--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hexrd_find_orientations.xml	Thu Apr 01 18:31:47 2021 +0000
@@ -0,0 +1,87 @@
+<tool id="hexrd_find_orientations" name="HEXRD find-orientations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
+    <description>Process rotation image series to find grain orientations</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        cp '$config_yml' $config &&
+        cp '$config_yml' config.yml &&
+        ## symlink input files
+        @CMD_LINKS@
+        hexrd find-orientations config.yml &&
+        @CONVERT2TAB@ &&
+        cp find-orientations_analysis_*.log '$log' &&
+        cp  accepted_orientations_analysis_*.dat '$accepted_orientations' &&
+        cp  scored_orientations_analysis_*.npz '$score_orientations' &&
+        cp analysis_*_eta-ome_maps.npz '$ome_maps' 
+    ]]></command>
+    <configfiles>
+        <configfile name="config_yml"><![CDATA[@FIND_ORIENTATIONS_YML@
+]]></configfile>
+    </configfiles>
+
+    <inputs>
+        <expand macro="find_orientations_config"/> 
+    </inputs>
+    <outputs>
+        <data name="config" format="hexrd.yml" 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.npz" label="${tool.name} on ${on_string}: analysis_${active_material}_eta-ome_maps.npz"/>
+        <data name="score_orientations" format="hexrd.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="grains" format="tabular" label="${tool.name} on ${on_string}: grains.out" from_work_dir="analysis/grains.out" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputs" ftype="hexrd.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"/>
+            <conditional name="detector">
+                <param name="panel_assignment" value="infer_from_name"/>
+            </conditional>
+            <param name="instrument" ftype="hexrd.yml" value="ge_detector.yml"/>
+            <param name="material" ftype="hexrd.materials.h5" value="materials.h5"/>
+            <param name="active_material" value="ruby"/>
+            <section name="orientation_maps">
+                <param name="threshold" value="25"/>
+                <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="label"/>
+                        <param name="filter_radius" value="1"/>
+                        <param name="threshold" value="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="6.6655" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**HEXRD find-orientations**
+@HEXRD_HELP@
+@COMMON_INPUTS_HELP@
+@FIND_ORIENTATIONS_OUTPUTS_HELP@
+    ]]></help>
+    <expand macro="citations" />
+</tool>