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"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald commit f282701cadbb0c90c2c77a52579f18b44a357e24"
author | climate |
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date | Wed, 21 Oct 2020 20:30:35 +0000 |
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<tool id="ctsm-fates" name="CTSM/FATES-EMERALD" version="2.0.1"> <description>Functionally Assembled Terrestrial Ecosystem Simulator</description> <requirements> <requirement type="package" version="2.0.1">fates-emerald</requirement> <requirement type="package" version="1.32">tar</requirement> <requirement type="package" version="2.35">binutils</requirement> <requirement type="package" version="3">python</requirement> <requirement type="package" version="2.0132">perl-xml-libxml</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ ( export HOME=`pwd` && export USER='jovyan' && mkdir -p .cime && cp '$__tool_directory__/config' .cime/config && cp '$__tool_directory__/config_compilers.xml' '.cime/config_compilers.xml' && cp '$__tool_directory__/config_machines.xml' '.cime/config_machines.xml' && mkdir inputdata && tar -xf '$inputdata' -C 'inputdata/' && mkdir output_dir && mkdir usermods_dirs && #if str($adv.condi_user_mods).strip() == 'yes' # should create a new type user_mods.tar cd usermods_dirs && tar xf '$user_mods' && cd .. && #end if create_newcase --case '$casename' --compset 2000_DATM%1PTGSWP3_CLM50%FATES_SICE_SOCN_MOSART_SGLC_SWAV --machine espresso --run-unsupported #if str($adv.condi_user_mods).strip() == 'yes' --user-mods-dir usermods_dirs #end if --res '$resolution' && cd '$casename' && ./case.setup > $case_info 2>&1 && #if (str($adv_period.condi_type_run.run_type) == 'hybrid' or str($adv_period.condi_type_run.run_type) == 'branch') ./xmlchange RUN_TYPE=$adv_period.condi_type_run.run_type && ./xmlchange RUN_REFDATE=$adv_period.condi_type_run.run_refdate && ./xmlchange RUN_REFCASE=$adv_period.condi_type_run.run_refcase && #end if #if ((str($adv_period.condi_type_run.run_type) == 'hybrid' or str($adv_period.condi_type_run.run_type) == 'startup') and ($adv_period.condi_type_run.run_startdate != '')) ./xmlchange RUN_STARTDATE=$adv_period.condi_type_run.run_startdate && #end if ./xmlchange STOP_N=$adv_period.stopn && ./xmlchange STOP_OPTION=$adv_period.stop_option && ./xmlchange CCSM_CO2_PPMV=$adv.co2 && ./xmlchange DOUT_S=FALSE && cp '$user_nl_clm_customization' user_nl_clm && ./case.build >> $case_info 2>&1 && #if (str($adv_period.condi_type_run.run_type) == 'hybrid' or str($adv_period.condi_type_run.run_type) == 'branch') tar -xf '$adv_period.condi_type_run.restart' -C '../work/$casename/run/' && #end if ./case.submit >> $case_info 2>&1 && mkdir -p restart && (cat '../work/$casename/run/rpointer'.* > $rinfo || printf "No restarts\n") && (cp '../work/$casename/run/$casename'.*.r*.*.nc restart/ || printf "No netCDF restarts\n") && (cp '../work/$casename/run/$casename'.*.r*.*.bin restart/ || printf "No bin restarts\n") && (cp '../work/$casename/run/rpointer'.* restart/ || printf "no rpointer\n") && cd restart && tar cvf $restart . && cd .. && (cp '../work/$casename/run/$casename'.*.h*.*.nc ../output_dir/ || printf "no netCDF outputs\n") && (gunzip '../work/$casename/run/'*.log.* || printf "no compressed logs") && cat '../work/$casename/run/'atm.log.* >> $atm_log && cat '../work/$casename/run/'cesm.log.* >> $cesm_log && cat '../work/$casename/run/'cpl.log.* >> $cpl_log && cat '../work/$casename/run/'lnd.log.* >> $lnd_log && cat '../work/$casename/run/'rof.log.* >> $rof_log && sleep 1000 ) || (printf "Case failed" && tar cf $work \${HOME}/work) ]]></command> <configfiles> <configfile name="user_nl_clm_customization"><![CDATA[ &clm_inparm hist_mfilt = 120, use_fates = .true., fates_spitfire_mode = $adv_clm.fates_spitfire_mode, use_fates_planthydro = $adv_clm.use_fates_planthydro, use_fates_cohort_age_tracking = $adv_clm.use_fates_cohort_age_tracking, use_fates_ed_st3 = $adv_clm.use_fates_ed_st3, use_fates_ed_prescribed_phys = $adv_clm.use_fates_ed_prescribed_phys, use_fates_logging = $adv_clm.use_fates_logging, use_fates_fixed_biogeog = $adv_clm.use_fates_fixed_biogeog, #if (str($adv_clm.fates_parteh_mode).strip() != '') fates_parteh_mode = $adv_clm.fates_parteh_mode #end if / ]]> </configfile> </configfiles> <inputs> <param name="inputdata" type="data" format='tar' label="inputdata for running FATES EMERALD"></param> <param name="casename" type="text" value="usecase" label="Name of your case"> <validator type="regex" message="start with a letter and no blanks">^[A-Za-z][A-Za-z0-9]*</validator> </param> <param name="resolution" type="select" label="Model resolution"> <option value="1x1_ALP1">ALP1</option> <option value="1x1_ALP2">ALP2</option> <option value="1x1_ALP3">ALP3</option> <option value="1x1_ALP4">ALP4</option> <option value="1x1_SUB1">SUB1</option> <option value="1x1_SUB2">SUB2</option> <option value="1x1_SUB3">SUB3</option> <option value="1x1_SUB4">SUB4</option> <option value="1x1_BOR1">BOR1</option> <option value="1x1_BOR2">BOR2</option> <option value="1x1_BOR3">BOR3</option> <option value="1x1_BOR4">BOR4</option> <option value="1x1_LYG">LYG</option> <option value="1x1_BUO">BUO</option> <option value="1x1_HAV">HAV</option> <option value="1x1_SKO">SKO</option> <option value="1x1_VIKE">VIKE</option> <option value="1x1_LIAH">LIAH</option> <option value="1x1_FINN">FINN</option> </param> <section name="adv_period" title="Customize the model run period" expanded="false"> <conditional name="condi_type_run"> <param name="run_type" type="select" label="Determines the model run initialization type."> <option value="startup" selected="true">startup</option> <option value="hybrid">hybrid</option> <option value="branch">branch</option> </param> <when value="startup"> <param name="run_startdate" type="text" value="" label="Run start date (yyyy-mm-dd). Only used for startup or hybrid runs."> <validator type="regex" message="YYYY-MM-DD">(^$|(\d{4}-(0[1-9]|1[0-2])-(0[1-9]|[12]\d|3[01])))</validator> </param> </when> <when value="branch"> <param name="run_refcase" type="text" value="" label="Reference case for hybrid or branch runs"></param> <param name="run_refdate" type="text" value="" label="Reference date for hybrid or branch runs (yyyy-mm-dd)"> <validator type="regex" message="YYYY-MM-DD">(^$|(\d{4}-(0[1-9]|1[0-2])-(0[1-9]|[12]\d|3[01])))</validator> </param> <param name="restart" type="data" format='tar' label="restart for running FATES EMERALD"></param> </when> <when value="hybrid"> <param name="run_refcase" type="text" value="" label="Reference case for hybrid or branch runs"></param> <param name="run_refdate" type="text" value="" label="Reference date for hybrid or branch runs (yyyy-mm-dd)"> <validator type="regex" message="YYYY-MM-DD">(^$|(\d{4}-(0[1-9]|1[0-2])-(0[1-9]|[12]\d|3[01])))</validator> </param> <param name="run_startdate" type="text" value="" label="Run start date (yyyy-mm-dd). Only used for startup or hybrid runs."> <validator type="regex" message="YYYY-MM-DD">(^$|(\d{4}-(0[1-9]|1[0-2])-(0[1-9]|[12]\d|3[01])))</validator> </param> <param name="restart" type="data" format='tar' label="restart for running FATES EMERALD"></param> </when> </conditional> <param name="stopn" type="integer" value="5" label="Provides a numerical count for STOP_OPTION."></param> <param name="stop_option" type="select" label=" Sets the run length along with STOP_N and STOP_DATE"> <option value="ndays" selected="true">ndays</option> <option value="none">none</option> <option value="never">never</option> <option value="nsteps">nsteps</option> <option value="nseconds">nseconds</option> <option value="nminutes">nminutes</option> <option value="nhours">nhours</option> <option value="nday">ndays</option> <option value="nmonths">nmonths</option> <option value="nyears">nyears</option> <option value="date">date</option> <option value="ifdays0">ifday0</option> <option value="end">end</option> </param> </section> <section name="adv_clm" title="CLM namelist customization" expanded="false"> <param name="use_fates_planthydro" type="boolean" label="Toggle to turn on plant hydraulics" truevalue=".true." falsevalue=".false." checked="false"/> <param name="use_fates_cohort_age_tracking" type="boolean" label="Toggle to turn on cohort age tracking" truevalue=".true." falsevalue=".false." checked="false"/> <param name="use_fates_ed_st3" type="boolean" label="Toggle to turn on Static Stand Structure Mode" truevalue=".true." falsevalue=".false." checked="false"/> <param name="use_fates_ed_prescribed_phys" type="boolean" label="Toggle to turn on prescribed physiology" truevalue=".true." falsevalue=".false." checked="false"/> <param name="use_fates_logging" type="boolean" label="Toggle to turn on the logging module" truevalue=".true." falsevalue=".false." checked="false"/> <param name="use_fates_fixed_biogeog" type="boolean" label="Toggle to turn on fixed biogeography mode" truevalue=".true." falsevalue=".false." checked="false"/> <param name="fates_spitfire_mode" type="select" label="Spitfire module to simulate fire"> <option value="0" selected="true">None</option> <option value="1">Use a global constant lightning rate found in fates_params</option> <option value="2">Use an external lightning dataset</option> <option value="3">Use an external confirmed ignitions dataset</option> <option value="4">Use external lightning and population datasets to simulate both natural and anthropogenic ignitions</option> </param> <param name="fates_parteh_mode" type="select" label="Switch deciding which nutrient model to use in FATES"> <option value="" selected="true">None</option> <option value="1">1</option> <option value="2">2</option> </param> </section> <section name="adv" title="Advanced customization" expanded="false"> <param name="co2" type="float" value="367.0" label="Atmospheric CO2 molar ratio (by volume) only used when co2_type==constant (umol/mol)"></param> <conditional name="condi_user_mods"> <param name="add_changes" type="select" label="user-modified source code"> <option value="no" selected="true">no</option> <option value="yes">yes</option> </param> <when value="yes"> <param name="usermods" type="data" format="tar" label="SourceMods"></param> </when> <when value="no"/> </conditional> </section> </inputs> <outputs> <collection name="history_files" type="list" label="${tool.name} on ${inputdata.name} (history file)"> <discover_datasets pattern="__designation_and_ext__" directory="output_dir" visible="true" format="netcdf"/> </collection> <data name="atm_log" format="txt" label="${tool.name} on ${inputdata.name} (atm.log)"/> <data name="cesm_log" format="txt" label="${tool.name} on ${inputdata.name} (cesm.log)"/> <data name="cpl_log" format="txt" label="${tool.name} on ${inputdata.name} (cpl.log)"/> <data name="lnd_log" format="txt" label="${tool.name} on ${inputdata.name} (lnd.log)"/> <data name="rof_log" format="txt" label="${tool.name} on ${inputdata.name} (rof.log)"/> <data name="restart" format="tar" label="${tool.name} on ${inputdata.name} (restart)"></data> <data name="case_info" format="txt" label="${tool.name} on ${inputdata.name} (case info)"></data> <data name="rinfo" format="txt" label="${tool.name} on ${inputdata.name} (restart info)"></data> <data name="work" format="tar" label="${tool.name} on ${inputdata.name} (workdir)"> </data> </outputs> <tests> <test> <param name="inputdata" value="inputdata_test.tar" /> <param name="casename" value="test" /> <param name="resolution" value="1x1_ALP1" /> <param name="run_startdate" value="2000-01-01" /> <param name="stop_option" value="nsteps" /> <param name="stopn" value="1" /> <output name="atm_log" ftype="txt" file="atm.log"> <assert_contents> <has_text text="(datm_comp_final) atm: end of main integration loop" /> </assert_contents> </output> <output name="cesm_log" ftype="txt" file="cesm.log"> <assert_contents> <has_text text="pes participating in computation for CLM" /> </assert_contents> </output> <output name="cpl_log" ftype="txt" file="cpl.log"> <assert_contents> <has_text text="SUCCESSFUL TERMINATION" /> </assert_contents> </output> <output name="lnd_log" ftype="txt" file="lnd.log"> <assert_contents> <has_text text="Successfully" /> </assert_contents> </output> <output name="rof_log" ftype="txt" file="rof.log"> <assert_contents> <has_text text="MOSART model initialization" /> </assert_contents> </output> <output name="case_info" ftype="txt" file="case_info.txt"> <assert_contents> <has_text text="MODEL BUILD HAS FINISHED SUCCESSFULLY" /> <has_line_matching expression="Submitted job" /> </assert_contents> </output> <output name="work" ftype="tar" file="workdir.tar"> <assert_contents> <has_size value="0"/> </assert_contents> </output> <output name="restart" ftype="tar" file="restart.tar" compare="sim_size" delta="100" /> <output name="rinfo" ftype="txt" file="restart_info.txt"> <assert_contents> <has_line_matching expression="*datm.r.2000-01-01-01800.nc*" /> <has_line_matching expression="*datm.rs1.2000-01-01-01800.bin*" /> <has_line_matching expression="*cpl.r.2000-01-01-01800.nc*" /> <has_line_matching expression="*clm2.r.2000-01-01-01800.nc*" /> </assert_contents> </output> <output_collection name="history_files" count="0"> </output_collection> </test> </tests> <help><![CDATA[ **The Functionally Assembled Terrestrial Ecosystem Simulator (FATES)** ========================================================================== This tool create and run CTSM-FATES EMERALD experiments from fates-emerald release. This version of FATES is maintained by the University of Oslo. Currently available resolution are as following: SeedClim Sites: ~~~~~~~~~~~~~~~ - ALP1,61.0243N,8.12343E - ALP2,60.8231N,7.27596E - ALP3,60.8328N,7.17561E - ALP4,60.9335N,6.41504E - SUB1,60.8203N,8.70466E - SUB2,60.8760N,7.17666E - SUB3,61.0866N,6.63028E - SUB4,60.5445N,6.51468E - BOR1,61.0355N,9.07876E - BOR2,60.8803N,7.16982E - BOR3,60.6652N,6.33738E - BOR4,60.6901N,5.96487E LandPress Sites: ~~~~~~~~~~~~~~~~ - LYG,60.70084N,5.092566E - BUO,65.83677N,12.224506E - HAV,64.779N,11.2193E - SKO,65.79602N,12.219299E Three-D Sites: ~~~~~~~~~~~~~~ - VIKE,60.88019N,7.16990E - JOAS,60.86183N,7.16800E - LIAH,60.85994N,7.19504E Finnmark Site: ~~~~~~~~~~~~~~ - FINN,69.341088N,25.293524E ]]></help> <citations> </citations> <edam_topics> <edam_topic>topic_3855</edam_topic> <edam_topic>topic_3318</edam_topic> <edam_topic>topic_3050</edam_topic> <edam_topic>topic_0610</edam_topic> </edam_topics> <edam_operations> <edam_operation>operation_3946</edam_operation> <edam_operation>operation_2426</edam_operation> </edam_operations> </tool>