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annotate hexrd_find_orientations.xml @ 6:164e881c40e2 draft

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"planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
author ximgchess
date Thu, 14 Oct 2021 18:03:22 +0000
parents 36f0e168e5ef
children baba452d0613
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164e881c40e2 "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
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1 <tool id="hexrd_find_orientations" name="HEXRD find-orientations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="3.5">
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2 <description>Process rotation image series to find grain orientations</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 cp '$config_yml' $config &&
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9 cp '$config_yml' config.yml &&
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10 ## symlink input files
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11 @CMD_LINKS@
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12 hexrd find-orientations config.yml &&
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13 @CONVERT2TAB@ &&
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14 cp find-orientations_analysis_*.log '$log' &&
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15 cp accepted_orientations_analysis_*.dat '$accepted_orientations' &&
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16 cp scored_orientations_analysis_*.npz '$score_orientations' &&
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17 cp analysis_*_eta-ome_maps.npz '$ome_maps'
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18 ]]></command>
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19 <configfiles>
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20 <configfile name="config_yml"><![CDATA[@FIND_ORIENTATIONS_YML@
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21 ]]></configfile>
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22 </configfiles>
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23
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24 <inputs>
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25 <expand macro="find_orientations_config"/>
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26 </inputs>
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27 <outputs>
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28 <data name="config" format="hexrd.yml" label="${tool.name} on ${on_string}: ${active_material}_config.yml"/>
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29 <data name="log" format="txt" label="${tool.name} on ${on_string}: find-orientations_analysis_${active_material}.log"/>
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30 <data name="ome_maps" format="hexrd.eta_ome.npz" label="${tool.name} on ${on_string}: analysis_${active_material}_eta-ome_maps.npz"/>
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31 <data name="score_orientations" format="hexrd.npz" label="${tool.name} on ${on_string}: scored_orientations_analysis_${active_material}.npz"/>
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32 <data name="accepted_orientations" format="hexrd.accepted_orientations" label="${tool.name} on ${on_string}: accepted_orientations_analysis_${active_material}.dat"/>
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33 <data name="grains" format="tabular" label="${tool.name} on ${on_string}: grains.out" from_work_dir="analysis/grains.out" />
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34 </outputs>
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35 <tests>
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36 <test>
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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"/>
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38 <conditional name="detector">
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39 <param name="panel_assignment" value="infer_from_name"/>
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40 </conditional>
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41 <param name="instrument" ftype="hexrd.yml" value="ge_detector.yml"/>
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42 <param name="material" ftype="hexrd.materials.h5" value="materials.h5"/>
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43 <param name="active_material" value="ruby"/>
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44 <section name="orientation_maps">
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45 <param name="threshold" value="25"/>
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46 <param name="bin_frames" value="1"/>
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47 <param name="active_hkls" value="0,1,2,3,4,5"/>
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48 </section>
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49 <section name="search_options">
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50 <conditional name="search">
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51 <param name="search_type" value="seed_search"/>
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52 <param name="hkl_seeds" value="0,1,2"/>
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53 <param name="fiber_step" value="0.5"/>
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54 <conditional name="params">
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55 <param name="method" value="label"/>
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56 <param name="filter_radius" value="1"/>
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57 <param name="threshold" value="1"/>
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58 </conditional>
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59 </conditional>
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60 </section>
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61 <section name="omega">
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62 <param name="omega_tolerance" value="1.0"/>
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63 </section>
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64 <section name="eta">
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65 <param name="eta_tolerance" value="1.0"/>
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66 <param name="eta_mask" value="5.0"/>
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67 </section>
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68 <section name="clustering">
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69 <param name="clustering_algorithm" value="dbscan"/>
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70 <param name="clustering_radius" value="1.0"/>
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71 <param name="clustering_completeness" value="0.85"/>
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72 </section>
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73 <output name="grains">
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74 <assert_contents>
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75 <has_text text="6.6655" />
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76 </assert_contents>
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77 </output>
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78 </test>
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79 </tests>
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80 <help><![CDATA[
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81 **HEXRD find-orientations**
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82 @HEXRD_HELP@
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83 @COMMON_INPUTS_HELP@
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
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84 @FIND_ORIENTATIONS_OUTPUTS_HELP@
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
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85 ]]></help>
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
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86 <expand macro="citations" />
36f0e168e5ef "planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 0db0d2633f65e2ceca2e34c8899a52b18965d059-dirty"
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87 </tool>