view psy-maps.xml @ 1:706666d912d5 draft default tip

"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"

<tool id="psy_maps" name="map plot" version="1.2.1">
    <description>gridded (lat/lon) netCDF data</description>
    <requirements>
        <requirement type="package" version="3">python</requirement>
        <requirement type="package" version="1.2.1">psyplot</requirement>
        <requirement type="package" version="1.2.0">psy-maps</requirement>
        <requirement type="package" version="1.2.0">psy-reg</requirement>
        <requirement type="package" version="1.4.2">netcdf4</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
       HOME=`pwd`  &&
       python3 '$__tool_directory__/psymap_simple.py'
            '$ifilename' '$variable'
            --proj '$adv.projection'
            --cmap '$adv.colormap'
            --output image.png
       #if str($adv.multiple_plot.selector) == 'yes'
            --time '$adv.multiple_plot.time'
            --format '$adv.multiple_plot.format'
            --ncol '$adv.multiple_plot.ncol'
            --nrow '$adv.multiple_plot.nrow'
       #end if
       #if str($adv.multiple_plot.title).strip()
            --title '$adv.multiple_plot.title'
       #end if
    ]]></command>
    <inputs>
        <param name="ifilename" type="data" format="netcdf" label="input with geographical coordinates (netCDF format)"></param>
        <param name="variable" type="text" value="TS" label="variable name as given in the netCDF file" />
        <section name="adv" title="Advanced Options" expanded="false">
            <conditional name="multiple_plot">
                <param name="selector" type="select" label="multiple times">
                    <option value="yes">yes</option>
                    <option value="no" selected="true">no</option>
                </param>
                <when value="yes">
                    <param name="time" type="text" value="0" label="comma separated list of indexes for fields to plot" />
                    <param name="format" type="text" value="%Y-%m-%d %H:%M:%S" label="date and time format" />
                    <param name="ncol" type="integer" value="1" min="1" max="4" label="number of columns for subplot grid" />
                    <param name="nrow" type="integer" value="1" min="1" max="20" label="number of rows for subplot grid" />
                    <param name="title" type="text" value="" label="subplot title (repeated on each subplot)" />
                </when>
                <when value="no">
                    <param name="title" type="text" value="" label="plot title" />
                </when>
            </conditional>
            <param name="projection" type="select">
                <option value="" selected="true">PlateCarree</option>
                <option value="robin">Robinson</option>
                <option value="moll">Mollweide</option>
                <option value="geo">Geostationary</option>
                <option value="northpole">NorthPolarStereo</option>
                <option value="southpole">SouthPolarStereo</option>
                <option value="ortho">Orthographic</option>
                <option value="stereo">Stereographic</option>
                <option value="near">NearsidePerspective</option>
            </param>
            <param name="colormap" type="select">
                <option value="Accent">Accent</option>
                <option value="Blues">Blues</option>
                <option value="BrBG">BrBG</option>
                <option value="BuGn">BuGn</option>
                <option value="BuPu">BuPu</option>
                <option value="CMRmap">CMRmap</option>
                <option value="Dark2">Dark2</option>
                <option value="GnBu">GnBu</option>
                <option value="Greens">Greens</option>
                <option value="Greys">Greys</option>
                <option value="OrRd">OrRd</option>
                <option value="Oranges">Oranges</option>
                <option value="PRGn">PRGn</option>
                <option value="Paired">Paired</option>
                <option value="Pastel1">Pastel1</option>
                <option value="Pastel2">Pastel2</option>
                <option value="PiYG">PiYG</option>
                <option value="PuBu">PuBu</option>
                <option value="PuBuGn">PuBuGn</option>
                <option value="PuOr">PuOr</option>
                <option value="PuRd">PuRd</option>
                <option value="Purples">Purples</option>
                <option value="RdBu">RdBu</option>
                <option value="RdGy">RdGy</option>
                <option value="RdPu">RdPu</option>
                <option value="RdBu_r">RdBu_r</option>
                <option value="RdGy_r">RdGy_r</option>
                <option value="RdPu_r">RdPu_r</option>
                <option value="RdYlBu">RdYlBu</option>
                <option value="RdYlGn">RdYlGn</option>
                <option value="Reds">Reds</option>
                <option value="Set1">Set1</option>
                <option value="Set2">Set2</option>
                <option value="Set3">Set3</option>
                <option value="Spectral">Spectral</option>
                <option value="Wistia">Wistia</option>
                <option value="YlGn">YlGn</option>
                <option value="YlGnBu">YlGnBu</option>
                <option value="YlOrBr">YlOrBr</option>
                <option value="YlOrRd">YlOrRd</option>
                <option value="afmhot">afmhot</option>
                <option value="autumn">autumn</option>
                <option value="binary">binary</option>
                <option value="bone">bone</option>
                <option value="brg">brg</option>
                <option value="bwr">bwr</option>
                <option value="cool">cool</option>
                <option value="coolwarm">coolwarm</option>
                <option value="copper">copper</option>
                <option value="cubehelix">cubehelix</option>
                <option value="flag">flag</option>
                <option value="gist_earth">gist_earth</option>
                <option value="gist_gray">gist_gray</option>
                <option value="gist_heat">gist_heat</option>
                <option value="gist_ncar">gist_ncar</option>
                <option value="gist_rainbow">gist_rainbow</option>
                <option value="gist_stern">gist_stern</option>
                <option value="gist_yarg">gist_yarg</option>
                <option value="gnuplot">gnuplot</option>
                <option value="gnuplot2">gnuplot2</option>
                <option value="gray">gray</option>
                <option value="hot">hot</option>
                <option value="hsv">hsv</option>
                <option value="jet" selected="true">jet</option>
                <option value="nipy_spectral">nipy_spectral</option>
                <option value="ocean">ocean</option>
                <option value="pink">pink</option>
                <option value="prism">prism</option>
                <option value="rainbow">rainbow</option>
                <option value="seismic">seismic</option>
                <option value="spring">spring</option>
                <option value="summer">summer</option>
                <option value="tab10">tab10</option>
                <option value="tab20">tab20</option>
                <option value="tab20b">tab20b</option>
                <option value="tab20c">tab20c</option>
                <option value="terrain">terrain</option>
                <option value="winter">winter</option>
            </param>
        </section>
    </inputs>
    <outputs>
        <data name="ofilename" format="png" from_work_dir="image.png"/>
    </outputs>
    <tests>
        <test>
            <param name="ifilename" value="TS.f2000.T31T31.control.cam.h0.0014-12.nc" />
            <param name="variable" value="TS" />
            <param name="projection" value="" />
            <param name="colormap" value="jet" />
            <output name="ofilename" ftype="png" file="TS.f2000.T31T31.control.cam.h0.0014-12.png" compare="sim_size" delta="500"/>
        </test>
        <test>
            <param name="ifilename" value="TS.f2000.T31T31.control.cam.h0.0014-12.nc" />
            <param name="variable" value="TS" />
            <param name="projection" value="ortho" />
            <param name="colormap" value="RdBu_r" />
            <output name="ofilename" ftype="png" file="TS.f2000.T31T31.control.cam.h0.0014-12_ortho.png" compare="sim_size" delta="500"/>
        </test>
    </tests>
    <help><![CDATA[

**Visualization on a map with psyplot**
=========================================

This tool wraps the functionality of ``psyplot.plot.mapplot``.


.. class:: infomark

        The wrappers aims at providing the same functionality as ``psyplot.plot.mapplot`` but it has some limitations.
        The input file must be in netCDF format and must contain 2D arrays with geographical coordinatates
        (latitudes, longitudes) given in degrees.
        TODO: Fill in help.

**What it does**
----------------

This tools creates an image (png format) corresponding to the visualization on a geographical map of a variable extracted from a
netCDF file (input file). By default, the projection is ``PlateCarree`` and colormap is ``jet``. These settings can be changed in *Advanced settings*.


**Usage**

::

  usage: psymap_simple.py [-h] [--proj PROJ] [--cmap CMAP] [--output OUTPUT] [--time TIME]
                          [--format FORMAT] [--title TITLE] [--ncol NCOL] [--nrow NROW] [-v] input varname


Positional arguments:
~~~~~~~~~~~~~~~~~~~~~

- **input**:            input filename with geographical coordinates (netCDF format)
- **varname**:          Specify which variable to plot (case sensitive)

Optional arguments:
~~~~~~~~~~~~~~~~~~~~~

  -h, --help       show this help message and exit
  --proj PROJ      Specify the projection on which we draw
  --cmap CMAP      Specify which colormap to use for plotting
  --output OUTPUT  output filename to store resulting image (png format)
  -v, --verbose    switch on verbose mode
  --time TIME      list of times to plot for multiple plots
  --format FORMAT  format for date/time (default is Month d, yyyy)
  --title TITLE    plot title
  --ncol NCOL      number of columns for multiple plots
  --nrow NROW      number of rows for multiple plots

It uses psy-maps, a python package to generate plots. More information about
psyplot and psy-maps can be found at https://psyplot.readthedocs.io/projects/psy-maps/en/latest/

    ]]></help>
    <citations>
    </citations>
</tool>