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comparison BRT_model.xml @ 1:fc621f3f8226 draft

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 459ba1277acd7d8d4a02f90dbd7ff444bf8eac92
author ecology
date Wed, 24 Jan 2024 15:52:56 +0000
parents f0d6938d0451
children f8962f1c832a
comparison
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0:f0d6938d0451 1:fc621f3f8226
1 <tool id="ecoregion_brt_analysis" name="BRT tool prediction" version="0.1.0+galaxy0" profile="22.05"> 1 <tool id="ecoregion_brt_analysis" name="BRT prediction tool" version="0.1.0+galaxy0" profile="22.05">
2 <description>for species distribution modelling</description> 2 <description>for species distribution modelling</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="4.3.0">r-base</requirement> 4 <requirement type="package" version="4.3.0">r-base</requirement>
5 <requirement type="package" version="2.1.8">r-gbm</requirement> 5 <requirement type="package" version="2.1.8">r-gbm</requirement>
6 <requirement type="package" version="3.4.2">r-ggplot2</requirement> 6 <requirement type="package" version="3.4.2">r-ggplot2</requirement>
14 '$abioticname' 14 '$abioticname'
15 '$outputpred' 15 '$outputpred'
16 '$outputval' 16 '$outputval'
17 '$outputspdistri' 17 '$outputspdistri'
18 '$outputplots' 18 '$outputplots'
19 '$dec_env'
20 '$dec_species'
19 ]]></command> 21 ]]></command>
20 <inputs> 22 <inputs>
21 <param name="enviro" type="data" format="txt,csv,tabular" label="Environment Data"/> 23 <param name="enviro" type="data" format="tabular" label="Input your environment data file of your study area (tabular format only)" help="See example below"/>
22 <param type="data" name="species_files" label="Occurrences Data File" format="tabular,txt,csv" multiple="True" /> 24 <param name="dec_env" type="select" label="What's the decimal separator of your environement data file ?">
23 <param name="abioticname" type="text" label="Write the name of your abiotic parameters (comma separated)"/> 25 <option value=".">Dot</option>
26 <option value=",">Comma</option>
27 </param>
28 <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"/>
29 <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" >
30 <option value=".">Dot</option>
31 <option value=",">Comma</option>
32 </param>
33 <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"/>
24 </inputs> 34 </inputs>
25 <outputs> 35 <outputs>
26 <collection name="outputpred" type="list" label="Prediction files"> 36 <collection name="outputpred" type="list" label="Prediction files">
27 <discover_datasets pattern="(?P&lt;designation&gt;.+_brts_pred_ceamarc)\.txt" format="txt"/> 37 <discover_datasets pattern="(?P&lt;designation&gt;.+_brts_pred_ceamarc)\.tsv" format="tabular"/>
28 </collection> 38 </collection>
29 <collection name="outputval" type="list" label="Validation files (Taxa, AUC, Tree complexity, Total deviance explained)"> 39 <collection name="outputval" type="list" label="Validation files (Taxa, AUC, Tree complexity, Total deviance explained)">
30 <discover_datasets pattern="(?P&lt;designation&gt;.+_brts_validation_ceamarc)\.tsv" format="tabular" /> 40 <discover_datasets pattern="(?P&lt;designation&gt;.+_brts_validation_ceamarc)\.tsv" format="tabular" />
31 </collection> 41 </collection>
32 <collection name="outputspdistri" type="list" label="Species distribution prediction maps" > 42 <collection name="outputspdistri" type="list" label="Species distribution prediction maps" >
36 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pdf" format="pdf" /> 46 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pdf" format="pdf" />
37 </collection> 47 </collection>
38 </outputs> 48 </outputs>
39 <tests> 49 <tests>
40 <test> 50 <test>
41 <param name="enviro" value="ceamarc_env.csv"/> 51 <param name="enviro" value="ceamarc_env.tsv"/>
42 <param name="species_files" value="cnidaria_filtered.csv"/> 52 <param name="species_files" value="cnidaria_filtered.tsv"/>
43 <param name="abioticname" value="Carbo,Grav,Maxbearing,Maxmagnit,Meancurmag,Meansal,Meantheta,Mud,Prof,Rugosity,Sand,Seaice_prod,Sili,Slope,Standcurmag,Standsal,Standtheta"/> 53 <param name="abioticname" value="3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19"/>
54 <param name="dec_env" value="Dot"/>
55 <param name="dec_species" value="Comma"/>
44 <output_collection name='outputpred' type = "list" count="1"/> 56 <output_collection name='outputpred' type = "list" count="1"/>
45 <output_collection name='outputval' type = "list" count="1"/> 57 <output_collection name='outputval' type = "list" count="1"/>
46 <output_collection name='outputspdistri' type = "list" count="2"> 58 <output_collection name='outputspdistri' type = "list" count="2"/>
47 <element name="BRT- Actiniaria _pred_plot"> 59 <output_collection name='outputplots' type = "list" count="2"/>
48 <assert_contents>
49 <has_size value="76065" delta="10000"/>
50 </assert_contents>
51 </element>
52 </output_collection>
53 <output_collection name='outputplots' type = "list">
54 <element name="BRT- Actiniaria " >
55 <assert_contents>
56 <has_size value="16042" delta="1000"/>
57 </assert_contents>
58 </element>
59 </output_collection>
60 </test> 60 </test>
61 </tests> 61 </tests>
62 <help><![CDATA[ 62 <help><![CDATA[
63 ================== 63 ==================
64 **What it does ?** 64 **What it does ?**
69 69
70 =================== 70 ===================
71 **How to use it ?** 71 **How to use it ?**
72 =================== 72 ===================
73 73
74 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,... 74 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.
75 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. 75
76 .. class:: infomark
77 Your abiotic parameters must be present in your occurrence data file(s) and must be named the same as in your environment file.
78
79 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.
76 80
77 **Example of environmental data input :** 81 **Example of environmental data input :**
78 ----------------------------------------- 82 -----------------------------------------
79 83
80 +------+------+---------+------+--------------+-----+ 84 +------+------+---------+------+--------------+-----+
85 |139.22|-65.57| 0.88 |28.61 | 3.64 | ... | 89 |139.22|-65.57| 0.88 |28.61 | 3.64 | ... |
86 +------+------+---------+------+--------------+-----+ 90 +------+------+---------+------+--------------+-----+
87 | ... | ... | ... | ... | ... | ... | 91 | ... | ... | ... | ... | ... | ... |
88 +------+------+---------+------+--------------+-----+ 92 +------+------+---------+------+--------------+-----+
89 93
90
91 **Example of occurence data input :** 94 **Example of occurence data input :**
92 ------------------------------------- 95 -------------------------------------
93 96
94 +---------+----------+-----------+------------------------+-----------+-----+ 97 +---------+----------+-----------+------------------------+-----------+-----+------+--------------+-----+
95 | station | lat | long |Acanthorhabdus_fragilis | Acarnidae | ... | 98 | station | lat | long |Acanthorhabdus_fragilis | Acarnidae | ... | Grav | Maxbearing | ... |
96 +---------+----------+-----------+------------------------+-----------+-----+ 99 +---------+----------+-----------+------------------------+-----------+-----+------+--------------+-----+
97 | 1 |-65,999946|142,3360535| 0 | 1 | ... | 100 | 1 |-65,999946|142,3360535| 0 | 1 | ... |28.59 | 3.67 | ... |
98 +---------+----------+-----------+------------------------+-----------+-----+ 101 +---------+----------+-----------+------------------------+-----------+-----+------+--------------+-----+
99 | 10 |-66,335407| 141,3028 | 0 | 1 | ... | 102 | 10 |-66,335407| 141,3028 | 0 | 1 | ... |28.61 | 3.64 | ... |
100 +---------+----------+-----------+------------------------+-----------+-----+ 103 +---------+----------+-----------+------------------------+-----------+-----+------+--------------+-----+
101 | ... | ... | ... | ... | ... | ... | 104 | ... | ... | ... | ... | ... | ... | ... | ... | ... |
102 +---------+----------+-----------+------------------------+-----------+-----+ 105 +---------+----------+-----------+------------------------+-----------+-----+------+--------------+-----+
103
104
105
106 106
107 ]]></help> 107 ]]></help>
108 </tool> 108 </tool>
109 109
110 110