Merge pull request #17 from workflow4metabolomics/fix_ids

Fix ids

.gitignore

@@ -0,0 +1,2 @@
+tool_test_output.html
+tool_test_output.json

.travis.yml

@@ -13,5 +13,6 @@ before_install:
  - pip install planemo==0.37.0
 
 script:
-- planemo test --conda_auto_init --conda_auto_install --conda_dependency_resolution --galaxy_branch release_17.01 --no_cache_galaxy ${TRAVIS_BUILD_DIR}/galaxy/camera_suite/
+ - planemo lint ${TRAVIS_BUILD_DIR}/galaxy/camera_suite
+ - planemo test --conda_auto_init --conda_auto_install --conda_dependency_resolution --galaxy_branch release_17.01 --no_cache_galaxy ${TRAVIS_BUILD_DIR}/galaxy/camera_suite/
 

galaxy/camera_annotate/README.rst

@@ -2,6 +2,15 @@
 Changelog/News
 --------------
 
+**Version 2.1.6 - 09/02/2017**
+
+- BUGFIX: the diffreport ids didn't convert the rt in minute as the other export
+
+- UPDATE: the settings (digits, convertion in minutes) of the identifiants will no longer modify the native one. Because we want to be conservative and because it can be dangerous for the data integrity during a futur merge of the table, we decide to put those customization in a new column namecustom within the variableMetadata.
+
+- IMPROVEMENT: add the possibility to set the MZ digit within the identifiants
+
+
 **Version 2.1.5 - 21/04/2016**
 
 - UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0

galaxy/macro/macros.xml

@@ -19,20 +19,20 @@
     <token name="@COMMAND_CAMERA_SCRIPT@">
         LANG=C Rscript $__tool_directory__/CAMERA.r
     </token>
-    
+
     <!-- zipfile load for planemo test -->
     <token name="@COMMAND_ZIPFILE_LOAD@">
         #if $zipfile_load_conditional.zipfile_load_select == "yes":
             #if $zipfile_load_conditional.zip_file:
                 zipfile $zipfile_load_conditional.zip_file
             #end if
-        #end if    
+        #end if
     </token>
     <xml name="zipfile_load">
         <conditional name="zipfile_load_conditional">
             <param name="zipfile_load_select" type="select" label="Resubmit your zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." >
                 <option value="no" >no need</option>
-                <option value="yes" selected="peakgroups">yes</option>
+                <option value="yes" >yes</option>
             </param>
             <when value="no">
             </when>
@@ -41,11 +41,11 @@
             </when>
         </conditional>
     </xml>
-    
+
     <token name="@HELP_AUTHORS@">
 .. class:: infomark
 
-**Authors**  Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu 
+**Authors**  Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu
 
 .. class:: infomark
 

src/camera_w4m_script/CAMERA.r

@@ -16,7 +16,7 @@ for(p in pkgs) {
 }
 source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
 
-cat("\n\n"); 
+cat("\n\n");
 
 
 
@@ -42,7 +42,7 @@ if (listArguments[["xfunction"]] %in% c("combinexsAnnos")) {
   xaP=xa
   listOFlistArgumentsP=listOFlistArguments
   if (exists("xsAnnotate_object")) xaP=xsAnnotate_object
-  
+
   diffrepP=NULL
   if (exists("diffrep")) diffrepP=diffrep
 
@@ -119,12 +119,12 @@ if (thefunction %in% c("annotatediff"))  {
     suppressWarnings(unzip(zipfile, unzip="unzip"))
 
     #get the directory name
-    filesInZip=unzip(zipfile, list=T); 
+    filesInZip=unzip(zipfile, list=T);
     directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
     directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
     directory = "."
     if (length(directories) == 1) directory = directories
-    
+
     cat("files_root_directory\t",directory,"\n")
   }
 }