Mercurial > repos > ecology > cb_ivr

annotate cb_ivr.xml @ 1:b67730406f1b draft

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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
author ecology
date Wed, 04 Jan 2023 13:21:30 +0000
parents 8c6142630659
children bcbad4f83dec
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8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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1 <tool id="cb_ivr" name="IVR" version="@VERSION@" profile = "20.01">
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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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>
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6 <expand macro="cb_requirements">
1
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7 <requirement type="package" version="2.19">r-rmarkdown</requirement>
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8 <requirement type="package" version="0.2.4">r-officedown</requirement>
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9 <requirement type="package" version="1.3.2">r-tidyverse</requirement>
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10 <requirement type="package" version="0.5.0">r-officer</requirement>
b67730406f1b planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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11 <requirement type="package" version="0.8.3">r-flextable</requirement>
b67730406f1b planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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12 <requirement type="package" version="3.4">r-ggplot2</requirement>
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8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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13 </expand>
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14 <required_files>
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15 <include type="literal" path="test-data/champbloc_ivr.csv"/>
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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16 <include type="literal" path="test-data/ficheterrain.csv"/>
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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17 <include type="literal" path="CB_ivr.tif"/>
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18 <include type="literal" path="logo_merged.png"/>
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19 <include type="literal" path="cb_ivr_site_report_col_scale_loop.Rmd"/>
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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20 <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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21 <include type="literal" path="cb_ivr.r"/>
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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22 </required_files>
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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23 <command detect_errors="exit_code"><![CDATA[
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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24 Rscript
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25 '$__tool_directory__/cb_ivr.r'
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26 '$fiche_val'
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27 '$input_data'
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28 '$__tool_directory__/cb_ivr_site_report_col_scale_loop.Rmd'
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29 '$__tool_directory__/loop_col_scale.r'
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30 '$output_ivr'
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31 '$plots'
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32 '$output_report'
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33 ]]>
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34 </command>
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35 <inputs>
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36 <expand macro="cb_input"/>
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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37 <param name="input_data" type="data" format="data" label="Input champbloc_ivr.csv"/>
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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38 </inputs>
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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39 <outputs>
1
b67730406f1b planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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40 <data name="output_ivr" from_work_dir="ivr_val_qu.RDS" format="rdata" label="IVR Rdata"/>
0
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41 <collection type="list" name="plots" label="IVR plot">
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42 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" visible="false" format="png"/>
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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43 </collection>
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44 <collection type="list" name="output_report" label="Reports">
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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45 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.docx" directory="results" visible="false" format="docx"/>
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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46 </collection>
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47 </outputs>
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48 <tests>
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49 <test expect_num_outputs="3">
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50 <param name="fiche_val" value="ficheterrain.csv"/>
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51 <param name="input_data" value="champbloc_ivr.csv"/>
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52 <output name="output_ivr">
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53 <assert_contents>
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54 <has_text text="yo"/>
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55 </assert_contents>
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56 </output>
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57 <output_collection name="plots" type="list" count="23"/>
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58 <output_collection name="output_report" type="list" count="23"/>
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59 </test>
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60 </tests>
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61 <help><![CDATA[
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62 =============
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63 VTI indicator
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64 =============
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65
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66
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67 **What it does**
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68
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69 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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70 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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71
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72 **Input description**
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73
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74 TWO input files in csv format.
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75
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76 +---------------+------------------+
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77 | CSV | CSV |
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78 +===============+==================+
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79 | champbloc.csv | ficheterrain.csv |
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80 +---------------+------------------+
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81 | ... | ... |
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82 +---------------+------------------+
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83
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84
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85 **Output**
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86
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87 - .RDS file 1 of them for the ivr
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88 - Multiple png plots one for each of the locations
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89
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90
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91 ]]> </help>
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92 <expand macro="cb_bibref"/>
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93 </tool>