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Commit message:
planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables commit 6045302c39c9c11fb6a73966a364cc395f2f9b28 |
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modified:
README.md ecv_retrieve.py essential_climate_variables.xml test-data/prep_seaice.nc test-data/soil_moisture.nc |
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| diff -r 8b30be2cef81 -r b9d9fe0c2ce7 README.md --- a/README.md Tue May 07 03:26:08 2019 -0400 +++ b/README.md Sun Jun 23 11:16:11 2019 -0400 |
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| @@ -9,9 +9,23 @@ The CDS API Key needs to be: - located in a file called `.cdsapirc`in the HOME area - (as defined the `HOME` environment variable). - - or passed in an enviroment variable called `GALAXY_COPERNICUS_CDSAPIRC`. - When passed in `GALAXY_COPERNICUS_CDSAPIRC`, make sure the key does not contain - the string `key: ` but the key itself only (starting with a number). The file - `.cdsapirc` will then be created and placed in the HOME area (using HOME - environment variable). + (as defined the `HOME` environment variable). + The file `.cdsapirc` should look like that: + +``` +url: https://cds.climate.copernicus.eu/api/v2 +key: 111:8789787-qwerz4e47-888-not-real +verify: 0 +``` + - or passed in an enviroment variable called `GALAXY_COPERNICUS_CDSAPIRC_KEY`. + This environment variable should contain a string that looks like that: +``` +111:8789787-qwerz4e47-888-not-real +``` + When passed in `GALAXY_COPERNICUS_CDSAPIRC_KEY`, make sure the key does not + contain the string `key: ` but the key itself only (starting with a number). + The file `.cdsapirc` will then be created and placed in the HOME area (using + HOME environment variable). + - or use `GALAXY_COPERNICUS_CDSAPIRC_KEY_FILE` to specify where your key file + is stored on your system. + |
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| diff -r 8b30be2cef81 -r b9d9fe0c2ce7 ecv_retrieve.py --- a/ecv_retrieve.py Tue May 07 03:26:08 2019 -0400 +++ b/ecv_retrieve.py Sun Jun 23 11:16:11 2019 -0400 |
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| @@ -34,7 +34,11 @@ self.time_aggregation = '1_month' else: self.time_aggregation = time_aggregation - self.area = area + if area == '': + self.area = 'global' + else: + self.area = area + if format == '': self.format = 'tgz' else: @@ -57,6 +61,7 @@ 'variable': self.variable, 'year': self.year, 'month': self.month, + 'origin': 'era5', 'area': self.area, 'format': self.format, 'product_type': self.product_type, |
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| diff -r 8b30be2cef81 -r b9d9fe0c2ce7 essential_climate_variables.xml --- a/essential_climate_variables.xml Tue May 07 03:26:08 2019 -0400 +++ b/essential_climate_variables.xml Sun Jun 23 11:16:11 2019 -0400 |
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| b'@@ -7,21 +7,27 @@\n </requirements>\n <command detect_errors="exit_code"><![CDATA[\n HOME=`pwd` &&\n+ source \\$COPERNICUS_CDSAPIRC_KEY_FILE 2> /dev/null | true &&\n python3 \'$__tool_directory__/ecv_retrieve.py\'\n \'ecv-for-climate-change\' \'$variable\'\n- --year \'$year\'\n- #if str($time_aggregation.selector) == \'1_month\'\n- --month \'$time_aggregation.month\'\n+ --month \'$month\'\n+ #if str($product_type.product) == \'monthly_mean\'\n+ --year \'$product_type.year\'\n+ --time_aggregation \'1_month\'\n+ #else if str($product_type.product) == \'anomaly\'\n+ --time_aggregation \'$product_type.selector\'\n+ --year \'$product_type.year\'\n #else\n- --month \'01\'\n+ --year \'2018\'\n+ --time_aggregation \'1_month\'\n #end if\n- --time_aggregation \'$time_aggregation.selector\'\n- --product_type \'$product_type\'\n+ --product_type \'$product_type.product\'\n --format \'tgz\' --output \'tmp.tgz\'\n --verbose &&\n tar zxvf tmp.tgz &&\n- cat *.grib > tmp.grib &&\n- cdo -f nc -t ecmwf copy tmp.grib tmp.nc\n+ cat *.grib > tmpg.grib &&\n+ cdo remapcon,$adv.resol -setgridtype,regular tmpg.grib tmp.grib &&\n+ cdo -f nc -t ecmwf copy tmp.grib tmp.nc \n ]]></command>\n <inputs>\n <param name="variable" type="select" multiple="true" label="Variable(s)">\n@@ -29,78 +35,129 @@\n <option value="surface_air_relative_humidity" selected="true">Surface air relative humidity</option>\n <option value="0_7cm_volumetric_soil_moisture" selected="true">0-7cm volumetric soil moisture</option>\n <option value="precipitation" selected="true">Precipitation</option>\n- <option value="sea_ice" selected="true">Sea-ice</option>\n+ <option value="sea_ice_cover" selected="true">Sea-ice cover</option>\n </param>\n- <param name="product_type" type="select" label="Select type of data">\n- <option value="climatology" selected="true">Climatology</option>\n- <option value="anomaly">Anomaly</option>\n- </param>\n- <conditional name="time_aggregation">\n- <param name="selector" type="select" label="Time aggregation">\n- <option value="12_month" selected="true">yearly</option>\n- <option value="1_month">monthly</option>\n+ <conditional name="product_type">\n+ <param name="product" type="select" label="Select type of data">\n+ <option value="monthly_mean" selected="true">Monthly mean</option>\n+ <option value="climatology">Climatology</option>\n+ <option value="anomaly">Anomaly</option>\n </param>\n- <when value="1_month">\n- <param name="month" type="select" multiple="true" label="Select month(s)">\n- <option value="01" selected="true">January</option>\n- <option value="02" selected="true">February</option>\n- <option value="03" selected="true">March</option>\n- <option value="04" selected="true">April</option>\n- <option value="05" selected="true">May</option>\n- <option value="06" selected="true">June</option>\n- <option value="07" selected="true">July</option>\n- <option value="08" selected="true">August</option>\n- <option value="09" selected="true">September</option>\n- <option value="10" selected="true">October</option>\n- <option value="11" selected="true">November</option>\n- <option value="12" selected="true">December</option>\n+ <when value="monthly_mean'..b' <param name="year" type="select" multiple="true" label="Select year(s)">\n- <option value="1979">1979</option>\n- <option value="1980">1980</option>\n- <option value="1981">1981</option>\n- <option value="1982">1982</option>\n- <option value="1983">1983</option>\n- <option value="1984">1984</option>\n- <option value="1985">1985</option>\n- <option value="1986">1986</option>\n- <option value="1987">1987</option>\n- <option value="1988">1988</option>\n- <option value="1989">1989</option>\n- <option value="1990">1990</option>\n- <option value="1991">1991</option>\n- <option value="1992">1992</option>\n- <option value="1993">1993</option>\n- <option value="1994">1994</option>\n- <option value="1995">1995</option>\n- <option value="1996">1996</option>\n- <option value="1997">1997</option>\n- <option value="1998">1998</option>\n- <option value="1999">1999</option>\n- <option value="2000">2000</option>\n- <option value="2001">2001</option>\n- <option value="2002">2002</option>\n- <option value="2003">2003</option>\n- <option value="2004">2004</option>\n- <option value="2005">2005</option>\n- <option value="2006">2006</option>\n- <option value="2007">2007</option>\n- <option value="2008">2008</option>\n- <option value="2009">2009</option>\n- <option value="2010">2010</option>\n- <option value="2011">2011</option>\n- <option value="2012">2012</option>\n- <option value="2013">2013</option>\n- <option value="2014">2014</option>\n- <option value="2015">2015</option>\n- <option value="2016">2016</option>\n- <option value="2017">2017</option>\n- <option value="2018">2018</option>\n- <option value="2019" selected="true">2019</option>\n- </param>\n+ <section name="adv" title="Advanced Options" expanded="false">\n+ <param name="resol" type="select" label="Resolution">\n+ <option value="r1440x720" selected="true">high</option>\n+ <option value="r144x72">low</option>\n+ </param>\n+ </section>\n </inputs>\n <outputs>\n <data name="ofilename" format="netcdf" from_work_dir="tmp.nc"/>\n@@ -108,17 +165,23 @@\n <tests>\n <test>\n <param name="variable" value="0_7cm_volumetric_soil_moisture"/>\n- <param name="product_type" value="climatology"/>\n- <param name="time_aggregation" value="1_month"/>\n+ <conditional name="product_type">\n+ <param name="product" value="monthly_mean"/>\n+ <param name="year" value="2018"/>\n+ </conditional>\n <param name="month" value="12"/>\n- <param name="year" value="2018"/>\n+ <param name="resol" value="r144x72"/>\n <output name="ofilename" ftype="netcdf" file="soil_moisture.nc" compare="sim_size" delta="100"/>\n </test>\n <test>\n- <param name="variable" value="precipitation,sea_ice"/>\n- <param name="product_type" value="anomaly"/>\n- <param name="time_aggregation" value="12_month"/>\n- <param name="year" value="2017"/>\n+ <param name="variable" value="precipitation"/>\n+ <conditional name="product_type">\n+ <param name="product" value="anomaly"/>\n+ <param name="year" value="2017"/>\n+ <param name="time_aggregation" value="12_month"/>\n+ </conditional>\n+ <param name="month" value="12"/>\n+ <param name="resol" value="r144x72"/>\n <output name="ofilename" ftype="netcdf" file="prep_seaice.nc" compare="sim_size" delta="100"/>\n </test>\n </tests>\n' |
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| diff -r 8b30be2cef81 -r b9d9fe0c2ce7 test-data/prep_seaice.nc |
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| diff -r 8b30be2cef81 -r b9d9fe0c2ce7 test-data/soil_moisture.nc |
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| Binary file test-data/soil_moisture.nc has changed |