sigma: $search_options.search.params.max_sigma
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250 num_sigma: $search_options.search.params.num_sigma
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251 threshold: $search_options.search.params.threshold
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252 overlap: $search_options.search.params.overlap
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253 #end if
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254 # this is the on-map threshold using in the scoring
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255 # defaults to 1
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256 #end if
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257 threshold: $on_map_threshold
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258
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259 omega:
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260 tolerance: $omega.omega_tolerance # in degrees, defaults to 2x ome step
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261
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262 eta:
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263 tolerance: $eta.eta_tolerance # in degrees, defaults to 2x ome step
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264 mask: $eta.eta_mask # degrees, mask angles close to ome rotation axis, defaults to 5
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265
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266 clustering:
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267 # algorithm choices are
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268 # sph-dbscan
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269 # ort-dbscn
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270 # dbscan <default>
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271 # fclusterdata; this is a fallback and won't work for large problems
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272 algorithm: $clustering.clustering_algorithm
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273 radius: $clustering.clustering_radius
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274 completeness: $clustering.clustering_completeness
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275
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276 ]]></token>
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277
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278 <xml name="fit_grains_config">
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279 <expand macro="common_config" token_multiple_inputs="true"/>
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280 <param name="ome_map" type="data" format="hexrd.npz" label="analysis eta-ome_maps.npz from find_orientations"/>
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281 <param name="accepted_orientations" type="data" format="tabular" label="accepted_orientations from find_orientations"/>
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282 <param name="grains_estimate" type="data" format="tabular" label="grains.out from find_orientations"/>
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283 <param name="do_fit" type="boolean" truevalue="true" falsevalue="false" checked="true" label="fit grains" help="if false, extracts grains but doesn't fit"/>
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284 <param name="npdiv" type="integer" value="2" min="1" label="number of polar pixel grid subdivisions"/>
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285 <param name="threshold" type="integer" value="25" min="1" label="threshold"/>
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286 <section name="tolerance" title="Fit Grain Tolerance" expanded="true">
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287 <repeat name="tolerance_lists" title="Tolerance values" min="1">
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288 <param name="tth" type="float" value="" min="0" label="tth"/>
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289 <param name="eta" type="float" value="" min="0" label="eta"/>
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290 <param name="omega" type="float" value="" min="0" label="omega"/>
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291 </repeat>
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292 <param name="refit" type="text" value="1" label="refit">
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293 <validator type="regex" message="">^\d(,\d)*$</validator>
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294 </param>
1
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295 <conditional name="max_tth">
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296 <param name="tth_max_value" type="select" label="Set tth_max">
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297 <option value="true" selected="true">true</option>
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298 <option value="false">false</option>
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299 <option value="entered">enter value</option>
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300 </param>
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301 <when value="true"/>
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302 <when value="false"/>
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303 <when value="entered">
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304 <param name="tth_max" type="float" value="14.25" label="tth_max"/>
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305 </when>
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306 </conditional>
0
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307 </section>
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308 </xml>
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309
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310 <token name="@FIT_GRAINS_YML@"><![CDATA[@COMMON_YML@
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311 find_orientations:
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312 orientation_maps:
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313 # A file name must be specified. If it doesn't exist, one will be created
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314 file: $ln_name($ome_map,'npz')
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315
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316 fit_grains:
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317 do_fit: $do_fit # if false, extracts grains but doesn't fit. defaults to true
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318 # estimate: null
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319 npdiv: $npdiv # number of polar pixel grid subdivisions, defaults to 2
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320 threshold: $threshold
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321
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322 #set $tth = []
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323 #set $eta = []
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324 #set $omega = []
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325 #set refit = '[' + str($tolerance.refit) + ']'
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326 #for $tol in $tolerance.tolerance_lists
2
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327 #silent $tth.append(float($tol.tth))
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328 #silent $eta.append(float($tol.eta))
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329 #silent $omega.append(float($tol.omega))
0
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330 #end for
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331 tolerance:
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332 tth: $tth # tolerance lists must be identical length
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333 eta: $eta
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334 omega: $omega
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335
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336 refit: $refit
1
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337 #if $tolerance.max_tth.tth_max_value == 'entered':
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338 tth_max: $tolerance.max_tth.tth_max # true, false, or a non-negative value, defaults to true
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339 #else
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340 tth_max: $tolerance.max_tth.tth_max_value # true, false, or a non-negative value, defaults to true
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341 #end if
0
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342 ]]></token>
2
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343 <token name="@HEXRD_HELP@"><![CDATA[
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344 HEXRD_ provides analysis of x-ray diffraction data, especially high-energy x-ray diffraction. HEXRD is comprised of a library and API for writing scripts, a command line interface, and an interactive graphical user interface.
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345
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346 .. _HEXRD: https://github.com/HEXRD/hexrd
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347 ]]></token>
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348
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349 <token name="@COMMON_INPUTS_HELP@"><![CDATA[
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350
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351 **INPUTS**
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352
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353 - imageseries - Detector image files converted to sparse matrix compressed numpy arrays.
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354 - instrument - A yaml file that decribes the instrument
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355 - materials.hexrd - A "pickled" hexrd Materials object that desscribes the sample material
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356 ]]></token>
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357 <token name="@FIT_GRAIN_INPUTS_HELP@"><![CDATA[@COMMON_INPUTS_HELP@
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358 - analysis eta-ome_maps.npz from find_orientations
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359 - accepted_orientations from find_orientations
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360
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361 ]]></token>
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362
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363 <token name="@COMMON_OUTPUTS_HELP@"><![CDATA[
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364
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365 **OUTPUTS**
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366
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367 - config yaml - parameter for hexrd
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368 - log - the hexrd logging output
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369 - grains.out
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370 ]]></token>
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371 <token name="@FIND_ORIENTATIONS_OUTPUTS_HELP@"><![CDATA[@COMMON_OUTPUTS_HELP@
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372 - analysis eta-ome_maps.npz *(used as input for hexrd fit-grains)*
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373 - analysis accepted_orientations_analysis.dat *(used as input for hexrd fit-grains)*
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374 - analysis scored_orientations_analysis.npz
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375 ]]></token>
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376 <token name="@FIT_GRAINS_OUTPUTS_HELP@"><![CDATA[@COMMON_OUTPUTS_HELP@
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377 - Collection of spots.out
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378 ]]></token>
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379
0
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380
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381 </macros>