diff mainglm.xml @ 1:a961be0a964f draft default tip

"planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit d49a4da1ffac1f33a15fdb7ae98827d0034a7879"

--- a/mainglm.xml	Thu Apr 02 03:32:56 2020 -0400
+++ b/mainglm.xml	Mon May 11 17:18:16 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="stoceps_glm" name="Estimate temporal population evolution" version="@VERSION@">
+<tool id="stoceps_glm" name="Estimate temporal population variation" version="@VERSION@">
     <description>by species</description>
     <macros>
         <import>stoceps_macros.xml</import>
@@ -94,12 +94,12 @@
     </tests>
     <help><![CDATA[
 =================================================
-STOC Estimate species population evolution
+STOC Estimate species population variation
 =================================================
 
 **What it does**
 
-Compute and plot evolution of species population, using a glm model.
+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.
 
 |
 
@@ -142,44 +142,6 @@
 UnPublished script available at http://www.vigienature.fr/sites/vigienature/files/atoms/files/analysestoceps_0.zip
 the first version written by Romain Lorrilliere
 
-Original script information:
-
-Estimate temporal evolution of population per species - ExeMainGlmGalaxy.r
-This script analyse the temporal evolution of species population and create graphical vizualisation.
-
-Script needs the followings inputs :
- - 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).
- - 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
- - file that stocks functions : "FunctTrendSTOCGalaxy.r"
-
-
-Arguments are :
- - spExclude: list of species (using the the species name or ID) that you want to exclude
- - assessIC : compute and show confidence interval in plots (TRUE / FALSE)
- - analysis custom id
-
-
-How to execute, eg :
- # all files are available in github repo
- #Exec id=mainglm, return IC on plot, no species excluded
- $ Rscript ExeMainGlmGalaxy.r' Datafilteredfortrendanalysis.tabular tabSpecies.csv 'mainglm' '' 'TRUE' FunctTrendSTOCGalaxy.r
-
-
-Outputs are created in an Output repo :
-GLM gives 1 graph per species and 2 tables:
-- nameofspecies_id.png (one plot per species)
-- tendanceGlobalEspece_id.tabular
-- variationsAnnuellesEspece_id.tabular
-
-
-R library needed
-r-lme4  version 1.1.18.1
-r-ggplot2  version 3.0.0
-r-speedglm  version 0.3.2
-r-arm  version 1.10.1
-r-reshape  version 0.8.8
-r-data.table  version 1.12.0
-r-reshape2   version 1.4.3
   ]]></help>
   <expand macro="stoceps_bibref" />
 </tool>