Mercurial > repos > ximgchess > hexrd

annotate hexrd_find_orientations.xml @ 10:a35bda7ed678 draft default tip

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"planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/hexrd commit 082120888ad38a8e84b32834c698c374db6f0b0c-dirty"
author ximgchess
date Thu, 07 Jul 2022 01:53:44 +0000
parents 4bb02acaaabc
children
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1 <tool id="hexrd_find_orientations" name="HEXRD find-orientations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="3.5">
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2 <description>Process rotation image series to find grain orientations</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 cp '$config_yml' $config &&
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9 cp '$config_yml' config.yml &&
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10 ## symlink input files
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11 @CMD_LINKS@
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12 hexrd find-orientations --clean config.yml &&
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13 @CONVERT2TAB@ &&
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14 cp find-orientations_analysis_*.log '$log' &&
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15 cp accepted_orientations_analysis_*.dat '$accepted_orientations' &&
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16 cp scored_orientations_analysis_*.npz '$score_orientations' &&
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17 cp analysis_*_eta-ome_maps.npz '$ome_maps'
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18 ]]></command>
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19 <configfiles>
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20 <configfile name="config_yml"><![CDATA[@FIND_ORIENTATIONS_YML@
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21 ]]></configfile>
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22 </configfiles>
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24 <inputs>
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25 <expand macro="find_orientations_config"/>
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26 </inputs>
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27 <outputs>
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28 <data name="config" format="yaml" label="${tool.name} on ${on_string}: ${active_material}_config.yml"/>
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29 <data name="log" format="txt" label="${tool.name} on ${on_string}: find-orientations_analysis_${active_material}.log"/>
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30 <data name="ome_maps" format="hexrd.eta_ome.npz" label="${tool.name} on ${on_string}: analysis_${active_material}_eta-ome_maps.npz"/>
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31 <data name="score_orientations" format="hexrd.scored_orientations.npz" label="${tool.name} on ${on_string}: scored_orientations_analysis_${active_material}.npz"/>
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32 <data name="accepted_orientations" format="hexrd.accepted_orientations" label="${tool.name} on ${on_string}: accepted_orientations_analysis_${active_material}.dat"/>
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33 <data name="grains" format="tabular" label="${tool.name} on ${on_string}: grains.out" from_work_dir="analysis/grains.out" />
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34 </outputs>
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35 <tests>
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36 <!-- Test-1 single_GE -->
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37 <test>
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38 <param name="analysis_name" value="ruby"/>
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39 <param name="inputs" ftype="hexrd.images.npz" value="single_GE/RUBY_0000-fc_GE.npz,single_GE/RUBY_0001-fc_GE.npz,single_GE/RUBY_0002-fc_GE.npz,single_GE/RUBY_0003-fc_GE.npz,single_GE/RUBY_0004-fc_GE.npz,single_GE/RUBY_0005-fc_GE.npz"/>
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40 <conditional name="detector">
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41 <param name="panel_assignment" value="infer_from_name"/>
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42 </conditional>
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43 <param name="instrument" ftype="hexrd.yml" value="single_GE/ge_detector.yml"/>
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44 <param name="material" ftype="hexrd.materials.h5" value="single_GE/materials.h5"/>
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45 <param name="active_material" value="ruby"/>
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46 <param name="dmin" value="0.7"/>
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47 <param name="tth_width" value="0.2"/>
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48 <param name="min_sfac_ratio" value="0.05"/>
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49 <section name="orientation_maps">
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50 <param name="threshold" value="25"/>
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51 <param name="bin_frames" value="1"/>
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52 <param name="active_hkls" value="0,1,2,3,4,5"/>
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53 </section>
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54 <section name="search_options">
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55 <conditional name="search">
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56 <param name="search_type" value="seed_search"/>
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57 <param name="hkl_seeds" value="0,1,2"/>
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58 <param name="fiber_step" value="0.5"/>
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59 <conditional name="params">
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60 <param name="method" value="label"/>
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61 <param name="filter_radius" value="1"/>
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62 <param name="threshold" value="1"/>
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63 </conditional>
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64 </conditional>
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65 </section>
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66 <section name="omega">
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67 <param name="omega_tolerance" value="1.0"/>
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68 </section>
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69 <section name="eta">
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70 <param name="eta_tolerance" value="1.0"/>
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71 <param name="eta_mask" value="5.0"/>
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72 </section>
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73 <section name="clustering">
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74 <param name="clustering_algorithm" value="dbscan"/>
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75 <param name="clustering_radius" value="1.0"/>
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76 <param name="clustering_completeness" value="0.85"/>
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77 </section>
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78 <output name="grains">
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79 <assert_contents>
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80 <has_text text="6.670" />
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81 </assert_contents>
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82 </output>
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83 </test>
10
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84 <!-- Test-2 multiruby_dexelas -->
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85 <test>
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86 <param name="analysis_name" value="ruby"/>
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87 <param name="inputs" ftype="hexrd.images.npz" value="multiruby_dexelas/mruby-0129_000004_ff1_000012-cachefile.npz,multiruby_dexelas/mruby-0129_000004_ff2_000012-cachefile.npz"/>
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88 <conditional name="detector">
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89 <param name="panel_assignment" value="infer_from_name"/>
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90 </conditional>
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91 <param name="instrument" ftype="hexrd.yml" value="multiruby_dexelas/dexelas_id3a_20200130.yml"/>
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92 <param name="material" ftype="hexrd.materials.h5" value="multiruby_dexelas/materials.h5"/>
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93 <param name="active_material" value="ruby"/>
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94 <param name="dmin" value="0.7"/>
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95 <param name="tth_width" value="0.2"/>
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96 <param name="min_sfac_ratio" value="0.05"/>
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97 <section name="orientation_maps">
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98 <param name="threshold" value="250"/>
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99 <param name="bin_frames" value="1"/>
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100 <param name="active_hkls" value="0,1,2,3,4,5"/>
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101 </section>
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102 <section name="search_options">
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103 <conditional name="search">
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104 <param name="search_type" value="seed_search"/>
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105 <param name="hkl_seeds" value="0,1,2"/>
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106 <param name="fiber_step" value="0.5"/>
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107 <conditional name="params">
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108 <param name="method" value="blob_log"/>
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109 <param name="min_sigma" value="0.5"/>
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110 <param name="max_sigma" value="5.0"/>
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111 <param name="num_sigma" value="10"/>
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112 <param name="threshold" value="0.01"/>
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113 <param name="overlap" value="0.1"/>
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114 </conditional>
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115 </conditional>
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116 </section>
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117 <section name="omega">
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118 <param name="omega_tolerance" value="1.0"/>
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119 </section>
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120 <section name="eta">
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121 <param name="eta_tolerance" value="1.0"/>
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122 <param name="eta_mask" value="5.0"/>
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123 </section>
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124 <section name="clustering">
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125 <param name="clustering_algorithm" value="dbscan"/>
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126 <param name="clustering_radius" value="1.0"/>
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127 <param name="clustering_completeness" value="0.85"/>
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128 </section>
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129 <output name="grains">
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130 <assert_contents>
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131 <has_text text="6.94" />
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132 </assert_contents>
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133 </output>
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134 </test>
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135
5
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136 </tests>
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137 <help><![CDATA[
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138 **HEXRD find-orientations**
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139 @HEXRD_HELP@
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140 @COMMON_INPUTS_HELP@
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141 @FIND_ORIENTATIONS_OUTPUTS_HELP@
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142 ]]></help>
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143 <expand macro="citations" />
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144 </tool>