--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/stat_presence_abs.xml	Tue Jul 27 16:57:02 2021 +0000
@@ -0,0 +1,88 @@
+<tool id="ecology_stat_presence_abs" name="Statistics on presence-absence" version="@VERSION@" profile = "20.01">
+    <description>of a numeric variable</description>
+    <macros>
+        <import>macro.xml</import>
+    </macros>
+    <expand macro="Explo_requirements">
+        <requirement type="package" version="1.1.1">r-cowplot</requirement>
+        <requirement type="package" version="0.1.3">r-ggcorrplot</requirement>
+        <requirement type="package" version="1.0.5">r-dplyr</requirement>
+    </expand>
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript
+            '$__tool_directory__/graph_stat_presence_abs.r'
+            '$input'
+            '$colnames'
+            '$variable1'
+            '$species'
+            '$location'
+            '$time'
+            '$output_md'
+        ]]>
+    </command>
+    <inputs>
+        <expand macro="explo_input"/>
+        <param name="variable1" label="Select a column containing numerical values (such as the abundance) " type="data_column" data_ref="input" numerical="true" use_header_names="true"/>
+         <param name="species" label="Select the column of the x-axis : most commonly species" type="data_column" data_ref="input" use_header_names="true" help= "Variable for dispersion plot and to see the correlation between zeros"/>
+        <param name="location" label="Select column containing locations " type="data_column" data_ref="input" use_header_names="true"/>
+        <param name="time" label="Select column containing temporal data (year, date, ...) " type="data_column" data_ref="input" use_header_names="true"/>
+    </inputs>
+    <outputs>
+        <data name="output_md" from_work_dir="Med_Disp.png" format="png" label="Boxplot and dispersion plot"/>
+        <data name="output_0" from_work_dir="0_pb.png" format="png" label="Absence-correlation plot"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="Reel_life_survey_fish_modif.tabular"/>
+            <param name="colnames" value="true"/>
+            <param name="variable1" value="18"/>
+            <param name="variable2" value="15"/>
+            <output name="output_md" ftype="png">
+                <assert_contents>
+                    <has_text text="PNG"/>
+                </assert_contents>
+            </output>
+            <output name="output_0" ftype="png">
+                <assert_contents>
+                    <has_text text="PNG"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <expand macro="topic"/>
+    <help><![CDATA[
+===================================================================================================================
+Create a boxplot, visualize the dispersion of a numeric variable and visualize correlation between species absences
+===================================================================================================================
+
+
+**What it does**
+
+
+This tool creates:
+
+- A boxplot of a numerical value (like the abundance) and a dispersion plot of this value according to a variable such as species.
+
+- A correlation plot using the presence of zeros in the numerical value. Handy to see if there is a correlation between the absence of two species and suggest a co-dependency.
+
+Don't use datasets with too much species, it won't be readable.
+
+**Input description**
+
+A tabular file with observation data. Must at least contain four columns a numerical value (ex: abundance), a temporal referential (year, date, ...), locations and species.
+
++-------------+------------+---------------+-------------+
+|   number    |    time    | species.code  |   location  |
++=============+============+===============+=============+
+|      2      |    date    |   speciesID   |     site    |
++-------------+------------+---------------+-------------+
+|     ...     |     ...    |      ...      |     ...     |
++-------------+------------+---------------+-------------+
+
+**Output**
+
+Two png files containing the three plots.
+    ]]>    </help>
+    <expand macro="explo_bibref"/>
+
+</tool>