Mercurial > repos > ecology > stoc_mainglm

annotate mainglm.xml @ 0:df3ce23d0d23 draft

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"planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
author ecology
date Thu, 02 Apr 2020 03:32:56 -0400
parents
children a961be0a964f
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0
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
ecology
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1 <tool id="stoceps_glm" name="Estimate temporal population evolution" version="@VERSION@">
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"/>
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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"/>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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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 =================================================
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97 STOC Estimate species population evolution
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98 =================================================
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99
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100 **What it does**
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101
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102 Compute and plot evolution of species population, using a glm model.
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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 Original script information:
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146
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147 Estimate temporal evolution of population per species - ExeMainGlmGalaxy.r
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148 This script analyse the temporal evolution of species population and create graphical vizualisation.
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149
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150 Script needs the followings inputs :
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151 - stoc or community data filtered with at least 4 columns: year, site, species, and abundance with 0. Corresponding to "observed" or predicted 0 abundance. May come from the tools "Preprocess population data for evolution trend analyzes" (ExemakeTableAnalyseGalaxy.r) followed by "Filter species with rare and low abundances" (ExeFilteringRareLowabundSPGalaxy.r).
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152 - species details file with name and indicator status file with at least 2 columns: the species name or species ID (found in the community data or in stoc data) and his status as indicator species
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153 - file that stocks functions : "FunctTrendSTOCGalaxy.r"
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154
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155
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156 Arguments are :
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157 - spExclude: list of species (using the the species name or ID) that you want to exclude
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158 - assessIC : compute and show confidence interval in plots (TRUE / FALSE)
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159 - analysis custom id
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160
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161
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162 How to execute, eg :
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163 # all files are available in github repo
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164 #Exec id=mainglm, return IC on plot, no species excluded
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165 $ Rscript ExeMainGlmGalaxy.r' Datafilteredfortrendanalysis.tabular tabSpecies.csv 'mainglm' '' 'TRUE' FunctTrendSTOCGalaxy.r
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166
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167
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168 Outputs are created in an Output repo :
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169 GLM gives 1 graph per species and 2 tables:
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170 - nameofspecies_id.png (one plot per species)
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171 - tendanceGlobalEspece_id.tabular
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172 - variationsAnnuellesEspece_id.tabular
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173
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174
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175 R library needed
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176 r-lme4 version 1.1.18.1
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177 r-ggplot2 version 3.0.0
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178 r-speedglm version 0.3.2
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179 r-arm version 1.10.1
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180 r-reshape version 0.8.8
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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181 r-data.table version 1.12.0
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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182 r-reshape2 version 1.4.3
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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183 ]]></help>
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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184 <expand macro="stoceps_bibref" />
df3ce23d0d23 "planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit f82f897ab22464de40c878e17616333855814e25"
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185 </tool>