Mercurial > repos > muon-spectroscopy-computational-project > larch_artemis
diff larch_artemis.xml @ 5:7acb53ffb96f draft
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 4814f53888643f1d3667789050914675fffb7d59
| author | muon-spectroscopy-computational-project |
|---|---|
| date | Fri, 23 Aug 2024 13:46:13 +0000 |
| parents | 39ab361e6d59 |
| children | d17c5d62802f |
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--- a/larch_artemis.xml Mon Jun 17 13:54:30 2024 +0000 +++ b/larch_artemis.xml Fri Aug 23 13:46:13 2024 +0000 @@ -2,32 +2,12 @@ <description>generate Artemis projects from XAFS data</description> <macros> <!-- version of underlying tool (PEP 440) --> - <token name="@TOOL_VERSION@">0.9.75</token> + <token name="@TOOL_VERSION@">0.9.80</token> <!-- version of this tool wrapper (integer) --> - <token name="@WRAPPER_VERSION@">1</token> + <token name="@WRAPPER_VERSION@">0</token> <!-- citation should be updated with every underlying tool version --> <!-- typical fields to update are version, month, year, and doi --> <token name="@TOOL_CITATION@">10.1088/1742-6596/430/1/012007</token> - <xml name="series_options"> - <param name="stop_on_error" type="boolean" label="Stop on error" help="Whether to stop gracefully or continue with subsequent projects if an error is encountered when fitting."/> - <repeat name="report_criteria" title="Report Criteria"> - <param name="variable" type="text" label="Variable" help="Name of the variable of that appears in the statistics or variables sections of the report."/> - <conditional name="action"> - <param name="action" type="select" display="radio" label="Action" help="What to do with the named variable."> - <option value="log" selected="true">Log</option> - <option value="warn">Warn</option> - <option value="stop">Early stopping</option> - </param> - <when value="log"/> - <when value="warn"> - <param name="threshold" type="float" value="0.0" min="0.0" label="Warning threshold" help="In addition to logging, a warning will be printed if the absolute value of this variable goes above this threshold."/> - </when> - <when value="stop"> - <param name="threshold" type="float" value="0.0" min="0.0" label="Early stopping threshold" help="In addition to logging, execution will stop if the absolute value of this variable goes above this threshold."/> - </when> - </conditional> - </repeat> - </xml> <import>macros.xml</import> </macros> <creator> @@ -45,9 +25,15 @@ <command detect_errors="exit_code"><![CDATA[ unzip '$feff_paths' && mkdir report rmr chikr - #if $execution.execution=="zipped": - && unzip '$execution.prj_file' - && python '${__tool_directory__}/larch_artemis.py' prj '$gds_file' '$sp_file' '$inputs' + #if $execution.execution=="series": + #if $execution.format.format=="zipped": + && unzip '$execution.format.prj_file' + && python '${__tool_directory__}/larch_artemis.py' prj '$gds_file' '$sp_file' '$inputs' + #else + && python '${__tool_directory__}/larch_artemis.py' '$execution.format.prj_file' '$gds_file' '$sp_file' '$inputs' + #end if + #elif $execution.execution=="simultaneous": + && python '${__tool_directory__}/larch_artemis.py' _ '$gds_file' '$sp_file' '$inputs' #else && python '${__tool_directory__}/larch_artemis.py' '$execution.prj_file' '$gds_file' '$sp_file' '$inputs' #end if @@ -56,25 +42,57 @@ #end if ]]></command> <configfiles> - <inputs name="inputs"/> + <inputs name="inputs" data_style="paths"/> </configfiles> <inputs> - <conditional name="execution" > - <param name="execution" type="select" display="radio" label="Execution mode" help="Whether to execute: on individual Athena projects as parallel jobs, as one job with each project fit occurring in series, or as one job using a zipped input."> + <conditional name="execution"> + <param name="execution" type="select" display="radio" label="Execution mode" help="Whether to execute: on individual Athena projects as parallel jobs, on several projects using a simultaneous fit, or as one job with each project fit occurring in series."> <option value="parallel" selected="true">Parallel</option> + <option value="simultaneous">Simultaneous</option> <option value="series">Series</option> - <option value="zipped">Zipped</option> </param> <when value="parallel"> <param name="prj_file" type="data" format="prj" label="Athena project file" help="Normalised X-ray Absorption Fine Structure (XAFS) data, in Athena project format. If a collection of files is provided, these will be submitted and executed in parallel."/> </when> - <when value="series"> - <param name="prj_file" type="data" format="prj" multiple="true" label="Athena project files" help="Normalised X-ray Absorption Fine Structure (XAFS) data, in Athena project format. These will be submitted as a single job working in series, enabling early stopping criteria."/> - <expand macro="series_options"/> + <when value="simultaneous"> + <repeat name="simultaneous" title="Simultaneous datasets" min="1" default="1"> + <param name="prj_file" type="data" format="prj" label="Athena project files" help="Normalised X-ray Absorption Fine Structure (XAFS) data, in Athena project format. These will be submitted as a single job performing a simultaneous fit."/> + <repeat name="paths" title="Path IDs to select" min="1" default="1"> + <param name="path_id" type="integer" min="1" label="Path ID"/> + </repeat> + </repeat> </when> - <when value="zipped"> - <param name="prj_file" type="data" format="zip" label="Zipped Athena outputs" help="Normalised X-ray Absorption Fine Structure (XAFS) data, in Athena project format, and zipped. These will be submitted as a single job working in series, enabling early stopping criteria."/> - <expand macro="series_options"/> + <when value="series"> + <conditional name="format"> + <param name="format" type="select" display="radio" label="Data format"> + <option value="prj" selected="true">Athena projects (.prj)</option> + <option value="zipped">Zipped</option> + </param> + <when value="prj"> + <param name="prj_file" type="data" format="prj" multiple="true" label="Athena project files" help="Normalised X-ray Absorption Fine Structure (XAFS) data, in Athena project format. These will be submitted as a single job working in series, enabling early stopping criteria."/> + </when> + <when value="zipped"> + <param name="prj_file" type="data" format="zip" label="Zipped Athena outputs" help="Normalised X-ray Absorption Fine Structure (XAFS) data, in Athena project format, and zipped. These will be submitted as a single job working in series, enabling early stopping criteria."/> + </when> + </conditional> + <param name="stop_on_error" type="boolean" label="Stop on error" help="Whether to stop gracefully or continue with subsequent projects if an error is encountered when fitting."/> + <repeat name="report_criteria" title="Report Criteria"> + <param name="variable" type="text" label="Variable" help="Name of the variable of that appears in the statistics or variables sections of the report."/> + <conditional name="action"> + <param name="action" type="select" display="radio" label="Action" help="What to do with the named variable."> + <option value="log" selected="true">Log</option> + <option value="warn">Warn</option> + <option value="stop">Early stopping</option> + </param> + <when value="log"/> + <when value="warn"> + <param name="threshold" type="float" value="0.0" min="0.0" label="Warning threshold" help="In addition to logging, a warning will be printed if the absolute value of this variable goes above this threshold."/> + </when> + <when value="stop"> + <param name="threshold" type="float" value="0.0" min="0.0" label="Early stopping threshold" help="In addition to logging, execution will stop if the absolute value of this variable goes above this threshold."/> + </when> + </conditional> + </repeat> </when> </conditional> <param name="feff_paths" type="data" format="zip" label="FEFF paths file" help="Zipped directory of the FEFF paths."/> @@ -110,38 +128,38 @@ <filter>zip_outputs</filter> </data> <data name="fit_report" format="feffit" from_work_dir="report/fit_report.txt" label="Fit report on ${on_string}"> - <filter>execution["execution"]=="parallel"</filter> + <filter>execution["execution"]!="series"</filter> <filter>not zip_outputs</filter> </data> <data name="rmr" format="png" from_work_dir="rmr/rmr.png" label="RMR plot on ${on_string}"> - <filter>execution["execution"]=="parallel"</filter> + <filter>execution["execution"]!="series"</filter> <filter>plot_graph</filter> <filter>not zip_outputs</filter> </data> <data name="chikr" format="png" from_work_dir="chikr/chikr.png" label="ChiKR plot on ${on_string}"> - <filter>execution["execution"]=="parallel"</filter> + <filter>execution["execution"]!="series"</filter> <filter>plot_graph</filter> <filter>not zip_outputs</filter> </data> <collection name="fit_report_collection" format="feffit" type="list" label="Fit reports on ${on_string}"> <discover_datasets pattern="__name_and_ext__" directory="report"/> - <filter>execution["execution"]!="parallel"</filter> + <filter>execution["execution"]=="series"</filter> <filter>not zip_outputs</filter> </collection> <collection name="rmr_collection" format="png" type="list" label="RMR plots on ${on_string}"> <discover_datasets pattern="__name_and_ext__" directory="rmr"/> - <filter>execution["execution"]!="parallel"</filter> + <filter>execution["execution"]=="series"</filter> <filter>plot_graph</filter> <filter>not zip_outputs</filter> </collection> <collection name="chikr_collection" format="png" type="list" label="ChiKR plots on ${on_string}"> <discover_datasets pattern="__name_and_ext__" directory="chikr"/> - <filter>execution["execution"]!="parallel"</filter> + <filter>execution["execution"]=="series"</filter> <filter>plot_graph</filter> <filter>not zip_outputs</filter> </collection> <data name="criteria_report" format="csv" from_work_dir="criteria_report.csv" label="Selected criteria from ${on_string}"> - <filter>execution["execution"]!="parallel"</filter> + <filter>execution["execution"]=="series"</filter> <filter>len(execution["report_criteria"])>0</filter> </data> </outputs> @@ -182,12 +200,12 @@ <output name="fit_report" file="fit_report.txt" compare="re_match"/> <output name="rmr"> <assert_contents> - <has_size value="55000" delta="1000"/> + <has_size value="50000" delta="10000"/> </assert_contents> </output> <output name="chikr"> <assert_contents> - <has_size value="65000" delta="1000"/> + <has_size value="70000" delta="10000"/> </assert_contents> </output> </test> @@ -294,7 +312,8 @@ </test> <!-- Zipped --> <test expect_num_outputs="1"> - <param name="execution" value="zipped"/> + <param name="execution" value="series"/> + <param name="format" value="zipped"/> <param name="prj_file" value="test.zip"/> <param name="feff_paths" value="[FEFF_paths_of_test.inp].zip"/> <param name="gds_file" value="gds.csv"/> @@ -311,13 +330,14 @@ <param name="zip_outputs" value="true"/> <output name="out_zip"> <assert_contents> - <has_size value="230000" delta="500"/> + <has_size value="250000" delta="10000"/> </assert_contents> </output> </test> <!-- 7: Zipped numerical sort --> <test expect_num_outputs="2"> - <param name="execution" value="zipped"/> + <param name="execution" value="series"/> + <param name="format" value="zipped"/> <param name="prj_file" value="numeric_sort.zip"/> <param name="variable" value="rfactor"/> <param name="action" value="log"/> @@ -335,6 +355,40 @@ <output_collection name="fit_report_collection" type="list" count="3"/> <output name="criteria_report" file="numeric_sort_criteria_report.csv" compare="re_match"/> </test> + <!-- 8: Simultaneous --> + <test expect_num_outputs="1"> + <param name="execution" value="simultaneous"/> + <repeat name="simultaneous"> + <param name="prj_file" value="test.prj"/> + <repeat name="paths"> + <param name="path_id" value="1"/> + <param name="path_id" value="2"/> + <param name="path_id" value="3"/> + <param name="path_id" value="4"/> + </repeat> + </repeat> + <repeat name="simultaneous"> + <param name="prj_file" value="test.prj"/> + <repeat name="paths"> + <param name="path_id" value="1"/> + <param name="path_id" value="2"/> + <param name="path_id" value="3"/> + <param name="path_id" value="4"/> + </repeat> + </repeat> + <param name="feff_paths" value="[FEFF_paths_of_test.inp].zip"/> + <param name="gds_file" value="gds.csv"/> + <param name="sp_file" value="sp.csv"/> + <param name="fitspace" value="r"/> + <param name="kmin" value="3"/> + <param name="kmax" value="14"/> + <param name="kweight" value="2"/> + <param name="dk" value="1"/> + <param name="window" value="hanning"/> + <param name="rmin" value="1.4"/> + <param name="rmax" value="3.0"/> + <output name="fit_report" file="fit_report.txt" compare="re_match"/> + </test> </tests> <help><![CDATA[ Using Larch, perform fitting on an Athena project file, originally from the input X-ray Absorption Fine Structure (XAFS) data file.