Mercurial > repos > ecology > regionalgam_flight_curve

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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 03:59:27 -0400
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1767753d578f planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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1 <tool id="regionalgam_flight_curve" name="Flight curve" version="@VERSION@">
1767753d578f planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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2 <description>compute the regional expected pattern of 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 <requirements>
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7 <requirement type="package" version="1.8_28">r-mgcv</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 Rscript '$__tool_directory__/flight-curve.R'
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11 '$__tool_directory__/dennis-gam-initial-functions.R'
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12 '$count_file'
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13 $minvisit
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14 $minoccur
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15 '$output'
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16 ]]>
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17 </command>
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18 <inputs>
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19 <expand macro="rg_count_file"/>
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20 <param name="minvisit" type="integer" value="3" min="0" label="Minimum number of visits" help="Subset the data with a minimum number of visits." />
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21 <param name="minoccur" type="integer" value="2" min="0" label="Minimum number of occurences" help="Subset the data with a minimum number of occurences."/>
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22 </inputs>
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23 <outputs>
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24 <data format="tabular" name="output" from_work_dir="pheno" />
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="count_file" value="gatekeeper_CM_200320042005"/>
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29 <param name="minvisit" value="3"/>
1767753d578f planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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30 <param name="minoccur" value="2"/>
1767753d578f planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
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31 <output name="output" ftype="tabular">
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32 <assert_contents>
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33 <has_line line="&quot;species&quot;&#009;&quot;year&quot;&#009;&quot;week&quot;&#009;&quot;DAYNO&quot;&#009;&quot;DAYNO_adj&quot;&#009;&quot;nm&quot;"/>
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34 <has_n_columns n="6"/>
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35 <has_text_matching expression="&quot;Pyronia&#032;tithonus&quot;&#009;2003&#009;[0-9]&#009;[0-9]&#009;[0-9]&#009;[0-9]"/>
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36 </assert_contents>
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37 </output>
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38 </test>
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39 </tests>
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40 <help><![CDATA[
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41 ==========================
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42 Regional phenology
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43 ==========================
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44
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45 This tool is an implementation of the flight_curve function RegionalGAM package: https://github.com/RetoSchmucki/regionalGAM/
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46
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47 This function computes the annual phenology on a specific region.
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48
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49 The output tabular file can be used to impute expected count values with the abundance index computation tool.
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50
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51 |
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52
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53 **Outputs**
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54
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55 Regional expected pattern computation in a tabular file.
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56 ]]></help>
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57 <expand macro="rg_citation"/>
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58 </tool>