Mercurial > repos > ecology > divand_full_analysis

annotate divandfull.xml @ 1:42b317c31d5c draft default tip

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author ecology
date Tue, 22 Oct 2024 15:54:37 +0000
parents dae0fb5e0ee0
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1 <tool id="divand_full_analysis" name="DIVAnd" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
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2 <description>Data-Interpolating Variational Analysis in n dimensions</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.1.0</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="1.8.5">julia</requirement>
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9 <requirement type="package" version="2.7.9">julia-divand</requirement>
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10 </requirements>
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11 <command detect_errors="exit_code"><![CDATA[
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12 ## The HOME .julia folder is not writable inside the Docker container, so we need to set one that is writable.
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13 export JULIA_DEPOT_PATH="\$PWD:\$JULIA_DEPOT_PATH" &&
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14 julia
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15 '$__tool_directory__/divandfull.jl'
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16 '$input_netcdf_identifier'
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17 '$longmin'
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18 '$longmax'
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19 '$latmin'
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20 '$latmax'
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21 '$startdate'
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22 '$enddate'
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23 '$varname'
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24 '$selmin'
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25 '$selmax'
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26 '$bathname'
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27 ]]></command>
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28 <inputs>
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29 <param name="input_netcdf_identifier" type="data" format="netcdf" label="Input your netcdf data"/>
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30 <param name="bathname" type="data" format="netcdf" label="Input your bathymetry netcdf file" help="for more info see below."/>
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31 <param name="longmin" type="float" min="-180" max="180" value="0" label="Longitude minimal"/>
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32 <param name="longmax" type="float" min="-180" max="180" value="0" label="Longitude maximal"/>
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33 <param name="latmin" type="float" min="-180" max="180" value="0" label="Latitude minimal"/>
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34 <param name="latmax" type="float" min="-180" max="180" value="0" label="Latitude maximal"/>
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35 <param name="startdate" type="text" value="yyyy-mm-dd" label="Input the starting date">
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36 <sanitizer invalid_char="">
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37 <valid initial="string.digits">
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38 <add value="-"/>
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39 </valid>
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40 </sanitizer>
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41 </param>
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42 <param name="enddate" type="text" value="yyyy-mm-dd" label="Input the ending date">
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43 <sanitizer invalid_char="">
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44 <valid initial="string.digits">
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45 <add value="-"/>
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46 </valid>
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47 </sanitizer>
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48 </param>
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49 <param name="varname" type="text" value="variable" label="Write the name of the variable of the analysis" help="Example: phosphate">
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50 <sanitizer invalid_char="">
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51 <valid initial="string.letters">
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52 <add value="_"/>
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53 </valid>
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54 </sanitizer>
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55 <validator type="regex">[0-9a-zA-Z_]+</validator>
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56 </param>
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57 <param name="selmin" type="integer" min="0" max="100" optional="true" value="0" label="Minimum of the salinity"/>
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58 <param name="selmax" type="integer" min="0" max="100" optional="true" value="0" label="Maximum of the salinity"/>
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59 </inputs>
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60 <outputs>
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61 <data name="output_netcdf" label="DIVAnd netcdf output" from_work_dir="outputs_netcdf/*.nc" format="netcdf"/>
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62 </outputs>
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63 <tests>
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64 <test expect_num_outputs="1">
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65 <param name="input_netcdf_identifier" value="data_from_Eutrophication_Med_profiles_2022_unrestricted.nc"/>
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66 <param name="bathname" location="https://dox.ulg.ac.be/index.php/s/U0pqyXhcQrXjEUX/download"/>
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67 <param name="longmin" value="19.0"/>
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68 <param name="longmax" value="30.0"/>
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69 <param name="latmin" value="32.0"/>
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70 <param name="latmax" value="38.0"/>
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71 <param name="varname" value="phosphate"/>
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72 <param name="startdate" value="1950-01-01"/>
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73 <param name="enddate" value="2017-12-31"/>
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74 <param name="selmin" value="0"/>
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75 <param name="selmax" value="100"/>
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76 <output name="output_netcdf">
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77 <assert_contents>
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78 <has_size value="68291" delta="0"/>
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79 </assert_contents>
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80 </output>
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81 </test>
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82 </tests>
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83 <help><![CDATA[
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84
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85 .. class:: infomark
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86
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87 **What it does**
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88
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89 This tool takes a observation netcdf file and create climatology
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90
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91 **Input**
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92
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93 - An ocean observation netcdf file
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94 - A bathymetry netcdf file, you can download it like this: download("https://dox.ulg.ac.be/index.php/s/U0pqyXhcQrXjEUX/download", "gebco_30sec_8.nc")
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95 - Some complementary information for the tool to better understand your data and create your climatology on the right area: latitudes, longitudes, dates, and salinity.$
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96
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97 **Output**
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98
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99 One netcdf file containing the climatology created by DIVAnd.
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100
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101
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102 **A bit of context**
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103
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104 DIVAnd (Data-Interpolating Variational Analysis in n dimensions) performs an n-dimensional variational analysis/gridding of
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105 arbitrarily located observations. Observations will be interpolated/analyzed on a curvilinear grid in 1, 2, 3 or more dimensions.
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106 In this sense it is a generalization of the original two-dimensional DIVA version (still available `here <https://github.com/gher-uliege/DIVA>`_ but
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107 not further developed anymore).
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108
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109 The method bears some similarities and equivalences with Optimal Interpolation or Krigging in that it allows to create a smooth
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110 and continous field from a collection of observations, observations which can be affected by errors. The analysis method is however
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111 different in practise, allowing to take into account topological features, physical constraints etc in a natural way.
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112 The method was initially developped with ocean data in mind, but it can be applied to any field where localized observations have
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113 to be used to produce gridded fields which are "smooth".
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114
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115 DIVAndrun is the core analysis function in n dimensions. It does not know anything about the physical parameters or units you work with.
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116 Coordinates can also be very general. The only constraint is that the metrics (pm,pn,po,...) when multiplied by the corresponding length
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117 scales len lead to non-dimensional parameters. Furthermore the coordinates of the output grid (xi,yi,zi,...) need to have the same units
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118 as the observation coordinates (x,y,z,...).
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119
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120 DIVAndfun is a version with a minimal set of parameters (the coordinates and values of observations, i.e. (x,f), the remaining parameters
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121 being optional) and provides an interpolation function rather than an already gridded field.
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122
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123 diva3D is a higher-level function specifically designed for climatological analysis of data on Earth, using longitude/latitude/depth/time
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124 coordinates and correlations length in meters. It makes the necessary preparation of metrics, parameter optimizations etc you normally would
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125 program yourself before calling the analysis function DIVAndrun.
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126
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127 DIVAnd_heatmap can be used for additive data and produces Kernel Density Estimations.
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128
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129 DIVAndgo is only needed for very large problems when a call to DIVAndrun leads to memory or CPU time problems. This function tries to decide
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130 which solver (direct or iterative) to use and how to make an automatic domain decomposition. Not all options from DIVAndrun are available.
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131
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132 If you want to try out multivariate approaches, you can look at DIVAnd_multivarEOF and DIVAnd_multivarJAC
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133
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134 If you want more informations about the functions and parameters see also the `documentations here <https://gher-uliege.github.io/DIVAnd.jl/latest/index.html>`_.
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135
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136 ]]></help>
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137 <citations>
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138 <citation type="doi">doi:10.5194/gmd-7-225-2014</citation>
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139 </citations>
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140 </tool>