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comparison 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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9:e67ad9795525 10:a35bda7ed678
26 </inputs> 26 </inputs>
27 <outputs> 27 <outputs>
28 <data name="config" format="yaml" label="${tool.name} on ${on_string}: ${active_material}_config.yml"/> 28 <data name="config" format="yaml" label="${tool.name} on ${on_string}: ${active_material}_config.yml"/>
29 <data name="log" format="txt" label="${tool.name} on ${on_string}: find-orientations_analysis_${active_material}.log"/> 29 <data name="log" format="txt" label="${tool.name} on ${on_string}: find-orientations_analysis_${active_material}.log"/>
30 <data name="ome_maps" format="hexrd.eta_ome.npz" label="${tool.name} on ${on_string}: analysis_${active_material}_eta-ome_maps.npz"/> 30 <data name="ome_maps" format="hexrd.eta_ome.npz" label="${tool.name} on ${on_string}: analysis_${active_material}_eta-ome_maps.npz"/>
31 <data name="score_orientations" format="npz" label="${tool.name} on ${on_string}: scored_orientations_analysis_${active_material}.npz"/> 31 <data name="score_orientations" format="hexrd.scored_orientations.npz" label="${tool.name} on ${on_string}: scored_orientations_analysis_${active_material}.npz"/>
32 <data name="accepted_orientations" format="tabular" label="${tool.name} on ${on_string}: accepted_orientations_analysis_${active_material}.dat"/> 32 <data name="accepted_orientations" format="hexrd.accepted_orientations" label="${tool.name} on ${on_string}: accepted_orientations_analysis_${active_material}.dat"/>
33 <data name="grains" format="tabular" label="${tool.name} on ${on_string}: grains.out" from_work_dir="analysis/grains.out" /> 33 <data name="grains" format="tabular" label="${tool.name} on ${on_string}: grains.out" from_work_dir="analysis/grains.out" />
34 </outputs> 34 </outputs>
35 <tests> 35 <tests>
36 <!-- Test-1 single_GE -->
36 <test> 37 <test>
37 <param name="inputs" ftype="hexrd.images.npz" value="RUBY_0000-fc_GE.npz,RUBY_0001-fc_GE.npz,RUBY_0002-fc_GE.npz,RUBY_0003-fc_GE.npz,RUBY_0004-fc_GE.npz,RUBY_0005-fc_GE.npz"/> 38 <param name="analysis_name" value="ruby"/>
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"/>
38 <conditional name="detector"> 40 <conditional name="detector">
39 <param name="panel_assignment" value="infer_from_name"/> 41 <param name="panel_assignment" value="infer_from_name"/>
40 </conditional> 42 </conditional>
41 <param name="instrument" ftype="yaml" value="ge_detector.yml"/> 43 <param name="instrument" ftype="hexrd.yml" value="single_GE/ge_detector.yml"/>
42 <param name="material" ftype="hexrd.materials.h5" value="materials.h5"/> 44 <param name="material" ftype="hexrd.materials.h5" value="single_GE/materials.h5"/>
43 <param name="active_material" value="ruby"/> 45 <param name="active_material" value="ruby"/>
46 <param name="dmin" value="0.7"/>
47 <param name="tth_width" value="0.2"/>
48 <param name="min_sfac_ratio" value="0.05"/>
44 <section name="orientation_maps"> 49 <section name="orientation_maps">
45 <param name="threshold" value="25"/> 50 <param name="threshold" value="25"/>
46 <param name="bin_frames" value="1"/> 51 <param name="bin_frames" value="1"/>
47 <param name="active_hkls" value="0,1,2,3,4,5"/> 52 <param name="active_hkls" value="0,1,2,3,4,5"/>
48 </section> 53 </section>
70 <param name="clustering_radius" value="1.0"/> 75 <param name="clustering_radius" value="1.0"/>
71 <param name="clustering_completeness" value="0.85"/> 76 <param name="clustering_completeness" value="0.85"/>
72 </section> 77 </section>
73 <output name="grains"> 78 <output name="grains">
74 <assert_contents> 79 <assert_contents>
75 <has_text text="6.6655" /> 80 <has_text text="6.670" />
76 </assert_contents> 81 </assert_contents>
77 </output> 82 </output>
78 </test> 83 </test>
84 <!-- Test-2 multiruby_dexelas -->
85 <test>
86 <param name="analysis_name" value="ruby"/>
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"/>
88 <conditional name="detector">
89 <param name="panel_assignment" value="infer_from_name"/>
90 </conditional>
91 <param name="instrument" ftype="hexrd.yml" value="multiruby_dexelas/dexelas_id3a_20200130.yml"/>
92 <param name="material" ftype="hexrd.materials.h5" value="multiruby_dexelas/materials.h5"/>
93 <param name="active_material" value="ruby"/>
94 <param name="dmin" value="0.7"/>
95 <param name="tth_width" value="0.2"/>
96 <param name="min_sfac_ratio" value="0.05"/>
97 <section name="orientation_maps">
98 <param name="threshold" value="250"/>
99 <param name="bin_frames" value="1"/>
100 <param name="active_hkls" value="0,1,2,3,4,5"/>
101 </section>
102 <section name="search_options">
103 <conditional name="search">
104 <param name="search_type" value="seed_search"/>
105 <param name="hkl_seeds" value="0,1,2"/>
106 <param name="fiber_step" value="0.5"/>
107 <conditional name="params">
108 <param name="method" value="blob_log"/>
109 <param name="min_sigma" value="0.5"/>
110 <param name="max_sigma" value="5.0"/>
111 <param name="num_sigma" value="10"/>
112 <param name="threshold" value="0.01"/>
113 <param name="overlap" value="0.1"/>
114 </conditional>
115 </conditional>
116 </section>
117 <section name="omega">
118 <param name="omega_tolerance" value="1.0"/>
119 </section>
120 <section name="eta">
121 <param name="eta_tolerance" value="1.0"/>
122 <param name="eta_mask" value="5.0"/>
123 </section>
124 <section name="clustering">
125 <param name="clustering_algorithm" value="dbscan"/>
126 <param name="clustering_radius" value="1.0"/>
127 <param name="clustering_completeness" value="0.85"/>
128 </section>
129 <output name="grains">
130 <assert_contents>
131 <has_text text="6.94" />
132 </assert_contents>
133 </output>
134 </test>
135
79 </tests> 136 </tests>
80 <help><![CDATA[ 137 <help><![CDATA[
81 **HEXRD find-orientations** 138 **HEXRD find-orientations**
82 @HEXRD_HELP@ 139 @HEXRD_HELP@
83 @COMMON_INPUTS_HELP@ 140 @COMMON_INPUTS_HELP@