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1 <tool id="flight-curve" name="Flight curve">
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2 <description>compute the regional expected pattern of abundance</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 '$__tool_directory__/flight_curve.R' '$__tool_directory__/dennis_gam_initial_functions.R' '$input' '$output' ]]>
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8 </command>
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9 <inputs>
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10 <param format="tabular,csv" name="input" 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 </inputs>
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12 <outputs>
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13 <data format="tabular" name="output" from_work_dir="pheno" />
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14 </outputs>
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15 <tests>
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16 <test> <!--FAILED-->
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17 <param name="input" value="gatekeeper_CM"/>
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18 <output name="output" value="flight_curve_result.tabular"/>
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19 </test>
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20 </tests>
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21 <help><![CDATA[
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22
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23 .. class:: infomark
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24
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25 ==========================
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26 Regional phenology
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27 ==========================
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28
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29 This tool is an implementation of the flight_curve function `RegionalGAM package: https://github.com/RetoSchmucki/regionalGAM/
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30 This function computes the annual phenology on a specific region.
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31
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32 ]]></help>
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33 <citations>
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34 <citation type="doi">10.1111/1365-2664.12561</citation>
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35 </citations>
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36 </tool>
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