Mercurial > repos > muon-spectroscopy-computational-project > larch_lcf
annotate larch_lcf.xml @ 3:6bb927e155fc draft
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8
| author | muon-spectroscopy-computational-project |
|---|---|
| date | Thu, 11 Apr 2024 09:02:19 +0000 |
| parents | 85284c3e1354 |
| children | c2d5bfef5b63 |
| rev | line source |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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1 <tool id="larch_lcf" name="Larch LCF" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT"> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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2 <description>perform linear combination fit on XAS data</description> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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3 <macros> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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4 <!-- version of underlying tool (PEP 440) --> |
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6bb927e155fc
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8
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5 <token name="@TOOL_VERSION@">0.9.75</token> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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6 <!-- version of this tool wrapper (integer) --> |
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85284c3e1354
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 0f66842e802430e887d1c6cb7be1cc5436408fd2
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7 <token name="@WRAPPER_VERSION@">0</token> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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8 <!-- citation should be updated with every underlying tool version --> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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9 <!-- typical fields to update are version, month, year, and doi --> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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10 <token name="@TOOL_CITATION@">10.1088/1742-6596/430/1/012007</token> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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11 <import>macros.xml</import> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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12 </macros> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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13 <creator> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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14 <person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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15 </creator> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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16 <requirements> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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17 <requirement type="package" version="@TOOL_VERSION@">xraylarch</requirement> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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18 <requirement type="package" version="3.5.2">matplotlib</requirement> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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19 </requirements> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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20 <required_files> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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21 <include type="literal" path="larch_lcf.py"/> |
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6c28339b73f7
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
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22 <include type="literal" path="common.py"/> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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23 </required_files> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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24 <command detect_errors="exit_code"><![CDATA[ |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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25 python '${__tool_directory__}/larch_lcf.py' '$prj_file' '$inputs' |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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26 ]]></command> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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27 <configfiles> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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28 <inputs name="inputs" data_style="paths"/> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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29 </configfiles> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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30 <inputs> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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31 <param name="label" type="text" optional="true" label="Main data label" help="The label to use for the main data (target of the fit). If unset, the label will be taken from the Athena project metadata."/> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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32 <param name="prj_file" type="data" format="prj" label="Athena project to fit" help="Normalised X-ray Absorption Fine Structure (XAFS) data, in Athena project format, to be fit."/> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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33 <repeat name="components" title="Fit components"> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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34 <param name="label" type="text" optional="true" label="Component label" help="The label to use for this component. If unset, the label will be taken from the Athena project metadata."/> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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35 <param name="component_file" type="data" format="prj" label="Athena project to fit" help="Reference X-ray Absorption Fine Structure (XAFS) data, in Athena project format, to be used as components in the fit."/> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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36 </repeat> |
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6c28339b73f7
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
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37 <!-- Energy range for LCF --> |
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6c28339b73f7
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
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38 <param name="energy_min" type="float" label="Minimum fit energy (eV)" optional="true" help="If set, only data above this value will be used for the LCF."/> |
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6c28339b73f7
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
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39 <param name="energy_max" type="float" label="Maximum fit energy (eV)" optional="true" help="If set, only data below this value will be used for the LCF."/> |
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6c28339b73f7
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
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40 <!-- Plot limits --> |
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6c28339b73f7
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
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41 <expand macro="plot_limits_energy"/> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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42 </inputs> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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43 <outputs> |
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44 <data name="plot" format="png" from_work_dir="plot.png"/> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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45 </outputs> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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46 <tests> |
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47 <!-- 1 --> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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48 <test expect_num_outputs="1"> |
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49 <param name="prj_file" value="PtSn_OCO_Abu_1_29204.5.prj"/> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
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50 <param name="component_file" value="Sn_foil_29200.prj"/> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
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51 <param name="component_file" value="SnO2_29206.prj"/> |
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6c28339b73f7
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
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52 <param name="energy_min" value="29190"/> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
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53 <param name="energy_max" value="29230"/> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
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54 <param name="x_limit_min" value="29190"/> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
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55 <param name="x_limit_max" value="29230"/> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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56 <output name="plot"> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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57 <assert_contents> |
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58 <has_size value="59500" delta="100"/> |
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59 </assert_contents> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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60 </output> |
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61 <assert_stdout> |
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62 <has_text text="Goodness of fit (rfactor): 0.532130%"/> |
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63 </assert_stdout> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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64 </test> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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65 </tests> |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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66 <help><![CDATA[ |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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67 Performs a Linear Combination Fit (LCF) on an Athena project, using a number of other projects as components to the fit. |
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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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68 The extent to which each component contributes to the target is recorded in the output plot of the normalised absorption co-efficient. |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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69 ]]></help> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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70 <citations> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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71 <citation type="doi">@TOOL_CITATION@</citation> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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72 <citation type="doi">10.1107/S0909049505012719</citation> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
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73 </citations> |
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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
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74 </tool> |