comparison essential_climate_variables.xml @ 2:b9d9fe0c2ce7 draft

planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables commit 6045302c39c9c11fb6a73966a364cc395f2f9b28

1:8b30be2cef81

        <requirement type="package" version="0.1.4">cdsapi</requirement>
        <requirement type="package" version="1.9.6">cdo</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
       HOME=`pwd`  &&
       python3 '$__tool_directory__/ecv_retrieve.py'
            'ecv-for-climate-change' '$variable'
            --year '$year'
        #if str($time_aggregation.selector) == '1_month'
            --month '$time_aggregation.month'
        #else
            --month '01'
        #end if
           --time_aggregation '$time_aggregation.selector'
           --product_type '$product_type'
           --format 'tgz' --output 'tmp.tgz'
           --verbose                                       &&
           tar zxvf tmp.tgz                                &&
           cat *.grib > tmp.grib                           &&
           cdo -f nc -t ecmwf copy tmp.grib tmp.nc
    ]]></command>
    <inputs>
        <param name="variable" type="select" multiple="true" label="Variable(s)">
            <option value="surface_air_temperature" selected="true">Surface air temperature</option>
            <option value="surface_air_relative_humidity" selected="true">Surface air relative humidity</option>
            <option value="0_7cm_volumetric_soil_moisture" selected="true">0-7cm volumetric soil moisture</option>
            <option value="precipitation" selected="true">Precipitation</option>
            <option value="sea_ice" selected="true">Sea-ice</option>
        </param>
        <param name="product_type" type="select" label="Select type of data">
            <option value="climatology" selected="true">Climatology</option>
            <option value="anomaly">Anomaly</option>
        </param>
        <conditional name="time_aggregation">
            <param name="selector" type="select" label="Time aggregation">
                <option value="12_month" selected="true">yearly</option>
                <option value="1_month">monthly</option>
            </param>
            <when value="1_month">
                <param name="month" type="select" multiple="true" label="Select month(s)">
                    <option value="01" selected="true">January</option>
                    <option value="02" selected="true">February</option>
                    <option value="03" selected="true">March</option>
                    <option value="04" selected="true">April</option>
                    <option value="05" selected="true">May</option>
                    <option value="06" selected="true">June</option>
                    <option value="07" selected="true">July</option>
                    <option value="08" selected="true">August</option>
                    <option value="09" selected="true">September</option>
                    <option value="10" selected="true">October</option>
                    <option value="11" selected="true">November</option>
                    <option value="12" selected="true">December</option>
                </param>
            </when>
        </conditional>

        <param name="year" type="select" multiple="true"  label="Select year(s)">
            <option value="1979">1979</option>
            <option value="1980">1980</option>
            <option value="1981">1981</option>
            <option value="1982">1982</option>
            <option value="1983">1983</option>
            <option value="1984">1984</option>
            <option value="1985">1985</option>
            <option value="1986">1986</option>
            <option value="1987">1987</option>
            <option value="1988">1988</option>
            <option value="1989">1989</option>
            <option value="1990">1990</option>
            <option value="1991">1991</option>
            <option value="1992">1992</option>
            <option value="1993">1993</option>
            <option value="1994">1994</option>
            <option value="1995">1995</option>
            <option value="1996">1996</option>
            <option value="1997">1997</option>
            <option value="1998">1998</option>
            <option value="1999">1999</option>
            <option value="2000">2000</option>
            <option value="2001">2001</option>
            <option value="2002">2002</option>
            <option value="2003">2003</option>
            <option value="2004">2004</option>
            <option value="2005">2005</option>
            <option value="2006">2006</option>
            <option value="2007">2007</option>
            <option value="2008">2008</option>
            <option value="2009">2009</option>
            <option value="2010">2010</option>
            <option value="2011">2011</option>
            <option value="2012">2012</option>
            <option value="2013">2013</option>
            <option value="2014">2014</option>
            <option value="2015">2015</option>
            <option value="2016">2016</option>
            <option value="2017">2017</option>
            <option value="2018">2018</option>
            <option value="2019" selected="true">2019</option>
        </param>
    </inputs>
    <outputs>
        <data name="ofilename" format="netcdf" from_work_dir="tmp.nc"/>
    </outputs>
    <tests>
        <test>
            <param name="variable" value="0_7cm_volumetric_soil_moisture"/>
            <param name="product_type" value="climatology"/>
            <param name="time_aggregation" value="1_month"/>
            <param name="month" value="12"/>
            <param name="year" value="2018"/>
            <output name="ofilename" ftype="netcdf" file="soil_moisture.nc" compare="sim_size" delta="100"/>
        </test>
        <test>
            <param name="variable" value="precipitation,sea_ice"/>
            <param name="product_type" value="anomaly"/>
            <param name="time_aggregation" value="12_month"/>
            <param name="year" value="2017"/>
            <output name="ofilename" ftype="netcdf" file="prep_seaice.nc" compare="sim_size" delta="100"/>
        </test>
    </tests>
    <help><![CDATA[

2:b9d9fe0c2ce7

        <requirement type="package" version="0.1.4">cdsapi</requirement>
        <requirement type="package" version="1.9.6">cdo</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
       HOME=`pwd`  &&
       source \$COPERNICUS_CDSAPIRC_KEY_FILE 2> /dev/null | true &&
       python3 '$__tool_directory__/ecv_retrieve.py'
            'ecv-for-climate-change' '$variable'
            --month '$month'
        #if str($product_type.product) == 'monthly_mean'
            --year '$product_type.year'
            --time_aggregation '1_month'
        #else if str($product_type.product) == 'anomaly'
            --time_aggregation '$product_type.selector'
            --year '$product_type.year'
        #else
            --year '2018'
           --time_aggregation '1_month'
        #end if
           --product_type '$product_type.product'
           --format 'tgz' --output 'tmp.tgz'
           --verbose                                       &&
           tar zxvf tmp.tgz                                &&
           cat *.grib > tmpg.grib                          &&
           cdo remapcon,$adv.resol -setgridtype,regular tmpg.grib tmp.grib &&
           cdo -f nc -t ecmwf copy tmp.grib tmp.nc       
    ]]></command>
    <inputs>
        <param name="variable" type="select" multiple="true" label="Variable(s)">
            <option value="surface_air_temperature" selected="true">Surface air temperature</option>
            <option value="surface_air_relative_humidity" selected="true">Surface air relative humidity</option>
            <option value="0_7cm_volumetric_soil_moisture" selected="true">0-7cm volumetric soil moisture</option>
            <option value="precipitation" selected="true">Precipitation</option>
            <option value="sea_ice_cover" selected="true">Sea-ice cover</option>
        </param>
        <conditional name="product_type">
            <param name="product" type="select" label="Select type of data">
                <option value="monthly_mean" selected="true">Monthly mean</option>
                <option value="climatology">Climatology</option>
                <option value="anomaly">Anomaly</option>
            </param>
            <when value="monthly_mean">
                <param name="year" type="select" multiple="true"  label="Select year(s)">
                    <option value="1979">1979</option>
                    <option value="1980">1980</option>
                    <option value="1981">1981</option>
                    <option value="1982">1982</option>
                    <option value="1983">1983</option>
                    <option value="1984">1984</option>
                    <option value="1985">1985</option>
                    <option value="1986">1986</option>
                    <option value="1987">1987</option>
                    <option value="1988">1988</option>
                    <option value="1989">1989</option>
                    <option value="1990">1990</option>
                    <option value="1991">1991</option>
                    <option value="1992">1992</option>
                    <option value="1993">1993</option>
                    <option value="1994">1994</option>
                    <option value="1995">1995</option>
                    <option value="1996">1996</option>
                    <option value="1997">1997</option>
                    <option value="1998">1998</option>
                    <option value="1999">1999</option>
                    <option value="2000">2000</option>
                    <option value="2001">2001</option>
                    <option value="2002">2002</option>
                    <option value="2003">2003</option>
                    <option value="2004">2004</option>
                    <option value="2005">2005</option>
                    <option value="2006">2006</option>
                    <option value="2007">2007</option>
                    <option value="2008">2008</option>
                    <option value="2009">2009</option>
                    <option value="2010">2010</option>
                    <option value="2011">2011</option>
                    <option value="2012">2012</option>
                    <option value="2013">2013</option>
                    <option value="2014">2014</option>
                    <option value="2015">2015</option>
                    <option value="2016">2016</option>
                    <option value="2017">2017</option>
                    <option value="2018">2018</option>
                    <option value="2019" selected="true">2019</option>
                </param>
            </when>
            <when value="anomaly">
                <param name="year" type="select" multiple="true"  label="Select year(s)">
                    <option value="1979">1979</option>
                    <option value="1980">1980</option>
                    <option value="1981">1981</option>
                    <option value="1982">1982</option>
                    <option value="1983">1983</option>
                    <option value="1984">1984</option>
                    <option value="1985">1985</option>
                    <option value="1986">1986</option>
                    <option value="1987">1987</option>
                    <option value="1988">1988</option>
                    <option value="1989">1989</option>
                    <option value="1990">1990</option>
                    <option value="1991">1991</option>
                    <option value="1992">1992</option>
                    <option value="1993">1993</option>
                    <option value="1994">1994</option>
                    <option value="1995">1995</option>
                    <option value="1996">1996</option>
                    <option value="1997">1997</option>
                    <option value="1998">1998</option>
                    <option value="1999">1999</option>
                    <option value="2000">2000</option>
                    <option value="2001">2001</option>
                    <option value="2002">2002</option>
                    <option value="2003">2003</option>
                    <option value="2004">2004</option>
                    <option value="2005">2005</option>
                    <option value="2006">2006</option>
                    <option value="2007">2007</option>
                    <option value="2008">2008</option>
                    <option value="2009">2009</option>
                    <option value="2010">2010</option>
                    <option value="2011">2011</option>
                    <option value="2012">2012</option>
                    <option value="2013">2013</option>
                    <option value="2014">2014</option>
                    <option value="2015">2015</option>
                    <option value="2016">2016</option>
                    <option value="2017">2017</option>
                    <option value="2018" selected="true">2018</option>
                </param>
                <param name="selector" type="select" label="Time aggregation">
                    <option value="12_month" selected="true">yearly</option>
                    <option value="1_month">monthly</option>
                </param>
            </when>
        </conditional>
        <param name="month" type="select" multiple="true" label="Select month(s)">
            <option value="01" selected="true">January</option>
            <option value="02" selected="true">February</option>
            <option value="03" selected="true">March</option>
            <option value="04" selected="true">April</option>
            <option value="05" selected="true">May</option>
            <option value="06" selected="true">June</option>
            <option value="07" selected="true">July</option>
            <option value="08" selected="true">August</option>
            <option value="09" selected="true">September</option>
            <option value="10" selected="true">October</option>
            <option value="11" selected="true">November</option>
            <option value="12" selected="true">December</option>
        </param>

        <section name="adv" title="Advanced Options" expanded="false">
            <param name="resol" type="select" label="Resolution">
                <option value="r1440x720" selected="true">high</option>
                <option value="r144x72">low</option>
            </param>
        </section>
    </inputs>
    <outputs>
        <data name="ofilename" format="netcdf" from_work_dir="tmp.nc"/>
    </outputs>
    <tests>
        <test>
            <param name="variable" value="0_7cm_volumetric_soil_moisture"/>
            <conditional name="product_type">
                <param name="product" value="monthly_mean"/>
                <param name="year" value="2018"/>
            </conditional>
            <param name="month" value="12"/>
            <param name="resol" value="r144x72"/>
            <output name="ofilename" ftype="netcdf" file="soil_moisture.nc" compare="sim_size" delta="100"/>
        </test>
        <test>
            <param name="variable" value="precipitation"/>
            <conditional name="product_type">
                <param name="product" value="anomaly"/>
                <param name="year" value="2017"/>
                <param name="time_aggregation" value="12_month"/>
            </conditional>
            <param name="month" value="12"/>
            <param name="resol" value="r144x72"/>
            <output name="ofilename" ftype="netcdf" file="prep_seaice.nc" compare="sim_size" delta="100"/>
        </test>
    </tests>
    <help><![CDATA[