diff xarray_coords_info.xml @ 0:fea8a53f8099 draft

"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
author ecology
date Sun, 06 Jun 2021 08:50:43 +0000
parents
children 6015f30a7258
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xarray_coords_info.xml	Sun Jun 06 08:50:43 2021 +0000
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+<tool id="xarray_coords_info" name="NetCDF xarray Coordinate Info" version="@TOOL_VERSION+galaxy@VERSION_SUFFIX@">
+    <description>Get values for each coordinate of a Netcdf file</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>
+        <requirement type="package" version="0.9.0">geopandas</requirement>
+        <requirement type="package" version="1.7.1">shapely</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir output_dir &&
+        echo "Galaxy xarray version @TOOL_VERSION@" > output_dir/version.tabular &&
+        python3 '$__tool_directory__/xarray_tool.py' '$input' --coords_info output_dir
+    ]]></command>
+    <inputs>
+        <param type="data" name="input" label="Netcdf file" format="netcdf,h5" help="Netcdf file you need to extract coordinate values."/>
+    </inputs>
+    <outputs>
+        <collection type="list" name="output_dir" label="Coordinates">
+            <discover_datasets pattern="__name_and_ext__" visible="true" directory="output_dir"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+             <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>
+              <output_collection name="output_dir" type="list" count="5">
+                <element name="time" file="time.tabular" ftype="tabular"/>
+                <element name="latitude" file="latitude.tabular" ftype="tabular"/>
+                <element name="longitude" file="longitude.tabular" ftype="tabular"/>
+                <element name="depth" file="depth.tabular" ftype="tabular"/>
+                <element name="version" file="version.tabular" ftype="tabular"/>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+The tool will generate a collection containing one file per coordinate. Each file contains the values of the 
+corresponding coordinate. The output of this tool is usually used as input to other tools.
+
+**Input**
+
+A netcdf file (xxx.nc).
+
+--------------------------------
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>