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1 <tool id="glmmpql" name="Expected temporal trend" version="0.1">
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2 <description>of species abundance</description>
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3 <requirements>
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4 <requirement type="package" version="3.1_131">r-nlme</requirement>
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5 <requirement type="package" version="7.3_48">r-mass</requirement>
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6 <requirement type="package" version="0.9.10">xorg-libxrender</requirement>
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7 <requirement type="package" version="1.2.2">xorg-libsm</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 Rscript '$__tool_directory__/glmmpql.R' '$input1' '$output' '$output2' ]]>
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11 </command>
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12 <inputs>
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13 <param format="tabular" name="input1" type="data" label="Tabular file generated by the ab_index tool"/>
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14 </inputs>
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15 <outputs>
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16 <data format="png" name="output" from_work_dir="output-plot.png" />
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17 <data format="tabular" name="output2" from_work_dir="output-glmmpql" />
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="input1" value="data_index.tabular"/>
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22 <param name="output" value="glmmpql-plot.png"/>
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23 <output name="output2" value="glmmpql.tabular"/>
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24 </test>
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25 </tests>
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26 <help><![CDATA[
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27
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28 .. class:: infomark
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29
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30 ==========================
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31 Temporal trends of species abundance
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32 ==========================
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33
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34 This tool is an implementation of the glmmpql function from `RegionalGAM package: https://github.com/RetoSchmucki/regionalGAM/
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35 This function computes a collated index for each year and estimates the temporal trend.
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36 ]]></help>
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37 <citations>
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38 <citation type="doi">10.1111/1365-2664.12561</citation>
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39 </citations>
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40 </tool>
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