Mercurial > repos > ecology > cb_ivr

annotate cb_ivr.xml @ 2:bcbad4f83dec 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 16:49:19 +0000
parents b67730406f1b
children
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2
bcbad4f83dec planemo upload for repository https://github.com/Marie59/champ_blocs commit 075fd90d1a39ae7912b48549e5537971635b9620
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1 <tool id="cb_ivr" name="IVR" version="@VERSION@" profile="20.01">
0
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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>
2
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6 <requirements>
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7 <requirement type="package" version="1.0.10">r-dplyr</requirement>
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8 <requirement type="package" version="1.2.1">r-tidyr</requirement>
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9 <requirement type="package" version="1.4.1">r-stringr</requirement>
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10 <requirement type="package" version="3.1.8">r-tibble</requirement>
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11 <requirement type="package" version="1.40">r-knitr</requirement>
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12 <requirement type="package" version="0.6_8">r-gmp</requirement>
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13 <requirement type="package" version="2.0.3">r-magrittr</requirement>
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14 <requirement type="package" version="2.18">r-rmarkdown</requirement>
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15 <requirement type="package" version="0.2.4">r-officedown</requirement>
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16 <requirement type="package" version="1.3.2">r-tidyverse</requirement>
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17 <requirement type="package" version="0.5.1">r-officer</requirement>
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18 <requirement type="package" version="0.8.3">r-flextable</requirement>
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19 <requirement type="package" version="3.4.0">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_ivr.csv"/>
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23 <include type="literal" path="test-data/ficheterrain.csv"/>
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24 <include type="literal" path="CB_ivr.tif"/>
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25 <include type="literal" path="logo_merged.png"/>
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26 <include type="literal" path="cb_ivr_site_report_col_scale_loop.Rmd"/>
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27 <include type="literal" path="loop_col_scale.r"/>
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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28 <include type="literal" path="cb_ivr.r"/>
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29 </required_files>
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30 <command detect_errors="exit_code"><![CDATA[
2
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31 cp '$__tool_directory__/cb_ivr_site_report_col_scale_loop.Rmd' ./cb_ivr_site_report_col_scale_loop.Rmd &&
0
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32 Rscript
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33 '$__tool_directory__/cb_ivr.r'
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34 '$fiche_val'
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35 '$input_data'
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36 ./cb_ivr_site_report_col_scale_loop.Rmd
0
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37 '$__tool_directory__/loop_col_scale.r'
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38 '$output_ivr'
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39 '$plots'
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40 '$output_report'
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41 ]]>
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42 </command>
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43 <inputs>
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44 <expand macro="cb_input"/>
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45 <param name="input_data" type="data" format="data" label="Input champbloc_ivr.csv"/>
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46 </inputs>
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47 <outputs>
1
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48 <data name="output_ivr" from_work_dir="ivr_val_qu.RDS" format="rdata" label="IVR Rdata"/>
0
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49 <collection type="list" name="plots" label="IVR plot">
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50 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" visible="false" format="png"/>
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51 </collection>
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52 <collection type="list" name="output_report" label="Reports">
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53 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.docx" directory="results" visible="false" format="docx"/>
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54 </collection>
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55 </outputs>
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56 <tests>
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57 <test expect_num_outputs="3">
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58 <param name="fiche_val" value="ficheterrain.csv"/>
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59 <param name="input_data" value="champbloc_ivr.csv"/>
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60 <output name="output_ivr">
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61 <assert_contents>
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62 <has_text text="yo"/>
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63 </assert_contents>
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64 </output>
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65 <output_collection name="plots" type="list" count="23"/>
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66 <output_collection name="output_report" type="list" count="23"/>
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67 </test>
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68 </tests>
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69 <help><![CDATA[
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70 =============
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71 VTI indicator
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72 =============
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73
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74
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75 **What it does**
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76
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77 Calculates the Visual Boulder Turning Indicator (VTI), which is similar to a "landscape" indicator to assess fishing pressure based on architectural criteria.
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78 Based on the proportion of "turned" and "not turned" blocs this indicator vary from 0 to 5 and can be quickly used.
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79
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80 **Input description**
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81
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82 TWO input files in csv format.
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83
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84 +---------------+------------------+
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85 | CSV | CSV |
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86 +===============+==================+
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87 | champbloc.csv | ficheterrain.csv |
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88 +---------------+------------------+
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89 | ... | ... |
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90 +---------------+------------------+
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91
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92
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93 **Output**
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94
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95 - .RDS file 1 of them for the ivr
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96 - Multiple png plots one for each of the locations
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97
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98
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99 ]]> </help>
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100 <expand macro="cb_bibref"/>
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101 </tool>