--- a/xarray_netcdf2netcdf.xml	Sun Aug 29 16:45:45 2021 +0000
+++ b/xarray_netcdf2netcdf.xml	Thu Jan 20 17:08:29 2022 +0000
@@ -1,190 +1,81 @@
-<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" delta="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" delta="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>
+<tool id="xarray_netcdf2netcdf" name="NetCDF xarray operations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>manipulate xarray from netCDF and save back to netCDF</description>
+    <macros>
+        <import>macros.xml</import>
+        <import>macros_netcdf2netcdf.xml</import>
+        <import>macros_tests_netcdf2netcdf.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">xarray</requirement>
+        <requirement type="package" version="3">python</requirement>
+        <requirement type="package" version="1.5.8">netcdf4</requirement>
+        <requirement type="package" version="2021.12.0">dask</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    mkdir output_dir &&
+    python '$__tool_directory__/xarray_netcdf2netcdf.py'
+          '$input'
+          '$variable.var'
+           --filter
+    #for $i,$uc in enumerate($subset_coords.tsel.user_choice)
+        #if $uc.condi_between.comparator == "sl"
+            '${uc.dim}#${uc.condi_between.comparator}#${uc.condi_between.t1}#${uc.condi_between.t2}'
+        #elif $subset_coords.tsel.by_click == "sel" and $uc.condi_between.method != 'None'
+            '${uc.dim}#${uc.condi_between.comparator}#${uc.condi_between.value}#${uc.condi_between.method}'
+        #else
+            '${uc.dim}#${uc.condi_between.comparator}#${uc.condi_between.value}'
+        #end if
+    #end for
+    #if $subset_coords.tsel.by_click == "sel"
+        --selection
+    #end if
+    #if $variable.scale
+        --scale '$variable.scale'
+    #end if
+    #if ($variable.write_all) or (str($variable.var) == 'None')
+         --write_all
+    #end if
+    #if $variable.keep_attributes
+         --keep_attributes
+    #end if
+    #if str($mask_values.mask_condi.mask_option) == 'drop'
+        --drop
+    #elif str($mask_values.mask_condi.mask_option) == 'other'
+        --other '$mask_values.mask_condi.set_other'
+    #end if
+    #if str($mask_values.where_condition) != ""
+        --where '$mask_values.where_condition'
+    #end if
+           --verbose
+           --output '$output_netcdf'
+    ]]>    </command>
+    <inputs>
+        <param type="data" name="input" multiple="true" min="1" label="Input netcdf file" format="netcdf"/>
+        <param type="data" label="Metadata Infos" name="var_tab" format="tabular" help="Select the tabular file which summarize the available variables and dimensions."/>
+        <expand macro="section_variables"/>
+        <expand macro="section_coords"/>
+        <expand macro="section_where"/>
+    </inputs>
+    <outputs>
+        <data name="output_netcdf" format="netcdf"/>
+    </outputs>
+    <expand macro="section_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>