annotate essential_climate_variables.xml @ 3:b261160f10ee draft

planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables commit 9a4156ff5fe0c74f33b115cf62c6d5c5732ee895

<tool id="cds_essential_variability" name="Copernicus Essential Climate Variables" version="0.1.4">
    <description>for assessing climate variability</description>
    <requirements>
        <requirement type="package" version="3">python</requirement>
        <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`  &&
       cp \$COPERNICUS_CDSAPIRC_KEY_FILE .cdsapirc | 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[

**Copernicus Essential climate variables for assessment of climate variability from 1979 to present**
=======================================================================================================

This tool is a wrapper to retrieve Copernicus Essential Climate Variables.
It corresponds to the European Contribution to the Monitoring of Essential Climate Variables from Space.
An Essential Climate Variable is a physical, chemical or biological variable or a group of linked variables
that critically contributes to the characterization of Earth’ s climate.

The Essential Climate Variables for assessment of climate variability from 1979 to present dataset contains
a selection of climatologies and monthly anomalies of Essential Climate Variables (ECVs) suitable for
monitoring and assessment of climate variability and change. Selection criteria are based on accuracy
and temporal consistency on monthly to decadal time scales. The ECV data products in this set have been
estimated from multiple sources and, depending on the source, may have been adjusted to account for biases
and other known deficiencies. Data sources and adjustment methods used are described in the Product User
Guide, as are various particulars such as the baseline periods used to calculate monthly climatologies and
the corresponding anomalies.


- ECV Factsheets: https://gcos.wmo.int/en/essential-climate-variables/ecv-factsheets
- Copernicus Climate Data Store documentation on Essential Climate Variables:
  https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview

  See climatedata.wmo.int/ for more information on Essential Climate Variables.

.. class:: infomark

   It allows to retrieve estimates of Essential Climate Variables (ECVs)
   derived from Earth observations.

License:
~~~~~~~~
   Copernicus License V1.1

   Generated using Copernicus Climate Change Service information [2019].
   Neither the European Commission nor ECMWF is responsible for any use 
   that may be made of the Copernicus information or data it contains.

    ]]></help>
    <citations>
        <citation type="doi">10.1002/qj.828</citation>
        <citation type="doi">10.1002/qj.2949</citation>
    </citations>
</tool>