Mercurial > repos > lecorguille > camera_annotate
changeset 15:77a191e37af4 draft
planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
| author | lecorguille |
|---|---|
| date | Mon, 25 Apr 2016 11:06:59 -0400 |
| parents | e98ca7f0dcbd |
| children | af2d29943e97 |
| files | CAMERA.r README.rst lib.r planemo_test.sh |
| diffstat | 4 files changed, 27 insertions(+), 5 deletions(-) [+] |
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--- 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()
--- 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
--- 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)))]
--- 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.