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comparison climate-stripes.xml @ 0:fec3147b0206 draft

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"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes commit aa08ea46712c1cfbaac2e6fcd07c93097751cad3"
author climate
date Sat, 05 Oct 2019 17:03:08 -0400
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-1:000000000000 0:fec3147b0206
1 <tool id="climate_stripes" name="climate stripes" version="1.0.0">
2 <description>from timeseries</description>
3 <requirements>
4 <requirement type="package" version="3">python</requirement>
5 <requirement type="package" version="3.1.1">matplotlib</requirement>
6 <requirement type="package" version="0.25.1">pandas</requirement>
7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[
9 python3 '$__tool_directory__/climate_stripes.py'
10 '$ifilename' '$variable'
11 --cmap '$adv.colormap'
12 #if str($title).strip()
13 --title '$title'
14 #end if
15 #if str($adv.xname).strip()
16 --xname '$adv.xname'
17 #end if
18 #if str($adv.format_date).strip()
19 --format_date '$adv.format_date'
20 #end if
21 #if str($adv.format_plot).strip()
22 --format_plot '$adv.format_plot'
23 #end if
24 --output image.png
25 ]]></command>
26 <inputs>
27 <param name="ifilename" type="data" format="tabular" label="timeseries to plot"></param>
28 <param name="variable" type="text" value="global" label="column name to use for plotting" />
29 <param name="title" type="text" value="" label="plot title" />
30 <section name="adv" title="Advanced Options" expanded="false">
31 <param name="xname" type="text" value="" label="column name to use for x-axis" />
32 <param name="format_date" type="text" value="" label="format for input date/time column" />
33 <param name="format_plot" type="text" value="" label="format for plotting dates on the x-axis" />
34 <param name="colormap" type="select">
35 <option value="Accent">Accent</option>
36 <option value="Blues">Blues</option>
37 <option value="BrBG">BrBG</option>
38 <option value="BuGn">BuGn</option>
39 <option value="BuPu">BuPu</option>
40 <option value="CMRmap">CMRmap</option>
41 <option value="Dark2">Dark2</option>
42 <option value="GnBu">GnBu</option>
43 <option value="Greens">Greens</option>
44 <option value="Greys">Greys</option>
45 <option value="OrRd">OrRd</option>
46 <option value="Oranges">Oranges</option>
47 <option value="PRGn">PRGn</option>
48 <option value="Paired">Paired</option>
49 <option value="Pastel1">Pastel1</option>
50 <option value="Pastel2">Pastel2</option>
51 <option value="PiYG">PiYG</option>
52 <option value="PuBu">PuBu</option>
53 <option value="PuBuGn">PuBuGn</option>
54 <option value="PuOr">PuOr</option>
55 <option value="PuRd">PuRd</option>
56 <option value="Purples">Purples</option>
57 <option value="RdBu">RdBu</option>
58 <option value="RdGy">RdGy</option>
59 <option value="RdPu">RdPu</option>
60 <option value="RdBu_r" selected="true">RdBu_r</option>
61 <option value="RdGy_r">RdGy_r</option>
62 <option value="RdPu_r">RdPu_r</option>
63 <option value="RdYlBu">RdYlBu</option>
64 <option value="RdYlGn">RdYlGn</option>
65 <option value="Reds">Reds</option>
66 <option value="Set1">Set1</option>
67 <option value="Set2">Set2</option>
68 <option value="Set3">Set3</option>
69 <option value="Spectral">Spectral</option>
70 <option value="Wistia">Wistia</option>
71 <option value="YlGn">YlGn</option>
72 <option value="YlGnBu">YlGnBu</option>
73 <option value="YlOrBr">YlOrBr</option>
74 <option value="YlOrRd">YlOrRd</option>
75 <option value="afmhot">afmhot</option>
76 <option value="autumn">autumn</option>
77 <option value="binary">binary</option>
78 <option value="bone">bone</option>
79 <option value="brg">brg</option>
80 <option value="bwr">bwr</option>
81 <option value="cool">cool</option>
82 <option value="coolwarm">coolwarm</option>
83 <option value="copper">copper</option>
84 <option value="cubehelix">cubehelix</option>
85 <option value="flag">flag</option>
86 <option value="gist_earth">gist_earth</option>
87 <option value="gist_gray">gist_gray</option>
88 <option value="gist_heat">gist_heat</option>
89 <option value="gist_ncar">gist_ncar</option>
90 <option value="gist_rainbow">gist_rainbow</option>
91 <option value="gist_stern">gist_stern</option>
92 <option value="gist_yarg">gist_yarg</option>
93 <option value="gnuplot">gnuplot</option>
94 <option value="gnuplot2">gnuplot2</option>
95 <option value="gray">gray</option>
96 <option value="hot">hot</option>
97 <option value="hsv">hsv</option>
98 <option value="jet">jet</option>
99 <option value="nipy_spectral">nipy_spectral</option>
100 <option value="ocean">ocean</option>
101 <option value="pink">pink</option>
102 <option value="prism">prism</option>
103 <option value="rainbow">rainbow</option>
104 <option value="seismic">seismic</option>
105 <option value="spring">spring</option>
106 <option value="summer">summer</option>
107 <option value="tab10">tab10</option>
108 <option value="tab20">tab20</option>
109 <option value="tab20b">tab20b</option>
110 <option value="tab20c">tab20c</option>
111 <option value="terrain">terrain</option>
112 <option value="winter">winter</option>
113 </param>
114 </section>
115 </inputs>
116 <outputs>
117 <data name="ofilename" format="png" from_work_dir="image.png"/>
118 </outputs>
119 <tests>
120 <test>
121 <param name="ifilename" value="T2Mclimatology.txt" />
122 <param name="variable" value="global" />
123 <output name="ofilename" ftype="png" file="T2Mstripes.png" compare="sim_size" delta="50"/>
124 </test>
125 <test>
126 <param name="ifilename" value="T2Mclimatology.txt" />
127 <param name="variable" value="global" />
128 <param name="title" value="Surface Temperature stripes (1979-2019)" />
129 <param name="colormap" value="OrRd" />
130 <param name="xname" value="Month" />
131 <param name="format_date" value="XYXm" />
132 <param name="format_plot" value="XY" />
133 <output name="ofilename" ftype="png" file="T2Mstripes_with_axis.png" compare="sim_size" delta="50"/>
134 </test>
135 </tests>
136 <help><![CDATA[
137
138 **Climate stripes**
139 =========================================
140
141 This tool generate stripes from timeseries and is often used to generate warming stripes.
142
143
144 .. class:: infomark
145
146 The wrappers aims at creating stripes from a timeseries.
147 The input file must be in tabular format and must contain at least one column that is used
148 for creating stripes. By default, no title and no axis are plotted. An additional column
149 can be specified for date/time and its date and time format must then be specified
150 with an additional options.
151
152 **What it does**
153 ----------------
154
155 This tools creates an image (png format) corresponding to the visualization of a timeseries as
156 stripes (see https://www.climate-lab-book.ac.uk/2018/warming-stripes/).
157 By default, the colormap is ``RdBu_r`` and no axis nor title are plotted. These settings can be
158 changed in *Advanced settings*.
159 ]]></help>
160 <citations>
161 </citations>
162 </tool>