# HG changeset patch
# User climate
# Date 1570309363 14400
# Node ID 2ea0576cb062eb0ad53160779d3e6e34aab163d4

"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes commit aa08ea46712c1cfbaac2e6fcd07c93097751cad3"

diff -r 000000000000 -r 2ea0576cb062 climate-stripes.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/climate-stripes.xml	Sat Oct 05 17:02:43 2019 -0400
@@ -0,0 +1,162 @@
+<tool id="climate_stripes" name="climate stripes" version="1.0.0">
+    <description>from timeseries</description>
+    <requirements>
+        <requirement type="package" version="3">python</requirement>
+        <requirement type="package" version="3.1.1">matplotlib</requirement>
+        <requirement type="package" version="0.25.1">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
+            --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="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="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>
diff -r 000000000000 -r 2ea0576cb062 climate_stripes.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/climate_stripes.py	Sat Oct 05 17:02:43 2019 -0400
@@ -0,0 +1,152 @@
+#!/usr/bin/env python3
+#
+#
+# usage: climate_stripes.py [-h] [--cmap CMAP]
+#                           [--output OUTPUT]
+#                           [--xname XNAME]
+#                           [--format_plot FORMAT_PLOT]
+#                           [--format_date FORMAT_DATE]
+#                           [--title TITLE]
+#                           [--nxsplit NXSPLIT]
+#                          input varname
+#
+# positional arguments:
+#   input                 input filename with timeseries (tabular format)
+#   varname               column name to use for plotting (case sensitive)
+#
+# optional arguments:
+#   -h, --help            show this help message and exit
+#   --cmap CMAP           Specify which colormap to use for plotting
+#   --output OUTPUT       output filename to store resulting image (png format)
+#   --xname XNAME         column name to use for x-axis
+#   --format_plot FORMAT_PLOT
+#                         format for plotting dates on the x-axis
+#   --format_date FORMAT_DATE
+#                         format for input date/time column
+#   --title TITLE         plot title
+#   --nxsplit NXSPLIT     number of ticks on the x-axis
+#
+
+import argparse
+import warnings
+
+import matplotlib as mpl
+mpl.use('Agg')
+
+import matplotlib.pyplot as plt   # noqa: I202,E402
+
+import numpy as np  # noqa: I202,E402
+
+import pandas as pd  # noqa: I202,E402
+
+
+class Stripes ():
+    def __init__(self, input, valname, cmap, output, xname="",
+                 date_format='%Y%m',
+                 plot_format='%Y',
+                 nxsplit=10,
+                 title=""):
+        self.input = input
+        self.valname = valname
+        self.xname = xname
+        if not nxsplit:
+            self.nxsplit = 10
+        else:
+            self.nxsplit = nxsplit
+        if not cmap:
+            self.cmap = 'RdBu_r'
+        else:
+            self.cmap = cmap
+        if not output:
+            self.output = "stripes.png"
+        else:
+            self.output = output
+        self.title = title
+        if not date_format:
+            self.format = '%Y%m'
+        else:
+            self.format = date_format.replace('X', '%')
+        if not plot_format:
+            self.plot_format = self.format
+        else:
+            self.plot_format = plot_format.replace('X', '%')
+
+    def read_data(self):
+        self.data = pd.read_csv(self.input, sep='\t')
+
+    def create_stripes(self):
+        data = np.zeros((2, self.data[self.valname].shape[0]), dtype='float')
+        data[:] = np.NaN
+        data[0, :] = self.data[self.valname]
+        data[1, :] = self.data[self.valname]
+        fig = plt.figure(figsize=(10, 2))
+        ax = plt.subplot(111)
+        plt.pcolor(data, cmap=self.cmap,
+                   vmin=self.data[self.valname].min(),
+                   vmax=self.data[self.valname].max())
+        if self.title:
+            plt.title(self.title)
+        if self.xname:
+            nrange = self.data.index.values
+            n = int(np.floor((nrange.max() - nrange.min())/int(self.nxsplit)))
+            date_list = self.data[self.xname].loc[::n].apply(
+                             lambda x: pd.to_datetime(str(x),
+                                                      format=self.format))
+            date_list = [i.strftime(self.plot_format) for i in date_list]
+            nval = int(self.data[self.xname].loc[::n].shape[0])
+            ax.xaxis.set_major_locator(plt.MaxNLocator(nval))
+            ax.xaxis.set_ticklabels(date_list)
+            ax.xaxis.set_tick_params(rotation=45)
+        else:
+            ax.set_xticks([])
+        ax.set_yticks([])
+        fig.tight_layout()
+        fig.savefig(self.output)
+
+
+if __name__ == '__main__':
+    warnings.filterwarnings("ignore")
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        'input',
+        help='input filename with geographical coordinates (netCDF format)'
+    )
+    parser.add_argument(
+        'varname',
+        help='column name to use for plotting (case sensitive)'
+    )
+    parser.add_argument(
+        '--cmap',
+        help='Specify which colormap to use for plotting'
+    )
+    parser.add_argument(
+        '--output',
+        help='output filename to store resulting image (png format)'
+    )
+    parser.add_argument(
+        '--xname',
+        help='column name to use for x-axis'
+    )
+    parser.add_argument(
+        '--format_plot',
+        help='format for plotting dates on the x-axis'
+    )
+    parser.add_argument(
+        '--format_date',
+        help='format for input date/time column (default is Month d, yyyy)'
+    )
+    parser.add_argument(
+        '--title',
+        help='plot title'
+    )
+    parser.add_argument(
+        '--nxsplit',
+        help='number of ticks on the x-axis'
+    )
+    args = parser.parse_args()
+    stripes = Stripes(args.input, args.varname, args.cmap, args.output,
+                      xname=args.xname, date_format=args.format_date,
+                      plot_format=args.format_plot, title=args.title,
+                      nxsplit=args.nxsplit)
+    stripes.read_data()
+    stripes.create_stripes()
diff -r 000000000000 -r 2ea0576cb062 test-data/T2Mclimatology.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/T2Mclimatology.txt	Sat Oct 05 17:02:43 2019 -0400
@@ -0,0 +1,489 @@
+Month	global
+197901	-0.2309
+197902	-0.4906
+197903	-0.2922
+197904	-0.3259
+197905	-0.2858
+197906	-0.258
+197907	-0.3306
+197908	-0.2336
+197909	-0.1801
+197910	-0.1248
+197911	-0.147
+197912	0.0667
+198001	-0.1084
+198002	-0.0513
+198003	-0.0826
+198004	-0.0015
+198005	0.0697
+198006	-0.0799
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+198011	-0.192
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+198104	-0.0305
+198105	-0.069
+198106	-0.0755
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+198109	-0.1398
+198110	-0.1792
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diff -r 000000000000 -r 2ea0576cb062 test-data/T2Mstripes.png
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diff -r 000000000000 -r 2ea0576cb062 test-data/T2Mstripes_with_axis.png
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