cb_dissimilarity.xml

<tool id="cb_dissim" name="Dissimilarity" 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="2.6_2">r-vegan</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_qecb.csv"/>
        <include type="literal" path="test-data/ficheterrain.csv"/>
        <include type="literal" path="cb_dissimilarity.r"/>
    </required_files>
    <command detect_errors="exit_code"><![CDATA[
        Rscript
            '$__tool_directory__/cb_dissimilarity.r'
            '$fiche_val'
            '$input_data'
            '$choice'
            '$choice_date'
            '$__tool_directory__/cb_qecb_site_report_col_scale_loop.Rmd'
            '$__tool_directory__/loop_col_scale.r'
            '$output_qecb'
            '$output_matri'
            '$plots_bf'
            '$plots_bm'
            '$plots'
        ]]>
    </command>
    <inputs>
        <expand macro="cb_input"/>
        <param name="input_data" type="data" format="data" label="Input champbloc_qecb.csv"/>
        <param name="choice" type="select" label="Do you have data after the year 2021 ?" display="radio">
            <option value="N">No</option>
            <option value="Y">Yes</option>
        </param>
        <param name="choice_date" type="integer" value="2021" label="Until when do you have data (write only the YEAR) ?" help="Example write : 2021 "/>
    </inputs>
    <outputs>
        <data name="output_qecb" from_work_dir="qecbnato0.RDS" format="data" label="Clean Rdata"/>
        <data name="output_matri" from_work_dir="matri_full.RDS" format="data" label="Matrice full Rdata"/>
        <collection type="list" name="plots_bf" label="Bloc fixe et bloc mobile face sup plot">
            <discover_datasets pattern="bm(?P&lt;designation&gt;.+)\.png" visible="false" format="png"/>
        </collection>
        <collection type="list" name="plots_bm" label="Bloc mobile face sup et face inf plot">
            <discover_datasets pattern="fs(?P&lt;designation&gt;.+)\.png" visible="false" format="png"/>
        </collection><!--&lowbar; pour underscore-->
        <collection type="list" name="plots" label="Distance plot">
            <discover_datasets pattern="distance(?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="5">
            <param name="fiche_val" value="ficheterrain.csv"/>
            <param name="input_data" value="champbloc_qecb.csv"/>
            <param name="choice" value="N"/>
            <param name="choice_date" value="2021"/>
            <output name="output_qecb">
                <assert_contents>
                    <has_text text="E6P"/>
                </assert_contents>
            </output>
            <output name="output_matri">
                <assert_contents>
                    <has_text text="6t"/>
                </assert_contents>
            </output>
            <output_collection name="plots_bf" type="list" count="23"/>
            <output_collection name="plots_bm" type="list" count="23"/>
            <output_collection name="plots" type="list" count="2"/>
        </test>
    </tests>
    <help><![CDATA[
=======================
Dissimilarity indicator
=======================


**What it does**

This tool computes the the Boulder Field Ecological Quality Index (BFEQ) based on biotic and abiotic variables that respond to the disturbance "boulder turning".

**Input description**

One input files in Rdata format.

+----------------+
|      Rdata     |
+================+
|   clean Rdata  |
+----------------+
|       ...      |
+----------------+


**Output**

- .RDS file 1 of them to use as an input for diversity index 
- Multiple png plots one for each of the locations



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