comparison xarray_netcdf2netcdf.xml @ 0:b0780241f916 draft

"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"

0:b0780241f916

<tool id="xarray_netcdf2netcdf" name="NetCDF xarray operations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>manipulate xarray from netCDF and save back to netCDF</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <requirements>
        <requirement type="package" version="3">python</requirement>
        <requirement type="package" version="1.5.6">netcdf4</requirement>
        <requirement type="package" version="@TOOL_VERSION@">xarray</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    mkdir output_dir &&
    python '$__tool_directory__/xarray_netcdf2netcdf.py' '$input' '$var'
           --filter
    #for $i,$uc in enumerate($user_choice)
        #if $uc.condi_between.comparator=="sl"
             '${uc.dim}#${uc.condi_between.comparator}#${uc.condi_between.t1}#${uc.condi_between.t2}'
        #else
             '${uc.dim}#${uc.condi_between.comparator}#${uc.condi_between.value}'
        #end if
    #end for
    #if $scale
        --scale '$scale'
    #end if
    #if $write_all
         --write_all
    #end if
           --verbose
           --output '$output_netcdf'
    ]]></command>
    <inputs>
        <param type="data" name="input" label="Input netcdf file" format="netcdf"/>
        <param type="data" label="Tabular of variables" name="var_tab" format="tabular" help="Select the tabular file which summarize the available variables and dimensions."/>

        <param name="var" type="select" label="Choose the variable to extract">
            <options from_dataset="var_tab">
                <column name="name" index="0"/>
                <column name="value" index="0"/>
            </options>
        </param>

        <repeat name="user_choice" title="additional filter" min="0" max="20" help="Use this option to filter on the selected dataset">
            <param name="dim" type="select" label="Dimensions">
                <options from_dataset="var_tab">
                    <column name="value" index="0"/>
                </options>
            </param>
            <param type="data" label="Tabular containing values of this dimension" name="dim_tab" format="tabular" help="File containing values for this dimension."/>
            <conditional name="condi_between">
                <param name="comparator" type="select" label="Comparator">
                    <option value="is">is</option>
                    <option value="from">from</option>
                    <option value="to">to</option>
                    <option value="sl">slice(threshold1,threshold2)</option>
                </param>
                <when value="sl">
                    <param name="t1" type="select" multiple="false" label="Choose the start value for slice">
                        <options from_dataset="dim_tab">
                            <column name="name" index="1"/>
                            <column name="value" index="0"/>
                        </options>
                    </param>
                    <param name="t2" type="select" multiple="false" label="Choose the end value for slice">
                        <options from_dataset="dim_tab">
                            <column name="name" index="1"/>
                            <column name="value" index="0"/>
                        </options>
                    </param>
                </when>
                <when value="is">
                    <param name="value" type="select" multiple="false" label="Choose the value to select">
                        <options from_dataset="dim_tab">
                            <column name="name" index="1"/>
                            <column name="value" index="0"/>
                        </options>
                    </param>
                </when>
                <when value="to">
                    <param name="value" type="select" multiple="false" label="Choose the end value">
                        <options from_dataset="dim_tab">
                            <column name="name" index="1"/>
                            <column name="value" index="0"/>
                        </options>
                    </param>
                </when>
                <when value="from">
                    <param name="value" type="select" multiple="false" label="Choose the start value">
                        <options from_dataset="dim_tab">
                            <column name="name" index="1"/>
                            <column name="value" index="0"/>
                        </options>
                    </param>
                </when>
            </conditional>
        </repeat>
        <param type="float" name="scale" optional="true" help="scale factor (float) to apply to selection (optional)"/>
        
        <param name="write_all" type="boolean" value="false" label="Write all variables to new netCDF file"/>
    </inputs>
    <outputs>
        <data name="output_netcdf" format="netcdf"/>
    </outputs>
    <tests>
        <test>
             <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>
             <param name="var_tab" value="var_tab_dataset-ibi"/>
             <param name="var" value="chl"/>
             <repeat name="user_choice">
                 <param name="dim" value="time"/>
                 <conditional name="condi_between">
                     <param name="comparator" value="sl"/>
                     <param name="t1" value="10"/>
                     <param name="t2" value="12"/>
                 </conditional>
             </repeat>
             <repeat name="user_choice">
                 <param name="dim" value="latitude"/>
                 <param name="dim_tab" value="latitude.tabular"/>
                 <conditional name="condi_between">
                     <param name="comparator" value="sl"/>
                     <param name="t1" value="5"/>
                     <param name="t2" value="10"/>
                 </conditional>
             </repeat>
             <repeat name="user_choice">
                 <param name="dim" value="longitude"/>
                 <param name="dim_tab" value="longitude.tabular"/>
                 <conditional name="condi_between">
                     <param name="comparator" value="sl"/>
                     <param name="t1" value="4"/>
                     <param name="t2" value="10"/>
                 </conditional>
             </repeat>
             <param name="scale" value="1000.5"/>
             <output name="output_netcdf" file="small.netcdf" compare="sim_size" delat="1000"/>
        </test>
        <test>
             <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>
             <param name="var_tab" value="var_tab_dataset-ibi"/>
             <param name="var" value="chl"/>
             <repeat name="user_choice">
                 <param name="dim" value="time"/>
                 <conditional name="condi_between">
                     <param name="comparator" value="sl"/>
                     <param name="t1" value="10"/>
                     <param name="t2" value="12"/>
                 </conditional>
             </repeat>
             <repeat name="user_choice">
                 <param name="dim" value="latitude"/>
                 <param name="dim_tab" value="latitude.tabular"/>
                 <conditional name="condi_between">
                     <param name="comparator" value="sl"/>
                     <param name="t1" value="5"/>
                     <param name="t2" value="10"/>
                 </conditional>
             </repeat>
             <repeat name="user_choice">
                 <param name="dim" value="longitude"/>
                 <param name="dim_tab" value="longitude.tabular"/>
                 <conditional name="condi_between">
                     <param name="comparator" value="sl"/>
                     <param name="t1" value="4"/>
                     <param name="t2" value="10"/>
                 </conditional>
             </repeat>
             <param name="scale" value="1000.5"/>
             <param name="write_all" value="Yes"/> 
             <output name="output_netcdf" file="all.netcdf" compare="sim_size" delat="1000"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Select a variable ans can restrict over any of its dimension and apply a scaling (1 by default).
the result is stored in a new netCDF file.
One can also select the range of time (for timeseries) to apply these operations over the range only
when a range of time is selected and when scaling, one can choose to save the entire timeseries or
the selected range only.
when scaling, one can add additional filters on dimensions (typically used to filter 
over latitudes and longitudes)


-------------------------------------------------

The xarray select tool can be used after the xarray Info and xarray Coord.
    ]]></help>
    <expand macro="citations"/>
</tool>