Mercurial > repos > muon-spectroscopy-computational-project > larch_lcf
annotate larch_lcf.xml @ 0:f59731986b61 draft
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
| author | muon-spectroscopy-computational-project |
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| date | Tue, 14 Nov 2023 15:35:22 +0000 |
| parents | |
| children | 6c28339b73f7 |
| 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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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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5 <token name="@TOOL_VERSION@">0.9.71</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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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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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
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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
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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
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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
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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
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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
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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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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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22 </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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23 <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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24 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
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25 ]]></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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26 <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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27 <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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28 </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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29 <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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30 <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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31 <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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32 <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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33 <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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34 <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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35 </repeat> |
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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 <expand macro="energy_limits"/> |
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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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37 </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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38 <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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39 <data name="plot" format="png" from_work_dir="plot.png" label="Larch LCF ${label} ${on_string}"/> |
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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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40 </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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41 <tests> |
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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 <test expect_num_outputs="1"> |
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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 <param name="prj_file" value="PtSn_OCO_Abu_1.prj"/> |
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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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44 <param name="component_file" value="Sn_foil_extracted.prj"/> |
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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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45 <param name="component_file" value="SnO2_extracted.prj"/> |
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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 <param name="energy_format" value="relative"/> |
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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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47 <param name="energy_max" value="10"/> |
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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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48 <output name="plot"> |
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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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49 <assert_contents> |
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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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50 <has_size value="55100" delta="100"/> |
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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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51 </assert_contents> |
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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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52 </output> |
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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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53 </test> |
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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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54 </tests> |
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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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55 <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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56 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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f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
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57 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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58 ]]></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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59 <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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60 <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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61 <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
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62 </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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63 </tool> |