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Merge pull request #91 from PaulineSGN/PaulineSGN-patch-1
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Update ecoregionalization workflow
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@yvanlebras
yvanlebras authored Jan 24, 2024
2 parents 313d35a + 881aea4 commit 459ba12
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74 changes: 37 additions & 37 deletions tools/Ecoregionalization_workflow/BRT_model.xml
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@@ -1,4 +1,4 @@
<tool id="ecoregion_brt_analysis" name="BRT tool prediction" version="0.1.0+galaxy0" profile="22.05">
<tool id="ecoregion_brt_analysis" name="BRT prediction tool" version="0.1.0+galaxy0" profile="22.05">
<description>for species distribution modelling</description>
<requirements>
<requirement type="package" version="4.3.0">r-base</requirement>
Expand All @@ -16,15 +16,25 @@
'$outputval'
'$outputspdistri'
'$outputplots'
'$dec_env'
'$dec_species'
]]></command>
<inputs>
<param name="enviro" type="data" format="txt,csv,tabular" label="Environment Data"/>
<param type="data" name="species_files" label="Occurrences Data File" format="tabular,txt,csv" multiple="True" />
<param name="abioticname" type="text" label="Write the name of your abiotic parameters (comma separated)"/>
<param name="enviro" type="data" format="tabular" label="Input your environment data file of your study area (tabular format only)" help="See example below"/>
<param name="dec_env" type="select" label="What's the decimal separator of your environement data file ?">
<option value=".">Dot</option>
<option value=",">Comma</option>
</param>
<param type="data" name="species_files" label="Input your occurrences data file(s) containing also the environemental caracteristics where the species has been observe (tabular format only)" format="tabular" multiple="True" help="See example below"/>
<param name="dec_species" type="select" label="What's the decimal separator of your occurrences data file(s) ?" help="It must be the same for all your occurences data files" >
<option value=".">Dot</option>
<option value=",">Comma</option>
</param>
<param name="abioticname" type="data_column" label="Choose column(s) where your abiotic parameter are in your environment data file." data_ref="enviro" multiple="true"/>
</inputs>
<outputs>
<collection name="outputpred" type="list" label="Prediction files">
<discover_datasets pattern="(?P&lt;designation&gt;.+_brts_pred_ceamarc)\.txt" format="txt"/>
<discover_datasets pattern="(?P&lt;designation&gt;.+_brts_pred_ceamarc)\.tsv" format="tabular"/>
</collection>
<collection name="outputval" type="list" label="Validation files (Taxa, AUC, Tree complexity, Total deviance explained)">
<discover_datasets pattern="(?P&lt;designation&gt;.+_brts_validation_ceamarc)\.tsv" format="tabular" />
Expand All @@ -38,25 +48,15 @@
</outputs>
<tests>
<test>
<param name="enviro" value="ceamarc_env.csv"/>
<param name="species_files" value="cnidaria_filtered.csv"/>
<param name="abioticname" value="Carbo,Grav,Maxbearing,Maxmagnit,Meancurmag,Meansal,Meantheta,Mud,Prof,Rugosity,Sand,Seaice_prod,Sili,Slope,Standcurmag,Standsal,Standtheta"/>
<param name="enviro" value="ceamarc_env.tsv"/>
<param name="species_files" value="cnidaria_filtered.tsv"/>
<param name="abioticname" value="3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19"/>
<param name="dec_env" value="Dot"/>
<param name="dec_species" value="Comma"/>
<output_collection name='outputpred' type = "list" count="1"/>
<output_collection name='outputval' type = "list" count="1"/>
<output_collection name='outputspdistri' type = "list" count="2">
<element name="BRT- Actiniaria _pred_plot">
<assert_contents>
<has_size value="76065" delta="10000"/>
</assert_contents>
</element>
</output_collection>
<output_collection name='outputplots' type = "list">
<element name="BRT- Actiniaria " >
<assert_contents>
<has_size value="16042" delta="1000"/>
</assert_contents>
</element>
</output_collection>
<output_collection name='outputspdistri' type = "list" count="2"/>
<output_collection name='outputplots' type = "list" count="2"/>
</test>
</tests>
<help><![CDATA[
Expand All @@ -71,8 +71,12 @@ detected. Two steps are performed in this script: the creation of the taxon dist
**How to use it ?**
===================
This tool takes in input the environmental data as well as the species occurrence data. See examples of inputs below. You also need to input the list of abiotic parameters (respecting the case, without spaces and separating them by commas). For example : Carbo,Grav,Maxbearing,...
This tool gives in output a file containing the predictions of probability of presence of each taxon for each pixel (latitude, longitude) environmental, a visualization of these pixels for each taxon and graphs showing the percentage of model explanation for each environmental parameter.
This tool takes in input the environmental data (for all the study areas) as well as the species occurrence data and the environmental characteristics where the species has been observed. See examples of inputs below. These files need to be in tabular format. You also need to select the column where your abiotic parameters are in your environment data file.
.. class:: infomark
Your abiotic parameters must be present in your occurrence data file(s) and must be named the same as in your environment file.
This tool gives in output a file containing the predictions of the probability of the presence of each taxon for each pixel (latitude, longitude) environmental, a visualization of these pixels for each taxon and graphs showing the percentage of model explanation for each environmental parameter.
**Example of environmental data input :**
-----------------------------------------
Expand All @@ -87,22 +91,18 @@ This tool gives in output a file containing the predictions of probability of pr
| ... | ... | ... | ... | ... | ... |
+------+------+---------+------+--------------+-----+
**Example of occurence data input :**
-------------------------------------
+---------+----------+-----------+------------------------+-----------+-----+
| station | lat | long |Acanthorhabdus_fragilis | Acarnidae | ... |
+---------+----------+-----------+------------------------+-----------+-----+
| 1 |-65,999946|142,3360535| 0 | 1 | ... |
+---------+----------+-----------+------------------------+-----------+-----+
| 10 |-66,335407| 141,3028 | 0 | 1 | ... |
+---------+----------+-----------+------------------------+-----------+-----+
| ... | ... | ... | ... | ... | ... |
+---------+----------+-----------+------------------------+-----------+-----+
+---------+----------+-----------+------------------------+-----------+-----+------+--------------+-----+
| station | lat | long |Acanthorhabdus_fragilis | Acarnidae | ... | Grav | Maxbearing | ... |
+---------+----------+-----------+------------------------+-----------+-----+------+--------------+-----+
| 1 |-65,999946|142,3360535| 0 | 1 | ... |28.59 | 3.67 | ... |
+---------+----------+-----------+------------------------+-----------+-----+------+--------------+-----+
| 10 |-66,335407| 141,3028 | 0 | 1 | ... |28.61 | 3.64 | ... |
+---------+----------+-----------+------------------------+-----------+-----+------+--------------+-----+
| ... | ... | ... | ... | ... | ... | ... | ... | ... |
+---------+----------+-----------+------------------------+-----------+-----+------+--------------+-----+
]]></help>
</tool>
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22 changes: 13 additions & 9 deletions tools/Ecoregionalization_workflow/Nb_cluster.xml
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Expand Up @@ -21,9 +21,9 @@
]]>
</command>
<inputs>
<param name="envfile" type="data" format="txt,csv,tabular" label="Environment file"/>
<param name="taxafile" type="data" format="txt" label="Taxa selected file (List of taxa from TaxaSeeker tool)"/>
<param name="predictionfile" type="data" format="txt" multiple="true" label="Prediction files"/>
<param name="envfile" type="data" format="tabular" label="Environment file (tabular format only)" help="See example below"/>
<param name="taxafile" type="data" format="txt" label="Taxa selected file (File 'List of taxa' from TaxaSeeker tool)"/>
<param name="predictionfile" type="data" format="tabular" multiple="true" label="Prediction files"/>
<param name="max_k" type="integer" value="2" min="1" label="Number of Cluster to test"/>
<param name="metric" type="select" label="What metric to use to calculate dissimilarities between observations ?">
<option value="manhattan">manhattan</option>
Expand All @@ -34,18 +34,22 @@
</inputs>
<outputs>
<data name="output1" from_work_dir="Indices_SIH.png" format="png" label="SIH index plot"/>
<data name="output2" from_work_dir="data_to_clus.tsv" format="tsv" label="Data to cluster"/>
<data name="output3" from_work_dir="data_bio.tsv" format="tsv" label="Data.bio table "/>
<data name="output2" from_work_dir="data_to_clus.tsv" format="tabular" label="Data to cluster"/>
<data name="output3" from_work_dir="data_bio.tsv" format="tabular" label="Data.bio table "/>
</outputs>
<tests>
<test>
<param name="envfile" value="ceamarc_env.csv"/>
<param name="envfile" value="ceamarc_env.tsv"/>
<param name="taxafile" value="List_of_taxa.txt"/>
<param name="predictionfile" value="1_brts_pred_ceamarc.txt"/>
<param name="predictionfile" value="1_brts_pred_ceamarc.tsv"/>
<param name='max_k' value="2"/>
<param name='metric' value="manhattan"/>
<param name='sample' value="10"/>
<output name='output1' value="SIH_index_plot.png"/>
<output name='output1'>
<assert_contents>
<has_size value="4297" delta="500"/>
</assert_contents>
</output>
<output name='output2' value="Data_to_cluster.tsv"/>
<output name='output3' value="Data.bio_table.tsv"/>
</test>
Expand All @@ -71,7 +75,7 @@ Then there are few parameters :
- the sample size that will be used to perform clustering. Indeed, the clara function is used to clustering large data using a representative sample rather than the entire data set. This will speed up the clustering process and make the calculation more efficient. A fairly high value representative of the data is recommended. It is important to note that using too small a sample may result in loss of information compared to using the entire data set.
The tool will produce three outputs. The first two are files that will be used in the rest of the workflow: a file containing four pieces of information, latitude, longitude, presence prediction and corresponding taxon, and a file containing the data to be partitioned. The third output corresponds to the main information of the tool, a graph presenting the value of the HIS index according to the number of clusters. The silhouette index provides a measure of the separation between clusters and the compactness within each cluster. The silhouette index ranges from -1 to 1. Values close to 1 indicate that objects are well grouped and separated from other clusters, while values close to -1 indicate that objects are poorly grouped and may be closer to other clusters. A value close to 0 indicates a situation where objects are located at the border between two neighboring clusters.
The tool will produce three outputs. The first two are files that will be used in the rest of the workflow: a file containing four pieces of information, latitude, longitude, presence prediction and corresponding taxon, and a file containing the data to be partitioned. The third output corresponds to the main information of the tool, a graph presenting the value of the SIH index according to the number of clusters. The silhouette index provides a measure of the separation between clusters and the compactness within each cluster. The silhouette index ranges from -1 to 1. Values close to 1 indicate that objects are well grouped and separated from other clusters, while values close to -1 indicate that objects are poorly grouped and may be closer to other clusters. A value close to 0 indicates a situation where objects are located at the border between two neighboring clusters.
**Example of the environemental file :**
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