Mercurial > repos > ecology > cb_dissim

annotate cb_dissimilarity.xml @ 1:f941081e03f0 draft default tip

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planemo upload for repository https://github.com/Marie59/champ_blocs commit 075fd90d1a39ae7912b48549e5537971635b9620
author ecology
date Sat, 18 Mar 2023 16:48:52 +0000
parents 42b51a52e308
children
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42b51a52e308 planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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1 <tool id="cb_dissim" name="QECB-Dissimilarity" version="@VERSION@" profile = "20.01">
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2 <description>indicator</description>
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3 <macros>
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4 <import>macro.xml</import>
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5 </macros>
1
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6 <requirements>
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7 <requirement type="package" version="4.2.2">r-base</requirement>
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8 <requirement type="package" version="2.0.3">r-magrittr</requirement>
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9 <requirement type="package" version="1.1.0">r-dplyr</requirement>
f941081e03f0 planemo upload for repository https://github.com/Marie59/champ_blocs commit 075fd90d1a39ae7912b48549e5537971635b9620
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10 <requirement type="package" version="1.3.0">r-tidyr</requirement>
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11 <requirement type="package" version="1.5.0">r-stringr</requirement>
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12 <requirement type="package" version="3.1.8">r-tibble</requirement>
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13 <requirement type="package" version="1.42">r-knitr</requirement>
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14 <requirement type="package" version="0.7_1">r-gmp</requirement>
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15 <requirement type="package" version="2.20">r-rmarkdown</requirement>
f941081e03f0 planemo upload for repository https://github.com/Marie59/champ_blocs commit 075fd90d1a39ae7912b48549e5537971635b9620
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16 <requirement type="package" version="0.3.0">r-officedown</requirement>
0
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17 <requirement type="package" version="2.6_4">r-vegan</requirement>
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18 <requirement type="package" version="1.3.2">r-tidyverse</requirement>
1
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19 <requirement type="package" version="3.4.1">r-ggplot2</requirement>
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20 </requirements>
0
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21 <required_files>
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22 <include type="literal" path="test-data/champbloc_qecb.csv"/>
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23 <include type="literal" path="test-data/ficheterrain.csv"/>
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24 <include type="literal" path="cb_dissimilarity.r"/>
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25 </required_files>
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26 <command detect_errors="exit_code"><![CDATA[
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27 Rscript
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28 '$__tool_directory__/cb_dissimilarity.r'
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29 '$fiche_val'
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30 '$input_data'
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31 '$choice'
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32 '$choice_date'
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33 '$output_qecb'
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34 '$output_eco'
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35 '$output_matri'
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36 '$plots_bf'
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37 '$plots_bm'
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38 '$plots'
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39 ]]>
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40 </command>
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41 <inputs>
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42 <expand macro="cb_input"/>
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43 <param name="input_data" type="data" format="data" label="Input champbloc_qecb.csv"/>
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44 <param name="choice" type="select" display="radio" label="Do you have data after the year 2021?">
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45 <option value="N">No</option>
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46 <option value="Y">Yes</option>
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47 </param>
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48 <param name="choice_date" type="integer" value="2021" label="Until when do you have data (write only the YEAR) ?" help="Example write : 2021 "/>
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49 </inputs>
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50 <outputs>
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51 <data name="output_qecb" from_work_dir="qecbnato0.RDS" format="rdata" label="Clean Rdata"/>
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52 <data name="output_eco" from_work_dir="bret_egmp_basq_qecb.RDS" format="rdata" label="Bret Rdata"/>
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53 <data name="output_matri" from_work_dir="matri_full.RDS" format="rdata" label="Matrice full Rdata"/>
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54 <collection type="list" name="plots_bf" label="Bloc fixe et bloc mobile face sup plot">
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55 <discover_datasets pattern="bm(?P&lt;designation&gt;.+)\.png" visible="false" format="png"/>
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56 </collection>
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57 <collection type="list" name="plots_bm" label="Bloc mobile face sup et face inf plot">
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58 <discover_datasets pattern="fs(?P&lt;designation&gt;.+)\.png" visible="false" format="png"/>
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59 </collection><!--&lowbar; pour underscore-->
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60 <collection type="list" name="plots" label="Distance plot">
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61 <discover_datasets pattern="distance(?P&lt;designation&gt;.+)\.png" visible="false" format="png"/>
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62 </collection>
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63 </outputs>
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64 <tests>
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65 <test expect_num_outputs="6">
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66 <param name="fiche_val" value="ficheterrain.csv"/>
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67 <param name="input_data" value="champbloc_qecb.csv"/>
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68 <param name="choice" value="N"/>
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69 <param name="choice_date" value="2021"/>
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70 <output name="output_qecb">
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71 <assert_contents>
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72 <has_text text="E6P"/>
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73 </assert_contents>
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74 </output>
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75 <output name="output_eco">
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76 <assert_contents>
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77 <has_text text="6t"/>
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78 </assert_contents>
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79 </output>
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80 <output name="output_matri">
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81 <assert_contents>
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82 <has_text text="6t"/>
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83 </assert_contents>
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84 </output>
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85 <output_collection name="plots_bf" type="list" count="23"/>
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86 <output_collection name="plots_bm" type="list" count="23"/>
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87 <output_collection name="plots" type="list" count="2"/>
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88 </test>
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89 </tests>
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90 <help><![CDATA[
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91 =======================
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92 Dissimilarity indicator
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93 =======================
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94
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95
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96 **What it does**
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97
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98 This tool computes the the Boulder Field Ecological Quality Index (BFEQ) based on biotic and abiotic variables that respond to the disturbance "boulder turning".
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99
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100 **Input description**
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101
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102 One input files in Rdata format.
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103
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104 +----------------+
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105 | Rdata |
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106 +================+
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107 | clean Rdata |
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108 +----------------+
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109 | ... |
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110 +----------------+
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111
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112
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113 **Output**
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114
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115 - .RDS file 1 of them to use as an input for diversity index
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116 - Multiple png plots one for each of the locations
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117
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118
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119
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120 ]]> </help>
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121 <expand macro="cb_bibref"/>
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122 </tool>