cb_ivr.xml

<tool id="cb_ivr" name="IVR" version="@VERSION@" profile = "20.01">
    <description>indicator</description>
    <macros>
        <import>macro.xml</import>
    </macros>
    <expand macro="cb_requirements">
        <requirement type="package" version="2.16">r-rmarkdown</requirement>
        <requirement type="package" version="0.2.4">r-officedown</requirement>
        <requirement type="package" version="1.3.2">r-tidyverse</requirement>
        <requirement type="package" version="0.4.4">r-officer</requirement>
        <requirement type="package" version="0.8.1">r-flextable</requirement>
        <requirement type="package" version="3.3.6">r-ggplot2</requirement>
    </expand>
    <required_files>
        <include type="literal" path="test-data/champbloc_ivr.csv"/>
        <include type="literal" path="test-data/ficheterrain.csv"/>
        <include type="literal" path="CB_ivr.tif"/>
        <include type="literal" path="logo_merged.png"/>
        <include type="literal" path="cb_ivr_site_report_col_scale_loop.Rmd"/>
        <include type="literal" path="loop_col_scale.r"/>
        <include type="literal" path="cb_ivr.r"/>
    </required_files>
    <command detect_errors="exit_code"><![CDATA[
        Rscript
            '$__tool_directory__/cb_ivr.r'
            '$fiche_val'
            '$input_data'
            '$__tool_directory__/cb_ivr_site_report_col_scale_loop.Rmd'
            '$__tool_directory__/loop_col_scale.r'
            '$output_ivr'
            '$plots'
            '$output_report'
        ]]>
    </command>
    <inputs>
        <expand macro="cb_input"/>
        <param name="input_data" type="data" format="data" label="Input champbloc_ivr.csv"/>
    </inputs>
    <outputs>
        <data name="output_ivr" from_work_dir="ivr_val_qu.RDS" format="data" label="IVR Rdata"/>
        <collection type="list" name="plots" label="IVR plot">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" visible="false" format="png"/>
        </collection>
        <collection type="list" name="output_report" label="Reports">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.docx" directory="results" visible="false" format="docx"/>
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="3">
            <param name="fiche_val" value="ficheterrain.csv"/>
            <param name="input_data" value="champbloc_ivr.csv"/>
            <output name="output_ivr">
                <assert_contents>
                    <has_text text="yo"/>
                </assert_contents>
            </output>
            <output_collection name="plots" type="list" count="23"/>
            <output_collection name="output_report" type="list" count="23"/>
        </test>
    </tests>
    <help><![CDATA[
=============
VTI indicator
=============


**What it does**

Calculates the Visual Boulder Turning Indicator (VTI), which is similar to a "landscape" indicator to assess fishing pressure based on architectural criteria.
Based on the proportion of "turned" and "not turned" blocs this indicator vary from 0 to 5 and can be quickly used.

**Input description**

TWO input files in csv format.

+---------------+------------------+
|      CSV      |        CSV       |
+===============+==================+
| champbloc.csv | ficheterrain.csv |
+---------------+------------------+
|      ...      |        ...       |
+---------------+------------------+


**Output**

- .RDS file 1 of them for the ivr
- Multiple png plots one for each of the locations


    ]]>    </help>
        <expand macro="cb_bibref"/>
</tool>