view recup_list.xml @ 4:2152f424e7a2 draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit c41939f1cdc03331ec021d47495576a6b0c5fd14

<tool id="ecoregion_taxa_seeker" name="TaxaSeeker" version="0.1.0+galaxy0" profile="22.05">
    <description>for recover list of taxa</description>
    <requirements>
    <requirement type="package" version="4.2.3">r-base</requirement>
    <requirement type="package" version="1.1.3">r-dplyr</requirement>
    <requirement type="package" version="1.6.2">r-taxonomycleanr</requirement> 
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        Rscript
        '$__tool_directory__/recup_liste_taxon.R'
        '$occurencefile'
        '$predictionfile'
        '$envfile'
        '$output1'
        '$output2'
        '$output3' 
    ]]></command>
    <inputs>
         <param name="envfile" type="data" format="tabular" label="Environement file (tabular format only)" help="See example below"/>
         <param name="occurencefile" type="data" format="tabular" multiple="True" label="Occurences file(s) (tabular format only)" help="See example below"/>
         <param name="predictionfile" type="data" format="tabular" multiple="True" label="Predictions file(s)" help="See example below"/>
    </inputs>
    <outputs>
     <data name="output1" from_work_dir="have_model.tsv" format="tabular" label="Summary of taxa model "/>
     <data name="output2" from_work_dir="list_taxa.txt" format="txt" label="List of taxa"/>
     <data name="output3" from_work_dir="list_taxa_clean.txt" format="txt" label="List of taxa clean"/>
    </outputs>
    <tests>
        <test>
            <param name="occurencefile" value="cnidaria_filtered.tsv"/>
            <param name="predictionfile" value="1_brts_pred_ceamarc.tsv"/>
            <param name="envfile" value="ceamarc_env.tsv"/>
            <output name='output1' value="Summary_of_taxa_model.tsv"/>
            <output name='output2' value="List_of_taxa.txt"/>
            <output name='output3' value="List_of_taxa_clean.txt"/>
        </test>
    </tests>
    <help><![CDATA[
    
==================    
**What it does ?**
==================

This tool does three things:

- It allows obtaining a summary file for each taxon indicating whether a BRT model was obtained and the number of occurrences per taxon.

- It provides a list of taxons that obtained cleaned BRT models (without "_", "_sp", etc.) to propose the list to WorMS (World Register Of Marine Species) and obtain more information about the taxons.

- It generates a list of taxons that obtained a BRT model for use in the subsequent ecoregionalization workflow.

===================         
**How to use it ?**
===================

This tool takes three inputs : Occurrences file(s), predictions file(s) and environement file. See example below. 


**Example of environmentfile :** 

+------+------+---------+------+--------------+-----+
| long | lat  |  Carbo  | Grav |  Maxbearing  | ... |
+------+------+---------+------+--------------+-----+
|139.22|-65.57|   0.88  |28.59 |     3.67     | ... |
+------+------+---------+------+--------------+-----+
|139.22|-65.57|   0.88  |28.61 |     3.64     | ... |
+------+------+---------+------+--------------+-----+
| ...  | ...  |   ...   | ...  |     ...      | ... |
+------+------+---------+------+--------------+-----+


**Example of occurences file :** 

+---------+----------+-----------+------------------------+-----------+-----+------+--------------+-----+
| 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     | ... |
+---------+----------+-----------+------------------------+-----------+-----+------+--------------+-----+
|   ...   |   ...    |   ...     |          ...           |    ...    | ... | ...  |     ...      | ... |
+---------+----------+-----------+------------------------+-----------+-----+------+--------------+-----+

**Example of the predictions file :**

+-----------+----------+-----------------------+-------------+
|    lat    |   long   |   Prediction.index    |     spe     |
+-----------+----------+-----------------------+-------------+
|  -65.57   |  139.22  |   0.122438487221909   |  Acarnidae  |
+-----------+----------+-----------------------+-------------+
|  -65.57   |  139.32  |   0.119154535627801   |  Acarnidae  |
+-----------+----------+-----------------------+-------------+
|   ...     |   ...    |         ...           |     ...     |
+-----------+----------+-----------------------+-------------+

    ]]></help>
    <citations>
       <citation type="doi">10.32614/CRAN.package.dplyr</citation>
       <citation type="bibtex">@Manual{,
          title = {taxonomyCleanr: A workflow and set of functions to clean taxonomy data using R},
          author = {Colin Smith},
          year = {2023},
          note = {https://github.com/EDIorg/taxonomyCleanr,
          https://ediorg.github.io/taxonomyCleanr/},
      }</citation>
    </citations>
</tool>