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comparison ab_index_en.xml @ 0:5b126f770671 draft

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author mnhn65mo
date Fri, 03 Aug 2018 08:28:22 -0400
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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>