annotate xarray_select.xml @ 0:225d0d275a24 draft

"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit f1455c158011dc4aab0fd469cf794be6f4142992"

<tool id="xarray_select" name="NetCDF xarray Selection" version="0.15.1">
    <description>extracts variable values with custom conditions on dimensions</description>
    <requirements>
        <requirement type="package" version="3">python</requirement>
        <requirement type="package" version="1.5.3">netcdf4</requirement>
        <requirement type="package" version="0.15.1">xarray</requirement>
        <requirement type="package" version="0.7.0">geopandas</requirement>
        <requirement type="package" version="1.7.0">shapely</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    mkdir output_dir &&
    python '$__tool_directory__/xarray_tool.py' '$input' --select '$var'
           --verbose
           --filter
    #for $i,$uc in enumerate($user_choice)
        #if $uc.condi_between.comparator=="bi"
             '${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 $time.condi_datetime.datetime=="yes"
         --time
        #if $time.condi_datetime.condi_between.comparator=="sl"
             '${time.condi_datetime.dim}#${time.condi_datetime.condi_between.comparator}#${time.condi_datetime.condi_between.t1}#${time.condi_datetime.condi_between.t2}'
        #else
             '${time.condi_datetime.dim}#${time.condi_datetime.condi_between.comparator}#${time.condi_datetime.condi_between.t1}'
        #end if
    #end if

    #if $condi_source_coord.coord_source=="coord_from_file"
         --coords '$coord_tabular'
         --latname '$condi_source_coord.lat_dim' --lonname '$condi_source_coord.lon_dim'
         --outputdir output_dir
    #else
         --outfile 'final.tabular'
        #if $condi_source_coord.condi_coord.coord=='single'
           --latname $condi_source_coord.condi_coord.lat_dim
           --latvalN $condi_source_coord.condi_coord.lat_val
           --lonname $condi_source_coord.condi_coord.lon_dim
           --lonvalE $condi_source_coord.condi_coord.lon_val
        #elif $condi_source_coord.condi_coord.coord=='subregion'
           --latname $condi_source_coord.condi_coord.lat_dim
           --latvalN $condi_source_coord.condi_coord.lat_valN
           --latvalS $condi_source_coord.condi_coord.lat_valS
           --lonname $condi_source_coord.condi_coord.lon_dim
           --lonvalE $condi_source_coord.condi_coord.lon_valE
           --lonvalW $condi_source_coord.condi_coord.lon_valW
        #end if
    #end if
    ]]></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>

        <conditional name="condi_source_coord">
            <param name="coord_source" type="select" label="Source of coordinates">
                <option value="coord_from_stdin">Manually enter coordinates</option>
                <option value="coord_from_file">Use coordinates from input file</option>
            </param>

            <when value="coord_from_file">
                <param type="data" label="Tabular of coord" name="coord_tabular" format="tabular" help="Format : Latitude	Longitude"/>
                <param name="lat_dim" type="select" label="Name of latitude coordinate" >
                    <options from_dataset="var_tab">
                        <column name="value" index="0"/>
                    </options>
                </param>
                <param name="lon_dim" type="select" label="Name of longitude coordinate" >
                    <options from_dataset="var_tab">
                        <column name="value" index="0"/>
                    </options>
                </param>
            </when>

            <when value="coord_from_stdin">
                <conditional name="condi_coord">
                    <param name="coord" type="select" label="Geographical area" help="Use this option to get valid values at your custom coordinates.">
                        <option value="global">Whole available region</option>
                        <option value="single">Single location</option>
                        <option value="subregion">Sub-region extraction</option>
                    </param>
                    <when value="single">
                        <param name="lat_dim" type="select" label="Name of latitude coordinate" >
                            <options from_dataset="var_tab">
                                <column name="value" index="0"/>
                            </options>
                        </param>
                        <param name="lat_val" type="float" value="0" label="Latitude"/>
                        <param name="lon_dim" type="select" label="Name of longitude coordinate" >
                            <options from_dataset="var_tab">
                                <column name="value" index="0"/>
                            </options>
                        </param>
                        <param name="lon_val" type="float" value="0" label="Longitude"/>
                    </when>
                    <when value="subregion">
                        <param name="lat_dim" type="select" label="Name of latitude coordinate" >
                            <options from_dataset="var_tab">
                                <column name="value" index="0"/>
                            </options>
                        </param>
                        <param name="lat_valN" type="float" value="0" label="Latitude North"/>
                        <param name="lat_valS" type="float" value="0" label="Latitude South"/>
                        <param name="lon_dim" type="select" label="Name of longitude coordinate" >
                            <options from_dataset="var_tab">
                                <column name="value" index="0"/>
                            </options>
                        </param>
                        <param name="lon_valE" type="float" value="0" label="Longitude East"/>
                        <param name="lon_valW" type="float" value="0" label="Longitude West"/>
                    </when>
                    <when value="global"></when>
                </conditional>
            </when>

        </conditional>

        <section name="time" title="Select Time series" expanded="false">
            <conditional name="condi_datetime">
                <param name="datetime" type="select" label="Datetime selection" help="Use this option to extract timeseries from your dataset">
                    <option value="no">No</option>
                    <option value="yes">Yes</option>
                </param>
                <when value="no"></when>
                <when value="yes">
                    <param name="dim" type="select" label="Select datetime dimension" help="Use this option only if your dataset contains a date/time dimension">
                        <options from_dataset="var_tab">
                            <column name="value" index="0"/>
                        </options>
                    </param>
                    <conditional name="condi_between">
                        <param name="comparator" type="select" label="date/Time selection">
                            <option value="is">is</option>
                            <option value="sl">slice</option>
                            <option value="ne">nearest</option>
                            <option value="to">to</option>
                            <option value="from">from</option>
                        </param>
                        <when value="sl">
                            <param name="t1" type="text" value="" label="Start date/time"/>
                            <param name="t2" type="text" value="" label="End date/time"/>
                        </when>
                        <when value="is">
                            <param name="t1" type="text" value="" label="date/time"/>
                        </when>
                        <when value="ne">
                            <param name="t1" type="text" value="" label="date/time"/>
                        </when>
                        <when value="to">
                            <param name="t1" type="text" value="" label="date/time"/>
                        </when>
                        <when value="from">
                            <param name="t1" type="text" value="" label="date/time"/>
                        </when>
                    </conditional>
                </when>
            </conditional>
        </section>
        <repeat name="user_choice" title="additional filter" 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>
            <conditional name="condi_between">
                <param name="comparator" type="select" label="Comparator">
                    <option value="e">Equal</option>
                    <option value="ge">Greater or equal</option>
                    <option value="le">Less or equal</option>
                    <option value="bi">Between-include [threshold1,threshold2]</option>
                </param>
                <when value="bi">
                    <param name="t1" type="text" value="0" label="Inferior threshold"/>
                    <param name="t2" type="text" value="0" label="Superior threshold"/>
                </when>
                <when value="e">
                    <param name="value" type="text" value="0" label="Value"/>
                </when>
                <when value="ge">
                    <param name="value" type="text" value="0" label="Value"/>
                </when>
                <when value="le">
                    <param name="value" type="text" value="0" label="Value"/>
                </when>
            </conditional>
        </repeat>
    </inputs>
    <outputs>
        <collection type="list" name="output">
            <discover_datasets pattern="__designation_and_ext__" visible="false" format="tabular" directory="output_dir"/>
            <filter>condi_source_coord['coord_source'] == 'coord_from_file'</filter>
        </collection>
        <data name="simpleoutput" from_work_dir="final.tabular" format="tabular">
            <filter>condi_source_coord['coord_source'] == 'coord_from_stdin'</filter>
        </data>
    </outputs>
    <tests>
        <test>
             <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>
             <param name="var" value="phy"/>
             <param name="var_tab" value="var_tab_dataset-ibi"/>
             <conditional name="condi_source_coord">
                 <param name="coord_source" value="coord_from_stdin"/>
                  <conditional name="condi_coord">
                    <param name="coord" value="single"/>
                    <param name="lat_dim" value="latitude"/>
                    <param name="lat_val" value="44.0"/>
                    <param name="lon_dim" value="longitude"/>
                    <param name="lon_val" value="-2.0"/>
                  </conditional>
             </conditional>
             <output name="simpleoutput" value="Test1.tabular">
                 <assert_contents>
                     <has_text_matching expression="0\t2002-12-15\t0.5"/>
                     <has_text_matching expression="144\t2014-12-15\t0.5"/>
                 </assert_contents>
             </output>
        </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="nh4"/>

             <conditional name="condi_source_coord">
                 <param name="coord_source" value="coord_from_stdin"/>
                  <conditional name="condi_coord">
                    <param name="coord" value="global"/>
                  </conditional>
             </conditional>
             <section name="time">
                 <conditional name="condi_datetime">
                     <param name="datetime" value="yes"/>
                     <conditional name="condi_between">
                         <param name="comparator" value="sl"/>
                         <param name="t1" value="2003-12-15" />
                         <param name="t2" value="2004-12-15" />
                     </conditional>
                 </conditional>
             </section>
             <repeat name="user_choice">
                 <param name="dim" value="nh4"/>
                 <conditional name="condi_between">
                    <param name="comparator" value="ge"/>
                    <param name="value" value="50."/>
                 </conditional>
             </repeat>
             <output name="simpleoutput" value="Test2.tabular">
                 <assert_contents>
                     <has_text_matching expression="0\t2003-12-15\t0.5"/>
                     <has_text_matching expression="23\t2004-12-15\t0.5"/>
                 </assert_contents>
             </output>
        </test>
    </tests>

    <help><![CDATA[
**What it does**

This tool extracts variable values with custom conditions on dimensions.

It can use manualy given coordinates or automaticaly take them from a tabular file to filter informations.

If no values are availables at a coordinate X, the tool will search the closest coordinate with a non NA value.

Filter can be set on every dimension. Available filtering operations are : =, >, <, >=, <=, [interval], ]interval[.



**Input**

A netcdf file (.nc).

Variable tabular file from 'Netcdf Metadate Info'.

Tabular file with coordinates and the following structure : 'lat'	'lon'.


**Outputs**

A single output with values for the wanted variable if there is only one coordinate.

A data collection where one file is created for every coordinate, if multiple coordinates from tabular file.


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

The xarray select tool can be used after the xarray Info.
    ]]></help>
</tool>