# HG changeset patch
# User ecology
# Date 1589232272 14400
# Node ID af4987066235ed87b8d0ee063ceb9c62a4b8e299
# Parent  22a784d2b0e0f115525fd4444b7749a215ba9f63
"planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit d49a4da1ffac1f33a15fdb7ae98827d0034a7879"

diff -r 22a784d2b0e0 -r af4987066235 FunctTrendSTOCGalaxy.r
--- a/FunctTrendSTOCGalaxy.r	Thu Apr 02 03:33:29 2020 -0400
+++ b/FunctTrendSTOCGalaxy.r	Mon May 11 17:24:32 2020 -0400
@@ -62,7 +62,7 @@
     if(length(colNull)>0){
         cat("\n",length(colNull)," Species removed from the analysis, abundance is always 0.\n\n",sep="")  #Espèces enlevées de l'analyse car abondance toujours égale a 0\n\n",sep="")
         #tabNull <- data.frame(Code_espece = colNull, nom_espece = tabsp[colNull,"nom"])
-        #cat("\n\n",sep="")
+        cat("Removed absent species : \n-",paste(colNull,collapse="\n-"),sep="")
         tab <- tab[,c("carre","annee",colConserve)]
     }
 ################################################################################ FIN DE LA PARTIE ISOLABLE
@@ -119,7 +119,7 @@
         cat("\n",length(colSupr)," Rare species removed from the analysis.\n\n",sep="")
         #tabSupr <- subset(tabsp,espece %in% colSupr ,select=c("espece","nom"))
         #tabSupr <- tabSupr[order(tabSupr$espece),]
-        #cat("\n\n",sep="")
+        cat("Removed rare species : \n-",paste(colSupr,collapse="\n-"),sep="")
         
     }
     if(length(colConserve)==0) {
diff -r 22a784d2b0e0 -r af4987066235 stoceps_macros.xml
--- a/stoceps_macros.xml	Thu Apr 02 03:33:29 2020 -0400
+++ b/stoceps_macros.xml	Mon May 11 17:24:32 2020 -0400
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@VERSION@">0.0.1</token>
+    <token name="@VERSION@">0.0.2</token>
     <xml name="reshape_requirements">
         <requirements>
             <requirement type="package" version="0.8.8">r-reshape</requirement>
@@ -53,11 +53,10 @@
         <param name="compute_ic" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="yes" label="Compute confidence intervals"/>
     </xml>
     <xml name="stoceps_filter_glmmtmb">
-        <filter> settings['advanced'] == 'advanced'</filter>
-        <filter> settings['method'] == 'glmmtmb'</filter>
+        <filter> method['model'] == 'glmmtmb'</filter>
     </xml>
     <xml name="stoceps_filter_gam">
-        <filter> settings['method'] == 'gam'</filter>
+        <filter> method['model'] == 'gam'</filter>
     </xml>
     <xml name="stoceps_bibref">
         <citations>