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comparison hexrd_find_orientations.xml @ 5:36f0e168e5ef draft

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"planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
author ximgchess
date Thu, 01 Apr 2021 18:31:47 +0000
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children 164e881c40e2
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4:b49a8ef3351d 5:36f0e168e5ef
1 <tool id="hexrd_find_orientations" name="HEXRD find-orientations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
2 <description>Process rotation image series to find grain orientations</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 cp '$config_yml' $config &&
9 cp '$config_yml' config.yml &&
10 ## symlink input files
11 @CMD_LINKS@
12 hexrd find-orientations config.yml &&
13 @CONVERT2TAB@ &&
14 cp find-orientations_analysis_*.log '$log' &&
15 cp accepted_orientations_analysis_*.dat '$accepted_orientations' &&
16 cp scored_orientations_analysis_*.npz '$score_orientations' &&
17 cp analysis_*_eta-ome_maps.npz '$ome_maps'
18 ]]></command>
19 <configfiles>
20 <configfile name="config_yml"><![CDATA[@FIND_ORIENTATIONS_YML@
21 ]]></configfile>
22 </configfiles>
23
24 <inputs>
25 <expand macro="find_orientations_config"/>
26 </inputs>
27 <outputs>
28 <data name="config" format="hexrd.yml" 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"/>
30 <data name="ome_maps" format="hexrd.npz" label="${tool.name} on ${on_string}: analysis_${active_material}_eta-ome_maps.npz"/>
31 <data name="score_orientations" format="hexrd.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"/>
33 <data name="grains" format="tabular" label="${tool.name} on ${on_string}: grains.out" from_work_dir="analysis/grains.out" />
34 </outputs>
35 <tests>
36 <test>
37 <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"/>
38 <conditional name="detector">
39 <param name="panel_assignment" value="infer_from_name"/>
40 </conditional>
41 <param name="instrument" ftype="hexrd.yml" value="ge_detector.yml"/>
42 <param name="material" ftype="hexrd.materials.h5" value="materials.h5"/>
43 <param name="active_material" value="ruby"/>
44 <section name="orientation_maps">
45 <param name="threshold" value="25"/>
46 <param name="bin_frames" value="1"/>
47 <param name="active_hkls" value="0,1,2,3,4,5"/>
48 </section>
49 <section name="search_options">
50 <conditional name="search">
51 <param name="search_type" value="seed_search"/>
52 <param name="hkl_seeds" value="0,1,2"/>
53 <param name="fiber_step" value="0.5"/>
54 <conditional name="params">
55 <param name="method" value="label"/>
56 <param name="filter_radius" value="1"/>
57 <param name="threshold" value="1"/>
58 </conditional>
59 </conditional>
60 </section>
61 <section name="omega">
62 <param name="omega_tolerance" value="1.0"/>
63 </section>
64 <section name="eta">
65 <param name="eta_tolerance" value="1.0"/>
66 <param name="eta_mask" value="5.0"/>
67 </section>
68 <section name="clustering">
69 <param name="clustering_algorithm" value="dbscan"/>
70 <param name="clustering_radius" value="1.0"/>
71 <param name="clustering_completeness" value="0.85"/>
72 </section>
73 <output name="grains">
74 <assert_contents>
75 <has_text text="6.6655" />
76 </assert_contents>
77 </output>
78 </test>
79 </tests>
80 <help><![CDATA[
81 **HEXRD find-orientations**
82 @HEXRD_HELP@
83 @COMMON_INPUTS_HELP@
84 @FIND_ORIENTATIONS_OUTPUTS_HELP@
85 ]]></help>
86 <expand macro="citations" />
87 </tool>