Mercurial > repos > muon-spectroscopy-computational-project > larch_select_paths
comparison larch_select_paths.xml @ 4:204c4afe2f1e draft default tip
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_select_paths commit 4814f53888643f1d3667789050914675fffb7d59
| author | muon-spectroscopy-computational-project |
|---|---|
| date | Fri, 23 Aug 2024 14:10:59 +0000 |
| parents | 1d08395c1a9f |
| children |
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| 3:1d08395c1a9f | 4:204c4afe2f1e |
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| 1 <tool id="larch_select_paths" name="Larch Select Paths" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT"> | 1 <tool id="larch_select_paths" name="Larch Select Paths" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT"> |
| 2 <description>select FEFF paths for XAFS data</description> | 2 <description>select FEFF paths for XAFS data</description> |
| 3 <macros> | 3 <macros> |
| 4 <!-- version of underlying tool (PEP 440) --> | 4 <!-- version of underlying tool (PEP 440) --> |
| 5 <token name="@TOOL_VERSION@">0.9.75</token> | 5 <token name="@TOOL_VERSION@">0.9.80</token> |
| 6 <!-- version of this tool wrapper (integer) --> | 6 <!-- version of this tool wrapper (integer) --> |
| 7 <token name="@WRAPPER_VERSION@">0</token> | 7 <token name="@WRAPPER_VERSION@">0</token> |
| 8 <!-- citation should be updated with every underlying tool version --> | 8 <!-- citation should be updated with every underlying tool version --> |
| 9 <!-- typical fields to update are version, month, year, and doi --> | 9 <!-- typical fields to update are version, month, year, and doi --> |
| 10 <token name="@TOOL_CITATION@">10.1088/1742-6596/430/1/012007</token> | 10 <token name="@TOOL_CITATION@">10.1088/1742-6596/430/1/012007</token> |
| 43 <configfiles> | 43 <configfiles> |
| 44 <inputs name="inputs" data_style="paths"/> | 44 <inputs name="inputs" data_style="paths"/> |
| 45 </configfiles> | 45 </configfiles> |
| 46 <inputs> | 46 <inputs> |
| 47 <section name="variables" expanded="false" title="GDS variable defaults" help="Define default values for variables in the EXAFS equation to use for the paths selected below."> | 47 <section name="variables" expanded="false" title="GDS variable defaults" help="Define default values for variables in the EXAFS equation to use for the paths selected below."> |
| 48 <section name="degen" expanded="false" title="N: path degeneracy"> | |
| 49 <param name="is_common" type="boolean" checked="true" label="Use path default" help="If set, a single variable 'degen' will be used for all paths. Otherwise, each path has a distinct variable."/> | |
| 50 <param name="value" type="float" optional="true" min="0.0" label="Value" help="The initial value for 'degen'. This will depend on the structure and path in question. If unset, then the path default will be used."/> | |
| 51 <expand macro="vary"/> | |
| 52 </section> | |
| 48 <section name="s02" expanded="false" title="S02: passive electron reduction factor"> | 53 <section name="s02" expanded="false" title="S02: passive electron reduction factor"> |
| 49 <param name="is_common" type="boolean" checked="true" label="Common to all paths" help="If set, a single variable 's02' will be used for all paths. Otherwise, each path has a distinct variable."/> | 54 <param name="is_common" type="boolean" checked="true" label="Common to all paths" help="If set, a single variable 's02' will be used for all paths. Otherwise, each path has a distinct variable."/> |
| 50 <param name="value" type="float" value="1.0" min="0.0" max="1.0" label="Value" help="The initial value for 's02'. This is typically between 0.7 and 1.0."/> | 55 <param name="value" type="float" value="1.0" min="0.0" max="1.0" label="Value" help="The initial value for 's02'. This is typically between 0.7 and 1.0."/> |
| 51 <expand macro="vary"/> | 56 <expand macro="vary"/> |
| 52 </section> | 57 </section> |
| 78 <option value="manual">Manual</option> | 83 <option value="manual">Manual</option> |
| 79 </param> | 84 </param> |
| 80 <when value="all"> | 85 <when value="all"> |
| 81 <repeat name="paths" title="Define path variables" help="Overwrite the default variables defined above for chosen paths."> | 86 <repeat name="paths" title="Define path variables" help="Overwrite the default variables defined above for chosen paths."> |
| 82 <param name="id" type="integer" value="1" min="1" label="Path ID" help="Numerical id of a path to select, this appears at the end of the label and filename in the path summary CSV."/> | 87 <param name="id" type="integer" value="1" min="1" label="Path ID" help="Numerical id of a path to select, this appears at the end of the label and filename in the path summary CSV."/> |
| 88 <section name="degen" expanded="false" title="N: path degeneracy"> | |
| 89 <expand macro="name"/> | |
| 90 <param name="value" type="float" optional="true" min="0.0" label="Value" help="The initial value for 'degen'. This will depend on the structure and path in question."/> | |
| 91 <expand macro="expr"/> | |
| 92 <expand macro="vary"/> | |
| 93 </section> | |
| 83 <section name="s02" expanded="false" title="S02: passive electron reduction factor"> | 94 <section name="s02" expanded="false" title="S02: passive electron reduction factor"> |
| 84 <expand macro="name"/> | 95 <expand macro="name"/> |
| 85 <param name="value" type="float" value="1.0" min="0.0" max="1.0" label="Value" help="The initial value for 's02'. This is typically between 0.7 and 1.0."/> | 96 <param name="value" type="float" value="1.0" min="0.0" max="1.0" label="Value" help="The initial value for 's02'. This is typically between 0.7 and 1.0."/> |
| 86 <expand macro="expr"/> | 97 <expand macro="expr"/> |
| 87 <expand macro="vary"/> | 98 <expand macro="vary"/> |
| 121 <expand macro="max_degeneracy"/> | 132 <expand macro="max_degeneracy"/> |
| 122 </when> | 133 </when> |
| 123 <when value="manual"> | 134 <when value="manual"> |
| 124 <repeat name="paths" title="Select paths" help="Identify paths to use in the fitting by their id, and optionally define their variables. This will overwrite and defaults set above."> | 135 <repeat name="paths" title="Select paths" help="Identify paths to use in the fitting by their id, and optionally define their variables. This will overwrite and defaults set above."> |
| 125 <param name="id" type="integer" value="1" min="1" label="Path ID" help="Numerical id of a path to select, this appears at the end of the label and filename in the path summary CSV."/> | 136 <param name="id" type="integer" value="1" min="1" label="Path ID" help="Numerical id of a path to select, this appears at the end of the label and filename in the path summary CSV."/> |
| 137 <section name="degen" expanded="false" title="N: path degeneracy"> | |
| 138 <expand macro="name"/> | |
| 139 <param name="value" type="float" value="1.0" min="0.0" optional="true" label="Value" help="The initial value for 'degen'. This will depend on the structure and path in question. If unset, then the path default will be used."/> | |
| 140 <expand macro="expr"/> | |
| 141 <expand macro="vary"/> | |
| 142 </section> | |
| 126 <section name="s02" expanded="false" title="S02: passive electron reduction factor"> | 143 <section name="s02" expanded="false" title="S02: passive electron reduction factor"> |
| 127 <expand macro="name"/> | 144 <expand macro="name"/> |
| 128 <param name="value" type="float" value="1.0" min="0.0" max="1.0" label="Value" help="The initial value for 's02'. This is typically between 0.7 and 1.0."/> | 145 <param name="value" type="float" value="1.0" min="0.0" max="1.0" label="Value" help="The initial value for 's02'. This is typically between 0.7 and 1.0."/> |
| 129 <expand macro="expr"/> | 146 <expand macro="expr"/> |
| 130 <expand macro="vary"/> | 147 <expand macro="vary"/> |