|
0
|
1 <tool id="ab_index" name="Abundance index" version="0.1">
|
|
|
2 <description>computation across species, sites and years</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="3.4">r</requirement>
|
|
|
5 </requirements>
|
|
|
6 <command detect_errors="exit_code"><![CDATA[
|
|
|
7 Rscript '$__tool_directory__/ab_index.R' '$__tool_directory__/dennis_gam_initial_functions.R' '$input1' '$input2' '$output' ]]>
|
|
|
8 </command>
|
|
|
9 <inputs>
|
|
|
10 <param format="tabular,csv" name="input1" type="data" label="Count file" help="The file must contain the SPECIES, SITE, YEAR, MONTH, DAY and COUNT columns. CSV file separator ',' or tab."/>
|
|
|
11 <param format="tabular" name="input2" type="data" label="Flight curve output"/>
|
|
|
12 </inputs>
|
|
|
13 <outputs>
|
|
|
14 <data format="tabular" name="output" from_work_dir="data.index" />
|
|
|
15 </outputs>
|
|
|
16 <tests>
|
|
|
17 <test> <!-- FAILED -->
|
|
|
18 <param name="input1" value="gatekeeper_CM"/>
|
|
|
19 <param name="input2" value="flight_curve_result.tabular"/>
|
|
|
20 <output name="output" value="data_index.tabular"/>
|
|
|
21 </test>
|
|
|
22 </tests>
|
|
|
23 <help><![CDATA[
|
|
|
24
|
|
|
25 .. class:: infomark
|
|
|
26
|
|
|
27 ==========================
|
|
|
28 Compute abundance index
|
|
|
29 ==========================
|
|
|
30
|
|
|
31 This tool is an implementation of the abundance_index function from `RegionalGAM package: https://github.com/RetoSchmucki/regionalGAM/
|
|
|
32
|
|
|
33 This function compute the Abundance Index across sites and years from your dataset and the regional flight curve.
|
|
|
34
|
|
|
35 ]]></help>
|
|
|
36 <citations>
|
|
|
37 <citation type="doi">10.1111/1365-2664.12561</citation>
|
|
|
38 </citations>
|
|
|
39 </tool>
|
