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annotate gls.xml @ 0:a79f5f0f17ad 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 04:02:41 -0400
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a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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1 <tool id="regionalgam_gls" name="Model temporal trend" version="@VERSION@">
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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2 <description>with a simple linear regression</description>
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3 <macros>
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4 <import>regionalgam_macros.xml</import>
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5 </macros>
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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6 <expand macro="rg_nlme_mass_requirements"/>
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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7 <command detect_errors="exit_code"><![CDATA[
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8 Rscript '$__tool_directory__/gls.R'
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9 '$collated_index' '$ab_indices'
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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10 '$output' '$output2'
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11 ]]>
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12 </command>
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13 <inputs>
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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14 <expand macro="rg_collated_index"/>
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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15 <expand macro="rg_ab_indices"/>
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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16 </inputs>
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17 <outputs>
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18 <data format="txt" name="output" from_work_dir="mod-summary.txt" />
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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19 <data format="rdata" name="output2" from_work_dir="mod.rda" />
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="collated_index" value="s_glmmpql.tabular"/>
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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24 <param name="ab_indices" value="s_data_index.tabular"/>
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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25 <output name="output" file="s_gls_sum.txt"/>
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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26 <output name="output2" file="s_gls_rda.rda"/>
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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27 </test>
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28 </tests>
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29 <help><![CDATA[
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30 ==========================
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31 Model temporal trend
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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32 ==========================
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33
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34 This tool is an implementation of the gls function from RegionalGAM package: https://github.com/RetoSchmucki/regionalGAM/
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36 This function model temporal trend with a simple linear regression.
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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38 |
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39
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40 **Outputs**
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41
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42 The tool returns the linear regression model in an Rdata file.
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43
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44 It also returns a summary of this model in txt format.
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45 ]]></help>
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46 <expand macro="rg_citation"/>
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47 </tool>