cb_freq.xml

<tool id="cb_freq" name="Freq" version="0.0.0" profile = "20.01">
    <description>things</description>
    <requirements>
        <requirement type="package" version="1.0.10">r-dplyr</requirement>
        <requirement type="package" version="1.2.1">r-tidyr</requirement>
        <requirement type="package" version="1.14.2">r-data.table</requirement>
        <requirement type="package" version="1.4.1">r-stringr</requirement>
        <requirement type="package" version="1.4.1">r-readxl</requirement>
        <requirement type="package" version="3.1.8">r-tibble</requirement>
        <requirement type="package" version="3.3.6">r-ggplot2</requirement>
    </requirements>
    <required_files>
        <include type="literal" path="test-data/frequentation_habitat.csv"/>
        <include type="literal" path="test-data/frequentation_site.csv"/>
        <include type="literal" path="test-data/frequentation_soussite.csv"/>
        <include type="literal" path="test-data/ficheterrain_freq.csv"/>
        <include type="literal" path="test-data/champ_bloc_observation.csv"/>
        <include type="literal" path="cb_freq.r"/>
    </required_files>
    <command detect_errors="exit_code"><![CDATA[
        Rscript
            '$__tool_directory__/cb_freq.r'
            '$input_hab'
            '$input_site'
            '$input_soussite'
            '$fiche_terr'
            '$input_obs'
            '$fiche'
            '$qecb'
            '$output_freq'
            '$output_obs'
            '$plots_freq'
            '$plots_obs'
        ]]>
    </command>
    <inputs>
        <param name="input_hab" type="data" format="data" label="Input frequentation_habitat.csv"/>
        <param name="input_site" type="data" format="data" label="Input frequentation_site.csv"/>
        <param name="input_soussite" type="data" format="data" label="Input frequentation_soussite.csv"/>
        <param name="fiche_terr" type="data" format="data" label="Input ficheterrain.csv" help="You have to take the ficheterrain.csv from the 'Suivi de la fréquentation des pêcheurs' folder of Estamp"/>
        <param name="input_obs" type="data" format="data" label="Input champ_bloc_observation.csv"/>
        <param name="fiche" type="data" format="data" label="Input ficheterrain.csv" help="You have to take the ficheterrain.csv from the 'Suivi des champs de blocs' folder of Estamp"/>
        <param name="qecb" type="data" format="data" label="Input Clean Rdata"/>
    </inputs>
    <outputs>
        <data name="output_freq" from_work_dir="freq.RDS" format="data" label="Frequentation Rdata"/>
        <data name="output_obs" from_work_dir="obs.RDS" format="data" label="Observations Rdata"/>
        <collection type="list" name="plots_freq" label="Frequentation plots">
            <discover_datasets pattern="freq_(?P&lt;designation&gt;.+)\.png" visible="false" format="png"/>
        </collection>
        <collection type="list" name="plots_obs" label="Comportement plots">
            <discover_datasets pattern="obs_(?P&lt;designation&gt;.+)\.png" visible="false" format="png"/>
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="4">
            <param name="input_hab" value="frequentation_habitat.csv"/>
            <param name="input_site" value="frequentation_site.csv"/>
            <param name="input_soussite" value="frequentation_soussite.csv"/>
            <param name="fiche_terr" value="ficheterrain_freq.csv"/>
            <param name="input_obs" value="champ_bloc_observation.csv"/>
            <param name="qecb" value="Clean_Rdata.data"/>
            <output name="output_freq">
                <assert_contents>
                    <has_text text="cwE"/>
                </assert_contents>
            </output>
            <output name="output_obs">
                <assert_contents>
                    <has_text text="cwE"/>
                </assert_contents>
            </output>
            <output_collection name="plots_freq" type="list" count="17"/>
            <output_collection name="plots_obs" type="list" count="16"/>
        </test>
    </tests>
    <help><![CDATA[
========================
Fisher men frequentation
========================


**What it does**

Calculates the fisher men frequentation for each sites.

**Input description**

TWO input files in csv format.

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


**Output**

- .RDS files 2 of them for the frequentatio and observation
- Multiple png plots one for each of the locations



    ]]>    </help>

</tool>