Mercurial > repos > ecology > stoc_mainglm

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"planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit d49a4da1ffac1f33a15fdb7ae98827d0034a7879"
author ecology
date Mon, 11 May 2020 17:18:16 -0400
parents df3ce23d0d23
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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a961be0a964f "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit d49a4da1ffac1f33a15fdb7ae98827d0034a7879"
ecology
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1 <tool id="stoceps_glm" name="Estimate temporal population variation" version="@VERSION@">
0
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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2 <description>by species</description>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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3 <macros>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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4 <import>stoceps_macros.xml</import>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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5 </macros>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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6 <expand macro="mainglm_requirements"/>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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7 <command detect_errors="exit_code"><![CDATA[
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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8 Rscript
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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9 '$__tool_directory__/ExeMainGlmGalaxy.r'
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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10 '$input'
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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11 '$inputtabSpecies'
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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12 #if $settings.advanced=='advanced'
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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13 'mainglm'
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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14 $settings.sp_code
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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15 $settings.compute_ic
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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16 #else
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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17 'mainglm'
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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18 ''
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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19 'TRUE'
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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20 #end if
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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21 '$__tool_directory__/FunctTrendSTOCGalaxy.r'
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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22
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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23
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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24 '$yearly_variations'
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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25 '$global_tendencies'
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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26 #if $settings.advanced=='advanced'
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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27 #if $settings.return_plot=='plot'
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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28 '$plots'
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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29 #end if
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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30 #end if
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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31 ]]>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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32 </command>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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33 <inputs>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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34 <expand macro="stoceps_input_filtered"/>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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35 <param name="inputtabSpecies" type="data" format="tabular" label="Species file" help="Input species tabular file, with 5 columns (species ID, species name, species scientific name, specialization status)." />
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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36 <conditional name="settings">
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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37 <expand macro="stoceps_advanced_params_select"/>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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38 <when value="advanced">
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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39 <param name="sp_code" type="select" label="Filter species to exclude" help="Create a subsample by selecting species codes you don't want to use." multiple="true" optional="true">
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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40 <options from_dataset="input">
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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41 <column name="value" index="2"/>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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42 <filter type="unique_value" name="espece" column="2"/>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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43 </options>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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44 <sanitizer>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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45 <valid initial="string.printable">
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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46 <remove value="&quot;"/>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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47 </valid>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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48 </sanitizer>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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49 </param>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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50 <param name="return_plot" type="boolean" truevalue="plot" falsevalue="noplot" checked="yes" help="All the figures will be stocked in a datacollection" label="Return visualizations."/>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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51 <expand macro="stoceps_compute_ic"/>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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52 </when>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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53 </conditional>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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54 </inputs>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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55 <outputs>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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56 <data name="yearly_variations" from_work_dir="Output/mainglm/variationsAnnuellesEspece_mainglm.tabular" format="tabular" label="GLM - Yearly variations on ${on_string}"/>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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57 <data name="global_tendencies" from_work_dir="Output/mainglm/tendanceGlobalEspece_mainglm.tabular" format="tabular" label="GLM - Global species tendencies on ${on_string}"/>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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58 <collection type="list" name="plots">
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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59 <filter>return_plot == 'plot'</filter>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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60 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" visible="false" format="png" directory="Output/mainglm/"/>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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61 </collection>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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62 </outputs>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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63 <tests>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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64 <test>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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65 <param name="inputtabSpecies" value="tabSpecies.csv"/>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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66 <param name="input" value="Datafilteredfortrendanalysis.tabular"/>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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67 <param name="advanced" value="simple"/>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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68 <output name="yearly_variations">
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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69 <assert_contents>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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70 <has_n_lines n="37"/>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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71 <has_n_columns n="14"/>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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72 <has_size value="3247" delta="100"/>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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73 </assert_contents>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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74 </output>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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75 <output name="global_tendencies">
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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76 <assert_contents>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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77 <has_n_lines n="3"/>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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78 <has_size value="468" delta="50"/>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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79 </assert_contents>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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80 </output>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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81 <output_collection name="plots" type="list" count="2">
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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82 <element name="ALAARV_mainglm">
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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83 <assert_contents>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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84 <has_text text="PNG"/>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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85 </assert_contents>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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86 </element>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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87 <element name="PARCAE_mainglm">
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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88 <assert_contents>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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89 <has_text text="PNG"/>
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90 </assert_contents>
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91 </element>
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92 </output_collection>
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93 </test>
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94 </tests>
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95 <help><![CDATA[
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96 =================================================
1
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97 STOC Estimate species population variation
0
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98 =================================================
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99
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100 **What it does**
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101
1
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102 Compute and plot trends of species population, using a glm model of formula : abundance ~ site + year. Testing the effect of site and year on abundance with quasipoisson distribution.
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103
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104 |
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105
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106 **Input description**
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107
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108 A first mandatory tabular file with species count shaped and filtered with the STOCs 'Preprocess population data' ans 'Filter species' tools.
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109
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110 A second optional "species details file" containing indicator status of species (Column with TRUE or FALSE), including the species name or ID (one used in the species count data). If you are not analyzing the default STOC data, you need one file of this kind.
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111
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112 Example dataset ::
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113
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114 "espece" "nom" "nomscientific" "indicateur" "specialisation"
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115 "ACCGEN" "Autour des palombes" "Accipiter gentilis" FALSE ""
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116 "ACCNIS" "Epervier d'Europe" "Accipiter nisus" FALSE ""
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117 "ACRARU" "Rousserolle turdoïde" "Acrocephalus arundinaceus" FALSE ""
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118 "ACRMEL" "Lusciniole à moustaches" "Acrocephalus melanopogon" FALSE ""
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119 "ACRPAL" "Phragmite aquatique" "Acrocephalus paludicola" FALSE ""
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120 "ACRRIS" "Rousserolle verderolle" "Acrocephalus palustris" FALSE ""
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121 "ACRSCH" "Phragmite des joncs" "Acrocephalus schoenobaenus" FALSE ""
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122 "ACRSCI" "Rousserolle effarvatte" "Acrocephalus scirpaceus" FALSE ""
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123 "ACTHYP" "Chevalier guignette" "Actitis hypoleucos" FALSE ""
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124 "AEGCAU" "Mésange à longue queue" "Aegithalos caudatus" FALSE ""
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125 "AEGFUN" "Chouette de Tengmalm" "Aegolius funereus" FALSE ""
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126 "AIXGAL" "Canard mandarin" "Aix galericulata" FALSE ""
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127 "AIXSPO" "Canard carolin" "Aix sponsa" FALSE ""
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128 "ALAARV" "Alouette des champs" "Alauda arvensis" TRUE "milieux agricoles"
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129
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130 |
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131
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132 **Output**
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133
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134 For each species present in the data, a plot of populations trend is created and stocked in a common data collection.
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135
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136 Two tabular files are created, they describe global tendencies and yearly variations.
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137
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138 |
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139
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140 **Source**
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141
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142 UnPublished script available at http://www.vigienature.fr/sites/vigienature/files/atoms/files/analysestoceps_0.zip
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143 the first version written by Romain Lorrilliere
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144
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145 ]]></help>
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146 <expand macro="stoceps_bibref" />
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147 </tool>