Mercurial > repos > ecology > ecoregion_taxa_seeker
view recup_list.xml @ 0:e3cd588fd14a draft
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 2a2ae892fa2dbc1eff9c6a59c3ad8f3c27c1c78d
author | ecology |
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date | Wed, 18 Oct 2023 09:58:17 +0000 |
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children | 9dc992f80c25 |
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<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="occurencefile" type="data" format="txt" multiple="True" label="Occurences file"/> <param name="predictionfile" type="data" format="txt" multiple="True" label="Predictions file"/> <param name="envfile" type="data" format="txt,csv,tabular" label="Environement file"/> </inputs> <outputs> <data name="output1" from_work_dir="have_model.csv" format="csv" 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.csv"/> <param name="predictionfile" value="1_brts_pred_ceamarc.txt"/> <param name="envfile" value="ceamarc_env.csv"/> <output name='output1' value="Summary_of_taxa_model.csv"/> <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, predictions file 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 | ... | +---------+----------+-----------+------------------------+-----------+-----+ | 1 |-65,999946|142,3360535| 0 | 1 | ... | +---------+----------+-----------+------------------------+-----------+-----+ | 10 |-66,335407| 141,3028 | 0 | 1 | ... | +---------+----------+-----------+------------------------+-----------+-----+ | ... | ... | ... | ... | ... | ... | +---------+----------+-----------+------------------------+-----------+-----+ *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> </tool>