Mercurial > repos > ecology > regionalgam_glmmpql

annotate glmmpql.xml @ 0:0f58d28d1603 draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
author ecology
date Thu, 20 Jun 2019 04:00:24 -0400
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0f58d28d1603 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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1 <tool id="regionalgam_glmmpql" name="Expected temporal trend" version="@VERSION@">
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2 <description>of species abundance</description>
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3 <macros>
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4 <import>regionalgam_macros.xml</import>
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5 </macros>
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6 <expand macro="rg_nlme_mass_requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 Rscript '$__tool_directory__/glmmpql.R'
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9 '$ab_indices'
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10 '$output' '$output2'
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11 ]]>
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12 </command>
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13 <inputs>
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14 <expand macro="rg_ab_indices"/>
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15 </inputs>
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16 <outputs>
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17 <data format="png" name="output" from_work_dir="output-plot.png" />
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18 <data format="tabular" name="output2" from_work_dir="output-glmmpql" />
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="ab_indices" value="s_data_index.tabular"/>
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23 <output name="output2" ftype="tabular">
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24 <assert_contents>
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25 <has_line_matching expression="5.5.*"/>
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26 <has_line line="&quot;x&quot;"/>
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27 <has_n_columns n="1"/>
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28 </assert_contents>
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29 </output>
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30 </test>
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31 </tests>
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32 <help><![CDATA[
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33 =====================================
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34 Temporal trends of species abundance
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35 =====================================
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37 This tool is an implementation of the glmmpql function from RegionalGAM package: https://github.com/RetoSchmucki/regionalGAM/
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39 This function computes a collated index for each year and estimates the temporal trend.
0f58d28d1603 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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41 A collated index correspond to the expected value for a year, when taking into account the variation contained among sites.
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43 Here we also add an autoregressive term to account for temporal autocorrelation in the time series.
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45 |
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47 **Outputs**
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49 The tool returns the collated index in tabular format.
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51 It also and plot it against year for visualization in an output png file.
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53 ]]></help>
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54 <expand macro="rg_citation"/>
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55 </tool>