annotate ab_index_en.xml @ 1:b8fa05dbcff4 draft

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author mnhn65mo
date Fri, 03 Aug 2018 10:07:25 -0400
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1 <tool id="ab_index" name="Abundance index" version="0.1">
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2 <description>computation across species, sites and years</description>
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3 <requirements>
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4 <requirement type="package" version="3.4">r</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 Rscript '$__tool_directory__/ab_index.R' '$__tool_directory__/dennis_gam_initial_functions.R' '$input1' '$input2' '$output' ]]>
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8 </command>
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9 <inputs>
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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."/>
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11 <param format="tabular" name="input2" type="data" label="Flight curve output"/>
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12 </inputs>
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13 <outputs>
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14 <data format="tabular" name="output" from_work_dir="data.index" />
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15 </outputs>
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16 <tests>
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17 <test> <!-- FAILED -->
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18 <param name="input1" value="gatekeeper_CM"/>
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19 <param name="input2" value="flight_curve_result.tabular"/>
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20 <output name="output" value="data_index.tabular"/>
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21 </test>
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22 </tests>
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23 <help><![CDATA[
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24
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25 .. class:: infomark
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26
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27 ==========================
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28 Compute abundance index
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29 ==========================
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30
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31 This tool is an implementation of the abundance_index function from RegionalGAM package: https://github.com/RetoSchmucki/regionalGAM/
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32
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33 This function compute the Abundance Index across sites and years from your dataset and the regional flight curve.
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34
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35 ]]></help>
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36 <citations>
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37 <citation type="doi">10.1111/1365-2664.12561</citation>
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38 </citations>
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39 </tool>