diff hexrd_find_orientations.xml @ 10:a35bda7ed678 draft default tip

"planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/hexrd commit 082120888ad38a8e84b32834c698c374db6f0b0c-dirty"

--- a/hexrd_find_orientations.xml	Wed Feb 02 16:40:24 2022 +0000
+++ b/hexrd_find_orientations.xml	Thu Jul 07 01:53:44 2022 +0000
@@ -28,19 +28,24 @@
         <data name="config" format="yaml" label="${tool.name} on ${on_string}: ${active_material}_config.yml"/>
         <data name="log" format="txt" label="${tool.name} on ${on_string}: find-orientations_analysis_${active_material}.log"/>
         <data name="ome_maps" format="hexrd.eta_ome.npz" label="${tool.name} on ${on_string}: analysis_${active_material}_eta-ome_maps.npz"/>
-        <data name="score_orientations" format="npz" label="${tool.name} on ${on_string}: scored_orientations_analysis_${active_material}.npz"/>
-        <data name="accepted_orientations" format="tabular" label="${tool.name} on ${on_string}: accepted_orientations_analysis_${active_material}.dat"/>
+        <data name="score_orientations" format="hexrd.scored_orientations.npz" label="${tool.name} on ${on_string}: scored_orientations_analysis_${active_material}.npz"/>
+        <data name="accepted_orientations" format="hexrd.accepted_orientations" label="${tool.name} on ${on_string}: accepted_orientations_analysis_${active_material}.dat"/>
         <data name="grains" format="tabular" label="${tool.name} on ${on_string}: grains.out" from_work_dir="analysis/grains.out" />
     </outputs>
     <tests>
+        <!-- Test-1 single_GE -->
         <test>
-            <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"/>
+            <param name="analysis_name" value="ruby"/>
+            <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"/>
             <conditional name="detector">
                 <param name="panel_assignment" value="infer_from_name"/>
             </conditional>
-            <param name="instrument" ftype="yaml" value="ge_detector.yml"/>
-            <param name="material" ftype="hexrd.materials.h5" value="materials.h5"/>
+            <param name="instrument" ftype="hexrd.yml" value="single_GE/ge_detector.yml"/>
+            <param name="material" ftype="hexrd.materials.h5" value="single_GE/materials.h5"/>
             <param name="active_material" value="ruby"/>
+            <param name="dmin" value="0.7"/>
+            <param name="tth_width" value="0.2"/>
+            <param name="min_sfac_ratio" value="0.05"/>
             <section name="orientation_maps">
                 <param name="threshold" value="25"/>
                 <param name="bin_frames" value="1"/>
@@ -72,10 +77,62 @@
             </section>
             <output name="grains">
                 <assert_contents>
-                    <has_text text="6.6655" />
+                    <has_text text="6.670" />
                 </assert_contents>
             </output>
         </test>
+        <!-- Test-2 multiruby_dexelas -->
+        <test>
+            <param name="analysis_name" value="ruby"/>
+            <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"/>
+            <conditional name="detector">
+                <param name="panel_assignment" value="infer_from_name"/>
+            </conditional>
+            <param name="instrument" ftype="hexrd.yml" value="multiruby_dexelas/dexelas_id3a_20200130.yml"/>
+            <param name="material" ftype="hexrd.materials.h5" value="multiruby_dexelas/materials.h5"/>
+            <param name="active_material" value="ruby"/>
+            <param name="dmin" value="0.7"/>
+            <param name="tth_width" value="0.2"/>
+            <param name="min_sfac_ratio" value="0.05"/>
+            <section name="orientation_maps">
+                <param name="threshold" value="250"/>
+                <param name="bin_frames" value="1"/>
+                <param name="active_hkls" value="0,1,2,3,4,5"/>
+            </section>
+            <section name="search_options">
+                <conditional name="search">
+                    <param name="search_type" value="seed_search"/>
+                    <param name="hkl_seeds" value="0,1,2"/>
+                    <param name="fiber_step" value="0.5"/>
+                    <conditional name="params">
+                        <param name="method" value="blob_log"/>
+                            <param name="min_sigma" value="0.5"/>
+                            <param name="max_sigma" value="5.0"/>
+                            <param name="num_sigma" value="10"/>
+                            <param name="threshold" value="0.01"/>
+                            <param name="overlap" value="0.1"/>
+                    </conditional>
+                </conditional>
+            </section>
+            <section name="omega">
+                <param name="omega_tolerance" value="1.0"/>
+            </section>
+            <section name="eta">
+                <param name="eta_tolerance" value="1.0"/>
+                <param name="eta_mask" value="5.0"/>
+            </section>
+            <section name="clustering">
+                <param name="clustering_algorithm" value="dbscan"/>
+                <param name="clustering_radius" value="1.0"/>
+                <param name="clustering_completeness" value="0.85"/>
+            </section>
+            <output name="grains">
+                <assert_contents>
+                    <has_text text="6.94" />
+                </assert_contents>
+            </output>
+        </test>
+
     </tests>
     <help><![CDATA[
 **HEXRD find-orientations**