diff comparison_div.xml @ 0:cf69ad260611 draft default tip

planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/comparison_div.xml	Mon Jan 09 13:36:02 2023 +0000
@@ -0,0 +1,138 @@
+<tool id="srs_process_data" name="Compare diversity indicators" version="@VERSION@" profile="20.01">
+    <description>with remote sensing data</description>
+    <macros>
+        <import>macro.xml</import>
+    </macros>
+    <expand macro="SRS_requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        #import re 
+        #if $method.type == 'envi_bil': 
+          #set input_raster = $method.input_raster
+          #set input_raster_identifier = re.sub('[^\s\w\-]', '_', str($input_raster.element_identifier)) 
+          #set input_header = $method.input_header
+          #set input_header_identifier = re.sub('[^\s\w\-]+[^.hdr]', '_', str($input_header.element_identifier)) 
+          cp '${input_raster}' '${input_raster_identifier}' &&
+          cp '${input_header}' '${input_header_identifier}' &&
+        #end if
+        Rscript
+            '$__tool_directory__/comparison_div.r'
+             #if $method.type == 'envi_bil':
+              '$input_raster_identifier' 
+              '$input_header_identifier'
+              ''
+            #else:
+              ''
+              ''
+              '$method.input'
+            #end if
+            '$input_plot'
+            '$choice'
+            '$__tool_directory__/functions.r'
+            '$typepca'
+            '$output_div'
+            '$output_beta'
+            '$plots'
+        ]]>
+    </command>
+    <inputs>
+        <conditional name="method">
+            <param name="type" type="select" label="In which format are your data ?">
+                <option value="zipper">The data you are using are in a zip folder Reflectance</option>
+                <option value="envi_bil">Your already have the files in ENVI BIL format</option>
+            </param>
+            <when value="zipper">
+                <param name="input" type="data" format="zip" multiple="true" label="Input data"/>
+            </when>
+            <when value="envi_bil">
+                <param name="input_raster" type="data" format="bil" label="Input raster" help="It can be the raw data in bil or the PCA raster layer in bil"/>
+                <param name="input_header" type="data" format="hdr" label="Input header"/>
+            </when>
+        </conditional>
+        <param name="input_plot" type="data" format="data" label="Plots folder zip"/>
+        <param name="choice" type="select" label="Do you want to compute beta diversity (needs mutliple locations) ?" display="radio">
+            <option value="Y">Yes</option>
+            <option value="N">No</option>
+        </param>
+        <param name="typepca" type="select" label="Do you want to do a PCA or a SPCA ?" display="radio" help="If you choose PCA there is no rescaling of the data as oppposed as if you choose SPCA">
+            <option value="SPCA">SPCA</option>
+            <option value="PCA">PCA</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output_div" from_work_dir="Diversity.tabular" format="tabular" label="Global diversity">
+        </data>
+        <data name="output_beta" from_work_dir="BrayCurtis.tabular" format="tabular" label="Bray Curtis">
+            <filter>choice == 'Y'</filter>
+        </data>
+        <collection type="list" name="plots" label="Comparison plot">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" visible="false" format="png"/>
+            <filter>choice =='Y'</filter>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="type" value="envi_bil"/>
+            <param name="input_raster" value="S2A_Subset"/>
+            <param name="input_header" value="S2A_Subset.hdr"/>
+            <param name="input_plot" value="S2A_T33NUD_Plots.zip"/>
+            <param name="choice" value="Y"/>
+            <output name="output_div">
+                <assert_contents>
+                    <has_n_lines n="25"/>
+                </assert_contents>
+            </output>
+            <output name="output_beta">
+                <assert_contents>
+                    <has_n_lines n="25"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="1"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+========================================================================
+Process satellite remote sensing data to produce biodiversity indicators
+========================================================================
+
+
+**What it does**
+
+Féret and Asner (2014) developed a method for **tropical forest** diversity mapping based on very high spatial resolution airborne imaging spectroscopy.
+
+The goal of this tool using the package biodivMapR is to compute diversity indices over each spatial polygon of a shapefile of plots, if available, in order to compare field inventories with diversity indices estimated from remotely-sensed images.
+
+**Input description**
+
+It expects an image file as input, with a specific data format. ENVI HDR image with BIL interleave required.
+The image is an ENVI raster including :
+
+- A binary file (which has no extension here).
+
+- A header file (with .hdr extension).
+
+The header file is a text file including all necessary metadata which can be read with a text editor. It includes image dimensions, projection, and the name and central wavelength for each spectral band.
+
+In order to get such input we advise to use the tool preprocessing sentinel 2 data. 
+
++--------------+----------+--------------+
+|      BIL     | ENVI HDR |  Shapefiles  |
++==============+==========+==============+
+| raster stack | Metadata |  plots.zip   |
++--------------+----------+--------------+
+|      ...     |    ...   |      ...     |
++--------------+----------+--------------+
+
+**Output**
+
+- Two tabulars : 
+    - One matrix for Bray-Curtis indicator
+    - One table for the following indicators; Species richness, shannon, fisher, simpson, richness, eveness, divergence
+
+- One comparison png plot in the Pcoa space that summarizes α- and β-diversity in scatterplots and illustrates that the combination of the three components computed with PCoA allows proper differentiation among vegetation types:
+    - PCoA#1 allows differentiating medium and high diversity forests from low diversity forest and low vegetation, but does not discriminate medium and high diversity forests.
+    - PCoA#2 allows differentiating low diversity forest from medium/high diversity forests and low vegetation
+    - PCoA#3 allows differentiating medium diversity forests from high diversity forests and low vegetation.
+
+    ]]>    </help>
+        <expand macro="SRS_BDMRref"/>
+</tool>