Mercurial > repos > ecology > regionalgam_plot_trend

annotate plot-trend.xml @ 0:58ecd15e6836 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 04:04:43 -0400
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58ecd15e6836 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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1 <tool id="regionalgam_plot_trend" name="Plot abundance" version="@VERSION@">
58ecd15e6836 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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2 <description>with trend line</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 '$__tool_directory__/plot-trend.R'
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9 '$ab_indices' '$gls_model'
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10 '$output'
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11 '$output_tsv'
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12 ]]>
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13 </command>
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14 <inputs>
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15 <expand macro="rg_ab_indices"/>
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16 <expand macro="rg_gls_model"/>
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17 </inputs>
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18 <outputs>
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19 <data format="png" name="output" from_work_dir="output-plot-trend.png" />
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20 <data format="tabular" name="output_tsv" from_work_dir="s_trend.tsv" />
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="ab_indices" value="s_data_index.tabular"/>
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25 <param name="gls_model" value="s_gls-adju_rda.rda"/>
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26 <output name="output_tsv" ftype="tabular">
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27 <assert_contents>
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28 <has_line_matching expression="2003&#009;5.5699.*"/>
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29 <has_line_matching expression="2004&#009;5.6221.*"/>
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30 <has_line_matching expression="2005&#009;5.6915.*"/>
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31 <has_line line="&quot;year&quot;&#009;&quot;collated index&quot;"/>
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32 <has_n_columns n="2"/>
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33 </assert_contents>
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34 </output>
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38 ==========================
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39 Plot abundance trend
58ecd15e6836 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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40 ==========================
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41
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42 This tool is an implementation of the plot_trend function from RegionalGAM package: https://github.com/RetoSchmucki/regionalGAM/
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43
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44 This function plot abundance and add a trend line, it is the year effect estimated in the model.
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45
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46 |
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47
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48 **Outputs**
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49
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50 Trend estimation plotted in an image png file, and raw values in a tabular file.
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51
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52 ]]></help>
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53 <expand macro="rg_citation"/>
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54 </tool>