# HG changeset patch
# User lecorguille
# Date 1461596819 14400
# Node ID 77a191e37af465926d0c051cb1bcaaea09b502a3
# Parent  e98ca7f0dcbda2e86fb37ab335984b4fd4ba4fe7
planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b

diff -r e98ca7f0dcbd -r 77a191e37af4 CAMERA.r
--- a/CAMERA.r	Fri Apr 22 08:36:37 2016 -0400
+++ b/CAMERA.r	Mon Apr 25 11:06:59 2016 -0400
@@ -39,7 +39,8 @@
 
 if (listArguments[["xfunction"]] %in% c("combinexsAnnos")) {
   load(listArguments[["image_pos"]])
-  xaP=xa  
+  xaP=xa
+  listOFlistArgumentsP=listOFlistArguments
   if (exists("xsAnnotate_object")) xaP=xsAnnotate_object
   
   diffrepP=NULL
@@ -47,6 +48,7 @@
 
   load(listArguments[["image_neg"]])
   xaN=xa
+  listOFlistArgumentsN=listOFlistArguments
   if (exists("xsAnnotate_object")) xaN=xsAnnotate_object
 
   diffrepN=NULL
@@ -158,7 +160,7 @@
 }
 
 if (thefunction %in% c("combinexsAnnos")) {
-  cAnnot=combinexsAnnos_function(xaP=xaP,xaN=xaN,diffrepP=diffrepP,diffrepN=diffrepN,convert_param=listArguments[["convert_param"]],pos=listArguments[["pos"]],tol=listArguments[["tol"]],ruleset=listArguments[["ruleset"]],keep_meta=listArguments[["keep_meta"]],variableMetadataOutput=variableMetadataOutput)
+  cAnnot=combinexsAnnos_function(xaP=xaP,xaN=xaN,listOFlistArgumentsP=listOFlistArgumentsP,listOFlistArgumentsN=listOFlistArgumentsN,diffrepP=diffrepP,diffrepN=diffrepN,convert_param=listArguments[["convert_param"]],pos=listArguments[["pos"]],tol=listArguments[["tol"]],ruleset=listArguments[["ruleset"]],keep_meta=listArguments[["keep_meta"]],variableMetadataOutput=variableMetadataOutput)
 }
 
 dev.off()
diff -r e98ca7f0dcbd -r 77a191e37af4 README.rst
--- a/README.rst	Fri Apr 22 08:36:37 2016 -0400
+++ b/README.rst	Mon Apr 25 11:06:59 2016 -0400
@@ -40,7 +40,7 @@
 Test Status
 -----------
 
-Planemo test using conda: failed
+Planemo test using conda: passed
 
 Planemo test using source env.sh: passed
 
diff -r e98ca7f0dcbd -r 77a191e37af4 lib.r
--- a/lib.r	Fri Apr 22 08:36:37 2016 -0400
+++ b/lib.r	Mon Apr 25 11:06:59 2016 -0400
@@ -114,7 +114,7 @@
 }
 
 
-combinexsAnnos_function <- function(xaP, xaN, diffrepP=NULL,diffrepN=NULL,convert_param=FALSE,pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, variableMetadataOutput="variableMetadata.tsv"){
+combinexsAnnos_function <- function(xaP, xaN, listOFlistArgumentsP,listOFlistArgumentsN, diffrepP=NULL,diffrepN=NULL,convert_param=FALSE,pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, variableMetadataOutput="variableMetadata.tsv"){
 
   #Load the two Rdata to extract the xset objects from positive and negative mode
   cat("\tObject xset from positive mode\n")
@@ -143,12 +143,15 @@
 
   if(pos){
     xa=xaP
+    listOFlistArgumentsP=listOFlistArguments
     mode="neg. Mode"
   } else {
     xa=xaN
+    listOFlistArgumentsN=listOFlistArguments
     mode="pos. Mode"
   }
-  peakList=getPeaklist(xa,intval=listArguments[["intval"]])
+  intval = "into"; for (steps in names(listOFlistArguments)) { if (!is.null(listOFlistArguments[[steps]]$intval)) intval = listOFlistArguments[[steps]]$intval }
+  peakList=getPeaklist(xa,intval=intval)
   peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
   variableMetadata=cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup",mode)]);
   variableMetadata=variableMetadata[,!(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))]
diff -r e98ca7f0dcbd -r 77a191e37af4 planemo_test.sh
--- a/planemo_test.sh	Fri Apr 22 08:36:37 2016 -0400
+++ b/planemo_test.sh	Mon Apr 25 11:06:59 2016 -0400
@@ -1,3 +1,10 @@
+# Example of planemo command to launch test
+
+# Note: --galaxy_branch "dev" is set to deal with zip file
+
+
+# -- Use of installed package environments
+# after having installing package on a local galaxy instance
 source /w/galaxy/dev/shed_tools_tool_dependency_dir/R/3.1.2/iuc/package_r_3_1_2/1ca39eb16186/env.sh
 source /w/galaxy/dev/shed_tools_tool_dependency_dir/bioconductor-camera/1.22.0/lecorguille/package_bioconductor_camera_1_22_0/22cec61d66c2/env.sh
 planemo test --install_galaxy --galaxy_branch "dev"
@@ -6,6 +13,16 @@
 #abims_CAMERA_annotateDiffreport[0]: passed
 
 
+# -- Use of conda dependencies
+planemo conda_init --conda_prefix /tmp/mc
+planemo conda_install --conda_prefix /tmp/mc . 
+planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution --galaxy_branch "dev"
+
+#All 1 test(s) executed passed.
+#abims_CAMERA_annotateDiffreport[0]: passed
+
+
+# -- Use of shed_test
 planemo shed_test --install_galaxy -t testtoolshed --galaxy_branch "dev"
 
 #All 1 test(s) executed passed.