Mercurial > repos > ximgchess > hexrd

annotate hexrd_fit_grains.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 baba452d0613
children
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1 <tool id="hexrd_fit_grains" name="HEXRD fit-grains" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="3.5">
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2 <description>Extracts G vectors, grain position and strain</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 @FIT_GRAIN_LINKS@
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12 hexrd fit-grains config.yml -f &&
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13 cp analysis/*.log '$log' &&
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14 @CONVERT2TAB@
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15 && for i in analysis/*/spots*.out; do dest=`echo \${i\#*/} | tr '/' '_'`; mv \${i} analysis/\$dest; done
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16 ]]></command>
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17 <configfiles>
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18 <configfile name="config_yml"><![CDATA[@FIT_GRAINS_YML@
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19 ]]></configfile>
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20 </configfiles>
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21 <inputs>
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22 <expand macro="fit_grains_config"/>
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23 </inputs>
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24 <outputs>
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25 <data name="config" format="yaml" label="${tool.name} on ${on_string}: ${active_material}_config.yml"/>
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26 <data name="log" format="txt" label="${tool.name} on ${on_string}:fit_grains_analysis_${active_material}.log"/>
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27 <data name="grains" format="tabular" label="${tool.name} on ${on_string}: grains.out" from_work_dir="analysis/grains.out" />
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28 <collection name="spots" type="list" label="${tool.name} on ${on_string}:spots">
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29 <discover_datasets pattern="(?P&lt;designation&gt;.+_spots.+\.out)" ext="tabular" directory="analysis"/>
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30 </collection>
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31 </outputs>
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32 <tests>
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33 <!-- Test-1 single_GE -->
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34 <test>
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35 <param name="analysis_name" value="ruby"/>
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36 <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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37 <conditional name="detector">
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38 <param name="panel_assignment" value="infer_from_name"/>
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39 </conditional>
10
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40 <param name="instrument" ftype="hexrd.yml" value="single_GE/ge_detector.yml"/>
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41 <param name="material" ftype="hexrd.materials.h5" value="single_GE/materials.h5"/>
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42 <param name="active_material" value="ruby"/>
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43 <param name="dmin" value="0.7"/>
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44 <param name="tth_width" value="0.2"/>
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45 <param name="min_sfac_ratio" value="0.05"/>
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46 <param name="ome_map" ftype="hexrd.eta_ome.npz" value="single_GE/analysis_ruby_eta-ome_maps.npz"/>
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47 <param name="accepted_orientations" ftype="hexrd.accepted_orientations" value="single_GE/accepted_orientations_analysis_ruby.dat"/>
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48 <param name="grains_estimate" ftype="tabular" value="single_GE/grains_estimate.out"/>
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49 <param name="do_fit" value="true"/>
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50 <param name="npdiv" value="2"/>
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51 <param name="threshold" value="25"/>
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52 <section name="tolerance">
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53 <repeat name="tolerance_lists">
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54 <param name="tth" value="0.25"/>
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55 <param name="eta" value="3.0"/>
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56 <param name="omega" value="2.0"/>
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57 </repeat>
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58 <repeat name="tolerance_lists">
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59 <param name="tth" value="0.20"/>
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60 <param name="eta" value="2.0"/>
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61 <param name="omega" value="1.0"/>
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62 </repeat>
10
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63 <param name="refit" value="1,1"/>
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64 <param name="tth_max" value="14.25"/>
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65 </section>
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66 <output name="grains">
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67 <assert_contents>
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68 <has_text text="6.69" />
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69 </assert_contents>
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70 </output>
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71 </test>
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72 <!-- Test-2 multiruby_dexelas -->
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73 <test>
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74 <param name="analysis_name" value="ruby"/>
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75 <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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76 <conditional name="detector">
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77 <param name="panel_assignment" value="infer_from_name"/>
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78 </conditional>
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79 <param name="instrument" ftype="hexrd.yml" value="multiruby_dexelas/dexelas_id3a_20200130.yml"/>
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80 <param name="material" ftype="hexrd.materials.h5" value="multiruby_dexelas/materials.h5"/>
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81 <param name="active_material" value="ruby"/>
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82 <param name="dmin" value="0.7"/>
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83 <param name="tth_width" value="0.2"/>
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84 <param name="min_sfac_ratio" value="0.05"/>
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85 <param name="ome_map" ftype="hexrd.eta_ome.npz" value="multiruby_dexelas/mruby_monolithic_eta-ome_maps.npz"/>
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86 <param name="accepted_orientations" ftype="hexrd.accepted_orientations" value="multiruby_dexelas/accepted_orientations_analysis_ruby.dat"/>
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87 <param name="grains_estimate" ftype="tabular" value="multiruby_dexelas/grains_estimate.out"/>
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88 <param name="do_fit" value="true"/>
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89 <param name="npdiv" value="4"/>
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90 <param name="threshold" value="25"/>
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91 <section name="tolerance">
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92 <repeat name="tolerance_lists">
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93 <param name="tth" value="0.25"/>
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94 <param name="eta" value="3.0"/>
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95 <param name="omega" value="2.0"/>
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96 </repeat>
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97 <repeat name="tolerance_lists">
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98 <param name="tth" value="0.20"/>
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99 <param name="eta" value="2.0"/>
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100 <param name="omega" value="1.0"/>
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101 </repeat>
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102 <param name="refit" value="3,1"/>
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103 <param name="tth_max" value="true"/>
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104 </section>
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105 <output name="grains">
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106 <assert_contents>
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107 <has_text text="0.98" />
5
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108 </assert_contents>
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109 </output>
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110 </test>
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111 </tests>
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112 <help><![CDATA[
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113 **HEXRD fit-grains**
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114 @HEXRD_HELP@
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115 @FIT_GRAIN_INPUTS_HELP@
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116 @FIT_GRAINS_OUTPUTS_HELP@
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117 ]]></help>
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118 <expand macro="citations" />
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119 </tool>