Mercurial > repos > ximgchess > hexrd
diff hexrd_find_orientations.xml @ 5:36f0e168e5ef draft
"planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
author | ximgchess |
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date | Thu, 01 Apr 2021 18:31:47 +0000 |
parents | |
children | 164e881c40e2 |
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--- /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>