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comparison hexrd_fit_grains.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_fit_grains" name="HEXRD fit-grains" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
2 <description>Extracts G vectors, grain position and strain</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 @FIT_GRAIN_LINKS@
12 hexrd fit-grains config.yml -f &&
13 cp analysis/*.log '$log' &&
14 @CONVERT2TAB@
15 && for i in analysis/*/spots*.out; do dest=`echo \${i\#*/} | tr '/' '_'`; mv \${i} analysis/\$dest; done
16 ]]></command>
17 <configfiles>
18 <configfile name="config_yml"><![CDATA[@FIT_GRAINS_YML@
19 ]]></configfile>
20 </configfiles>
21 <inputs>
22 <expand macro="fit_grains_config"/>
23 </inputs>
24 <outputs>
25 <data name="config" format="hexrd.yml" label="${tool.name} on ${on_string}: ${active_material}_config.yml"/>
26 <data name="log" format="txt" label="${tool.name} on ${on_string}:fit_grains_analysis_${active_material}.log"/>
27 <data name="grains" format="tabular" label="${tool.name} on ${on_string}: grains.out" from_work_dir="analysis/grains.out" />
28 <collection name="spots" type="list" label="${tool.name} on ${on_string}:spots">
29 <discover_datasets pattern="(?P&lt;designation&gt;.+_spots.+\.out)" ext="tabular" directory="analysis"/>
30 </collection>
31 </outputs>
32 <tests>
33 <test>
34 <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"/>
35 <conditional name="detector">
36 <param name="panel_assignment" value="infer_from_name"/>
37 </conditional>
38 <param name="instrument" ftype="hexrd.yml" value="ge_detector.yml"/>
39 <param name="material" ftype="hexrd.materials.h5" value="materials.h5"/>
40 <param name="active_material" value="ruby"/>
41 <param name="ome_map" ftype="hexrd.npz" value="analysis_ruby_eta-ome_maps.npz"/>
42 <param name="accepted_orientations" ftype="tabular" value="accepted_orientations_analysis_ruby.dat"/>
43 <param name="grains_estimate" ftype="tabular" value="grains.out"/>
44 <param name="do_fit" value="true"/>
45 <param name="npdiv" value="2"/>
46 <param name="threshold" value="25"/>
47 <section name="tolerance">
48 <repeat name="tolerance_lists">
49 <param name="tth" value="0.25"/>
50 <param name="eta" value="3.0"/>
51 <param name="omega" value="2.0"/>
52 <param name="refit" value="1"/>
53 </repeat>
54 <repeat name="tolerance_lists">
55 <param name="tth" value="0.20"/>
56 <param name="eta" value="2.0"/>
57 <param name="omega" value="1.0"/>
58 <param name="refit" value="1"/>
59 </repeat>
60 <param name="tth_max" value="14.25"/>
61 </section>
62 <output name="grains">
63 <assert_contents>
64 <has_text text="6.6655" />
65 </assert_contents>
66 </output>
67 </test>
68 </tests>
69 <help><![CDATA[
70 **HEXRD fit-grains**
71 @HEXRD_HELP@
72 @FIT_GRAIN_INPUTS_HELP@
73 @FIT_GRAINS_OUTPUTS_HELP@
74 ]]></help>
75 <expand macro="citations" />
76 </tool>