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annotate hexrd_fit_grains.xml @ 3:54513f5fc836 draft

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"planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit f29a6f52c76e068908ab2e1161314eb3edcfe4c9"
author ximgchess
date Wed, 31 Mar 2021 14:56:35 +0000
parents f0db3e3b9d99
children
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1 <tool id="hexrd_fit_grains" name="HEXRD fit-grains" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
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2 <description>Extracts G vectors, grain position and strain</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 @FIT_GRAIN_LINKS@
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12 hexrd fit-grains config.yml -f &&
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13 cp analysis/*.log '$log' &&
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14 @CONVERT2TAB@
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15 && for i in analysis/*/spots*.out; do dest=`echo \${i\#*/} | tr '/' '_'`; mv \${i} analysis/\$dest; done
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16 ]]></command>
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17 <configfiles>
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18 <configfile name="config_yml"><![CDATA[@FIT_GRAINS_YML@
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19 ]]></configfile>
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20 </configfiles>
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21 <inputs>
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22 <expand macro="fit_grains_config"/>
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23 </inputs>
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24 <outputs>
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25 <data name="config" format="hexrd.yml" label="${tool.name} on ${on_string}: ${active_material}_config.yml"/>
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26 <data name="log" format="txt" label="${tool.name} on ${on_string}:fit_grains_analysis_${active_material}.log"/>
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27 <data name="grains" format="tabular" label="${tool.name} on ${on_string}: grains.out" from_work_dir="analysis/grains.out" />
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28 <collection name="spots" type="list" label="${tool.name} on ${on_string}:spots">
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29 <discover_datasets pattern="(?P&lt;designation&gt;.+_spots.+\.out)" ext="tabular" directory="analysis"/>
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30 </collection>
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31 </outputs>
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32 <tests>
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33 <test>
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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"/>
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35 <conditional name="detector">
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36 <param name="panel_assignment" value="infer_from_name"/>
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37 </conditional>
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38 <param name="instrument" ftype="hexrd.yml" value="ge_detector.yml"/>
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39 <param name="material" ftype="hexrd.materials.h5" value="materials.h5"/>
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40 <param name="active_material" value="ruby"/>
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41 <param name="ome_map" ftype="hexrd.npz" value="analysis_ruby_eta-ome_maps.npz"/>
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42 <param name="accepted_orientations" ftype="tabular" value="accepted_orientations_analysis_ruby.dat"/>
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43 <param name="grains_estimate" ftype="tabular" value="grains.out"/>
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44 <param name="do_fit" value="true"/>
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45 <param name="npdiv" value="2"/>
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46 <param name="threshold" value="25"/>
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47 <section name="tolerance">
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48 <repeat name="tolerance_lists">
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49 <param name="tth" value="0.25"/>
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50 <param name="eta" value="3.0"/>
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51 <param name="omega" value="2.0"/>
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52 <param name="refit" value="1"/>
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53 </repeat>
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54 <repeat name="tolerance_lists">
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55 <param name="tth" value="0.20"/>
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56 <param name="eta" value="2.0"/>
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57 <param name="omega" value="1.0"/>
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58 <param name="refit" value="1"/>
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59 </repeat>
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60 <param name="tth_max" value="14.25"/>
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61 </section>
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62 <output name="grains">
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63 <assert_contents>
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64 <has_text text="6.6655" />
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65 </assert_contents>
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66 </output>
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67 </test>
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68 </tests>
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69 <help><![CDATA[
2
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70 **HEXRD fit-grains**
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71 @HEXRD_HELP@
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72 @FIT_GRAIN_INPUTS_HELP@
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73 @FIT_GRAINS_OUTPUTS_HELP@
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74 ]]></help>
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75 <expand macro="citations" />
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76 </tool>