view climate-stripes.xml @ 2:7f84fb995f4e draft default tip

planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes commit e4c144851549600ffde5bcf875304d5edd98e2b1

<tool id="climate_stripes" name="climate stripes" version="1.0.2">
    <description>from timeseries</description>
    <edam_topics>
      <edam_topic>topic_3855</edam_topic>
      <edam_topic>topic_3318</edam_topic>
    </edam_topics>
    <edam_operations>
      <edam_operation>operation_0337</edam_operation>
    </edam_operations>
    <requirements>
        <requirement type="package" version="3">python</requirement>
        <requirement type="package" version="3.5.2">matplotlib</requirement>
        <requirement type="package" version="1.4.3">pandas</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
       python3 '$__tool_directory__/climate_stripes.py'
            '$ifilename' '$variable'
            --cmap '$adv.colormap'
            #if str($title).strip()
                --title '$title'
            #end if
            #if str($adv.xname).strip()
                --xname '$adv.xname'
            #end if
            #if str($adv.format_date).strip()
                --format_date '$adv.format_date'
            #end if
            #if str($adv.format_plot).strip()
                --format_plot '$adv.format_plot'
            #end if
            #if $adv.nxsplit
                --nxsplit '$adv.nxsplit'
            #end if
            --output image.png
    ]]></command>
    <inputs>
        <param name="ifilename" type="data" format="tabular" label="timeseries to plot"></param>
        <param name="variable" type="text" value="global" label="column name to use for plotting" />
        <param name="title" type="text" value="" label="plot title" />
        <section name="adv" title="Advanced Options" expanded="false">
            <param name="nxsplit" type="integer" optional="true" label="number of values per intervals" />
            <param name="xname" type="text" value="" label="column name to use for x-axis" />
            <param name="format_date" type="text" value="" label="format for input date/time column" />
            <param name="format_plot" type="text" value="" label="format for plotting dates on the x-axis" />
            <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" selected="true">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">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="T2Mclimatology.txt" />
            <param name="variable" value="global" />
            <output name="ofilename" ftype="png" file="T2Mstripes.png" compare="sim_size" delta="50"/>
        </test>
        <test>
            <param name="ifilename" value="T2Mclimatology.txt" />
            <param name="variable" value="global" />
            <param name="title" value="Surface Temperature stripes (1979-2019)" />
            <param name="colormap" value="OrRd" />
            <param name="nxsplit" value="50" />
            <param name="xname" value="Month" />
            <param name="format_date" value="XYXm" />
            <param name="format_plot" value="XY" />
            <output name="ofilename" ftype="png" file="T2Mstripes_with_axis.png" compare="sim_size" delta="50"/>
        </test>
    </tests>
    <help><![CDATA[

**Climate stripes**
=========================================

This tool generate stripes from timeseries and is often used to generate warming stripes.


.. class:: infomark

        The wrappers aims at creating stripes from a timeseries.
        The input file must be in tabular format and must contain at least one column that is used
        for creating stripes. By default, no title and no axis are plotted. An additional column
        can be specified for date/time and its date and time format must then be specified
        with an additional options.

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

This tools creates an image (png format) corresponding to the visualization of a timeseries as
stripes (see https://www.climate-lab-book.ac.uk/2018/warming-stripes/).
By default, the colormap is ``RdBu_r`` and no axis nor title are plotted. These settings can be
changed in *Advanced settings*.
    ]]></help>
    <citations>
    </citations>
</tool>