annotate cdo_operations.xml @ 0:d5355f6fa02b draft default tip

"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo commit da614bb8e3e9b19a5167ff19b625a71d9976108a"

<tool id="cdo_operations" name="CDO Operations" profile="20.05" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>Climate Data Manipulation Operators operations for standard processing of climate and NWP model output.</description>
    <macros>
        <import>macros.xml</import>
        <import>macros_operations.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <expand macro="cdo_requirements"/>
    <expand macro="cdo_stdio"/>
    <command detect_errors="exit_code"><![CDATA[
        mkdir output_dir &&
        cdo 
        #for $i, $cdo_option in enumerate( $section_option )
            #if $cdo_option.option_type.add_opt == '-f'
                $cdo_option.option_type.add_opt $cdo_option.option_type.output_format
            #elif $cdo_option.option_type.add_opt == '-g'
                $cdo_option.option_type.add_opt $cdo_option.option_type.grid
            #elif $cdo_option.option_type.add_opt == '-gf'
                $cdo_option.option_type.add_opt $cdo_option.option_type.gridfile
            #elif $cdo_option.option_type.add_opt == '-m'
                $cdo_option.option_type.add_opt $cdo_option.option_type.missval
            #elif $cdo_option.option_type.add_opt == '--percentile'
                $cdo_option.option_type.add_opt $cdo_option.option_type.percentile
            #elif $cdo_option.option_type.add_opt == '--seed'
                $cdo_option.option_type.add_opt $cdo_option.option_type.seed
            #else
                $cdo_option.option_type.add_opt
            #end if
        #end for
        #for $i, $cdo_oper in enumerate( $section_operators )
            #if $cdo_oper.operator.opt == 'duplicate'
                -'$cdo_oper.operator.opt',$cdo_oper.operator.ndup
            #elif $cdo_oper.operator.opt == 'addc' or $cdo_oper.operator.opt == 'subc' or $cdo_oper.operator.opt == 'mulc' or $cdo_oper.operator.opt == 'divc'
                -'$cdo_oper.operator.opt',$cdo_oper.operator.const_value
	    #elif $cdo_oper.operator.opt == 'ens' or $cdo_oper.operator.opt == 'zon' or  $cdo_oper.operator.opt == 'tim' or  $cdo_oper.operator.opt == 'vert' or  $cdo_oper.operator.opt == 'day' or  $cdo_oper.operator.opt == 'year' or  $cdo_oper.operator.opt == 'mon' or  $cdo_oper.operator.opt == 'seas' or $cdo_oper.operator.opt == 'fld'
                -'${cdo_oper.operator.opt}${cdo_oper.operator.stat}'
	    #elif $cdo_oper.operator.opt == 'sp2gp' or $cdo_oper.operator.opt == 'gp2sp'
                #if $cdo_oper.operator.trunc > 0
                    -'$cdo_oper.operator.opt',$cdo_oper.operator.trunc
                #else
                    -'$cdo_oper.operator.opt'
                #end if
            #elif $cdo_oper.operator.opt == 'collgrid'
                #if str($cdo_oper.operator.nx)
                    #if str($cdo_oper.operator.names)
                        -'$cdo_oper.operator.opt',$cdo_oper.operator.nx,'$cdo_oper.operator.names'
                    #else
                        -'$cdo_oper.operator.opt',$cdo_oper.operator.nx
                    #end if
                #else
                    -'$cdo_oper.operator.opt'
                #end if
            #elif $cdo_oper.operator.opt == 'distgrid'
                -'$cdo_oper.operator.opt',$cdo_oper.operator.nx,$cdo_oper.operator.ny
            #elif $cdo_oper.operator.opt == 'splitsel'
                    #if str($cdo_oper.operator.noffset)
                        #if str($cdo_oper.operator.nskip)
                            -'$cdo_oper.operator.opt',$cdo_oper.operator.nsets,$cdo_oper.operator.noffset,$cdo_oper.operator.nskip
                        #else
                            -'$cdo_oper.operator.opt',$cdo_oper.operator.nsets,$cdo_oper.operator.noffset
                        #end if
                    #else
                        -'$cdo_oper.operator.opt',$cdo_oper.operator.nsets
                    #end if
            #elif $cdo_oper.operator.opt == 'select' or $cdo_oper.operator.opt == 'delete' or $cdo_oper.operator.opt == 'selname' or $cdo_oper.operator.opt == 'delname' or  $cdo_oper.operator.opt == 'seltimestep' or $cdo_oper.operator.opt == 'sellonlatbox' or $cdo_oper.operator.opt == 'expr' or $cdo_oper.operator.opt == 'ml2pl' or $cdo_oper.operator.opt == 'ml2hl' or $cdo_oper.operator.opt == 'intlevel'
                -'$cdo_oper.operator.opt','$cdo_oper.operator.params'
            #elif $cdo_oper.operator.opt == 'setattribute'
                -'$cdo_oper.operator.opt',FILE='$cdo_oper.operator.attr_file'
            #else
                -'$cdo_oper.operator.opt'
            #end if
            #if $cdo_oper.operator.opt == 'copy' or $cdo_oper.operator.opt == 'cat' or $cdo_oper.operator.opt == 'merge' or $cdo_oper.operator.opt == 'mergetime' or $cdo_oper.operator.opt == 'collgrid' or $cdo_oper.operator.opt == 'select' or $cdo_oper.operator.opt == 'delete' or $cdo_oper.operator.opt == 'replace'
                #for $ifile in $cdo_oper.operator.add_file
                    '${ifile}'
                #end for
            #elif $cdo_oper.operator.add_file and '$cdo_oper.operator.add_file' != '' and '$cdo_oper.operator.add_file' != 'None' and $cdo_oper.operator.add_file is not None
                '$cdo_oper.operator.add_file'
            #end if
            #if $i == 0
                #if $cdo_oper.operator.opt == 'splitcode' or $cdo_oper.operator.opt == 'splitparam' or $cdo_oper.operator.opt == 'splitname' or $cdo_oper.operator.opt == 'splitlevel' or $cdo_oper.operator.opt == 'splitgrid' or  $cdo_oper.operator.opt == 'splitzaxis' or $cdo_oper.operator.opt == 'splittabnum' or $cdo_oper.operator.opt == 'splithour' or $cdo_oper.operator.opt == 'splitday' or $cdo_oper.operator.opt == 'splitseas' or $cdo_oper.operator.opt == 'splityear' or $cdo_oper.operator.opt == 'splityearmon' or $cdo_oper.operator.opt == 'splitmon' 
                    #set output = 'output_dir/outfile_'
                #else
                    #set output = 'output_dir/outfile.netcdf'
                #end if
            #end if
        #end for
        '${output}'
    ]]>    </command>
    <inputs>
        <repeat name="section_operators" title="CDO Operators" min="1" max="10">
            <expand macro="cdo_operator"/>
        </repeat>
        <repeat name="section_option" title="CDO Options" min="0" max="5">
            <expand macro="cdo_option"/>
        </repeat>
    </inputs>
    <outputs>
        <collection name="output_files" type="list" label="${tool.name} outfiles">
            <discover_datasets pattern="__name__" directory="output_dir" visible="true" format="netcdf"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <conditional name="operator">
                <param name="opt" value="select" />
                <param name="params" value="name=Drops" />
                <param name="add_file" value="WMI_Lear.nc" ftype="netcdf" />
            </conditional>
            <output_collection name="output_files" type="list" count="1">
                <element name="outfile.netcdf" ftype="netcdf" file="drops1.nc" compare="sim_size" delta="50"/>
            </output_collection>
        </test>
        <test>
            <conditional name="operator">
                <param name="opt" value="copy" />
                <param name="add_file" value="WMI_Lear.nc" ftype="netcdf" />
            </conditional>
            <output_collection name="output_files" type="list" count="1">
                <element name="outfile.netcdf" ftype="netcdf" file="WMI_Lear_copy.nc" compare="sim_size" delta="50"/>
            </output_collection>
        </test>
        <test>
            <conditional name="operator">
                <param name="opt" value="cat" />
                <param name="add_file" value="drops1.nc,drops2.nc" ftype="netcdf" />
            </conditional>
            <output_collection name="output_files" type="list" count="1">
                <element name="outfile.netcdf" ftype="netcdf" file="drops_cat.nc" compare="sim_size" delta="50"/>
            </output_collection>
        </test>
        <test>
            <conditional name="operator">
                <param name="opt" value="splitname" />
                <param name="add_file" value="lat_long.nc" ftype="netcdf" />
            </conditional>
            <output_collection name="output_files" type="list" count="2"/>
        </test>
        <test>
            <conditional name="operator">
                <param name="opt" value="replace" />
                <param name="add_file" value="lat_long.nc,latitude_modified.nc" ftype="netcdf" />
            </conditional>
            <output_collection name="output_files" type="list" count="1">
                <element name="outfile.netcdf" ftype="netcdf" file="lat_long_modified.nc" compare="sim_size" delta="50"/>
            </output_collection>
        </test>
        <test>
            <conditional name="operator">
                <param name="opt" value="duplicate" />
                <param name="ndup" value="3" ftype="integer" />
                <param name="add_file" value="latitude.nc" ftype="netcdf" />
            </conditional>
            <output_collection name="output_files" type="list" count="1">
                <element name="outfile.netcdf" ftype="netcdf" file="latitude3.nc" compare="sim_size" delta="50"/>
            </output_collection>
        </test>
        <test>
            <conditional name="operator">
                <param name="opt" value="selname" />
                <param name="add_file" value="WMI_Lear.nc" ftype="netcdf" />
                <param name="params" value="Drops" />
            </conditional>
            <output_collection name="output_files" type="list" count="1">
                <element name="outfile.netcdf" ftype="netcdf" file="drops1.nc" compare="sim_size" delta="50"/>
            </output_collection>
        </test>
        <test>
            <conditional name="operator">
                <param name="opt" value="seltimestep" />
                <param name="add_file" value="WMI_Lear.nc" ftype="netcdf" />
                <param name="params" value="1,13,25" />
            </conditional>
            <output_collection name="output_files" type="list" count="1">
                <element name="outfile.netcdf" ftype="netcdf" file="WMI_Lear_timesteps.nc" compare="sim_size" delta="50"/>
            </output_collection>
        </test>
        <test>
            <conditional name="operator">
                <param name="opt" value="sellonlatbox" />
                <param name="add_file" value="WMI_Lear.nc" ftype="netcdf" />
                <param name="params" value="-10,10,60,70" />
            </conditional>
            <output_collection name="output_files" type="list" count="1">
                <element name="outfile.netcdf" ftype="netcdf" file="WMI_Lear_sellonlatbox.nc" compare="sim_size" delta="50"/>
            </output_collection>
        </test>
        <test>
            <conditional name="operator">
                <param name="opt" value="invertlat" />
                <param name="add_file" value="WMI_Lear.nc" ftype="netcdf" />
            </conditional>
            <output_collection name="output_files" type="list" count="1">
                <element name="outfile.netcdf" ftype="netcdf" file="WMI_Lear_invertlat.nc" compare="sim_size" delta="50"/>
            </output_collection>
        </test>
        <test>
            <repeat name="section_operators">
                <conditional name="operator">
                    <param name="opt" value="selname" />
                    <param name="params" value="Drops" />
                </conditional>
            </repeat>
            <repeat name="section_operators">
                <conditional name="operator">
                    <param name="opt" value="addc" />
                    <param name="const_value" value="10.5" />
                    <param name="add_file" value="WMI_Lear.nc" ftype="netcdf" />
                </conditional>
            </repeat>
            <output_collection name="output_files" type="list" count="1">
                <element name="outfile.netcdf" ftype="netcdf" file="WMI_Lear_addc.nc" compare="sim_size" delta="50"/>
            </output_collection>
        </test>
        <test>
            <conditional name="operator">
                <param name="opt" value="expr" />
                <param name="params" value="Drops2=1000*exp(1+Drops)" />
                <param name="add_file" value="WMI_Lear.nc" ftype="netcdf" />
            </conditional>
            <output_collection name="output_files" type="list" count="1">
                <element name="outfile.netcdf" ftype="netcdf" file="WMI_Lear_expr.nc" compare="sim_size" delta="50"/>
            </output_collection>
        </test>
        <test>
            <repeat name="section_operators">
                <conditional name="operator">
                    <param name="opt" value="selname" />
                    <param name="params" value="CLEAR_SKY_BHI" />
                </conditional>
            </repeat>
            <repeat name="section_operators">
                <conditional name="operator">
                    <param name="opt" value="tim" />
                    <param name="stat" value="avg" />
                    <param name="add_file" value="timeseries.nc" ftype="netcdf" />
                </conditional>
            </repeat>
            <output_collection name="output_files" type="list" count="1">
                <element name="outfile.netcdf" ftype="netcdf" file="timeseries_timavg.nc" compare="sim_size" delta="50"/>
            </output_collection>
        </test>
        <test>
            <repeat name="section_operators">
                <conditional name="operator">
                    <param name="opt" value="sub" />
                    <param name="add_file" value="timeseries.nc" ftype="netcdf" />
                </conditional>
            </repeat>
            <repeat name="section_operators">
                <conditional name="operator">
                    <param name="opt" value="addc" />
                    <param name="const_value" value="10.5" />
                    <param name="add_file" value="timeseries.nc" ftype="netcdf" />
                </conditional>
            </repeat>
            <output_collection name="output_files" type="list" count="1">
                <element name="outfile.netcdf" ftype="netcdf" file="timeseries_sub.nc" compare="sim_size" delta="50"/>
            </output_collection>
        </test>
        <test>
            <repeat name="section_operators">
                <conditional name="operator">
                    <param name="opt" value="sellonlatbox" />
                    <param name="params" value="-10,10,60,70" />
                </conditional>
            </repeat>
            <repeat name="section_operators">
                <conditional name="operator">
                    <param name="opt" value="setattribute" />
                    <param name="attr_file" value="attributes.txt" />
                    <param name="add_file" value="WMI_Lear.nc" ftype="netcdf" />
                </conditional>
            </repeat>
            <output_collection name="output_files" type="list" count="1">
                <element name="outfile.netcdf" ftype="netcdf" file="WMI_Lear_sellonlatbox_units.nc" compare="sim_size" delta="50"/>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[

**Climate Data Operators (CDO)**
=======================================================================================================

This tool is a wrapper to the Climate Data Operators (CDO) for all operators manipulating input files and creating a new output file.

- CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.
- There are more than 600 operators available.

- `CDO online documentation <https://code.mpimet.mpg.de/projects/cdo/>`_.

    ]]>    </help>
    <expand macro="citations"/>
</tool>