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comparison cb_ivr.xml @ 0:8c6142630659 draft

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planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
author ecology
date Fri, 02 Dec 2022 16:13:07 +0000
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children b67730406f1b
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-1:000000000000 0:8c6142630659
1 <tool id="cb_ivr" name="IVR" version="@VERSION@" profile = "20.01">
2 <description>indicator</description>
3 <macros>
4 <import>macro.xml</import>
5 </macros>
6 <expand macro="cb_requirements">
7 <requirement type="package" version="2.16">r-rmarkdown</requirement>
8 <requirement type="package" version="0.2.4">r-officedown</requirement>
9 <requirement type="package" version="1.3.2">r-tidyverse</requirement>
10 <requirement type="package" version="0.4.4">r-officer</requirement>
11 <requirement type="package" version="0.8.1">r-flextable</requirement>
12 <requirement type="package" version="3.3.6">r-ggplot2</requirement>
13 </expand>
14 <required_files>
15 <include type="literal" path="test-data/champbloc_ivr.csv"/>
16 <include type="literal" path="test-data/ficheterrain.csv"/>
17 <include type="literal" path="CB_ivr.tif"/>
18 <include type="literal" path="logo_merged.png"/>
19 <include type="literal" path="cb_ivr_site_report_col_scale_loop.Rmd"/>
20 <include type="literal" path="loop_col_scale.r"/>
21 <include type="literal" path="cb_ivr.r"/>
22 </required_files>
23 <command detect_errors="exit_code"><![CDATA[
24 Rscript
25 '$__tool_directory__/cb_ivr.r'
26 '$fiche_val'
27 '$input_data'
28 '$__tool_directory__/cb_ivr_site_report_col_scale_loop.Rmd'
29 '$__tool_directory__/loop_col_scale.r'
30 '$output_ivr'
31 '$plots'
32 '$output_report'
33 ]]>
34 </command>
35 <inputs>
36 <expand macro="cb_input"/>
37 <param name="input_data" type="data" format="data" label="Input champbloc_ivr.csv"/>
38 </inputs>
39 <outputs>
40 <data name="output_ivr" from_work_dir="ivr_val_qu.RDS" format="Rdata" label="IVR Rdata"/>
41 <collection type="list" name="plots" label="IVR plot">
42 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" visible="false" format="png"/>
43 </collection>
44 <collection type="list" name="output_report" label="Reports">
45 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.docx" directory="results" visible="false" format="docx"/>
46 </collection>
47 </outputs>
48 <tests>
49 <test expect_num_outputs="3">
50 <param name="fiche_val" value="ficheterrain.csv"/>
51 <param name="input_data" value="champbloc_ivr.csv"/>
52 <output name="output_ivr">
53 <assert_contents>
54 <has_text text="yo"/>
55 </assert_contents>
56 </output>
57 <output_collection name="plots" type="list" count="23"/>
58 <output_collection name="output_report" type="list" count="23"/>
59 </test>
60 </tests>
61 <help><![CDATA[
62 =============
63 VTI indicator
64 =============
65
66
67 **What it does**
68
69 Calculates the Visual Boulder Turning Indicator (VTI), which is similar to a "landscape" indicator to assess fishing pressure based on architectural criteria.
70 Based on the proportion of "turned" and "not turned" blocs this indicator vary from 0 to 5 and can be quickly used.
71
72 **Input description**
73
74 TWO input files in csv format.
75
76 +---------------+------------------+
77 | CSV | CSV |
78 +===============+==================+
79 | champbloc.csv | ficheterrain.csv |
80 +---------------+------------------+
81 | ... | ... |
82 +---------------+------------------+
83
84
85 **Output**
86
87 - .RDS file 1 of them for the ivr
88 - Multiple png plots one for each of the locations
89
90
91 ]]> </help>
92 <expand macro="cb_bibref"/>
93 </tool>