Mercurial > repos > tomnl > cameradims
changeset 2:1965e2b5a3d0 draft
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit d4159f1962ef3fe37dd4f3047e4050afe013c15a-dirty
| author | tomnl |
|---|---|
| date | Thu, 03 May 2018 05:21:32 -0400 |
| parents | df281fb2c279 |
| children | 11597f112979 |
| files | cameradims.R cameradims.xml |
| diffstat | 2 files changed, 11 insertions(+), 1 deletions(-) [+] |
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--- a/cameradims.R Mon Apr 23 05:45:23 2018 -0400 +++ b/cameradims.R Thu May 03 05:21:32 2018 -0400 @@ -79,6 +79,15 @@ df <- df[df$i>opt$intensity_filter,] + +if (opt$rule_type=='extended_large'){ + if(opt$polarity=='pos'){ + opt$rule_path <- read.csv(system.file("rules", "CAMERA_rules_PosFinal_PlusLi.csv", package = "cameraDIMS"), header=TRUE) + }else{ + opt$rule_path <- read.csv(system.file("rules", "CAMERA_rules_NegFinal_PlusLi.csv", package = "cameraDIMS"), header=TRUE) + } +} + cameraOut <- cameraDIMS(data=df, params_iso=paramiso, params_adduct=paramadduct,
--- a/cameradims.xml Mon Apr 23 05:45:23 2018 -0400 +++ b/cameradims.xml Thu May 03 05:21:32 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="cameradims" name="CAMERA_DIMS" version="0.1.13"> +<tool id="cameradims" name="CAMERA_DIMS" version="0.1.14"> <description>Modification of the R package CAMERA to work on DIMS data</description> <requirements> <requirement type="package" version="3.4.1">R</requirement> @@ -59,6 +59,7 @@ <param name="ruleset" type="select" label="Rules for adducts" > <option value="primary adducts" >Primary adducts ([M+Na]+, [M+K]+ and [M+NH4]+")</option> <option value="extended" selected="true" >Extended adducts</option> + <option value="extended_large" selected="true" >Extended adducts (large)</option> <option value="user" >Provide a csv file of the rules to use</option> </param> <when value="user">