# HG changeset patch # User lecorguille # Date 1455112189 18000 # Node ID 57dce001024cd3ba55ce30b75c7b1ba7067d5753 # Parent 3cc51ada0ffaa2063ab36fd1929613c66e137df4 Uploaded diff -r 3cc51ada0ffa -r 57dce001024c abims_CAMERA_annotateDiffreport.xml --- a/abims_CAMERA_annotateDiffreport.xml Wed Jan 20 03:41:48 2016 -0500 +++ b/abims_CAMERA_annotateDiffreport.xml Wed Feb 10 08:49:49 2016 -0500 @@ -1,4 +1,4 @@ - + CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition. @@ -7,7 +7,10 @@ Rscript xcms camera - camera_w4m_script + camera_w4m_script + CAMERA.r + graphicsmagick + convert @@ -42,6 +45,7 @@ #end if #if $options.option == "show": + runDiffreport TRUE eicmax $options.eicmax eicwidth $options.eicwidth value $options.value @@ -50,15 +54,6 @@ w $options.w mzdec $options.mzdec new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_ - #else - eicmax 0 - eicwidth 200 - value "into" - sortpval TRUE - h 480 - w 640 - mzdec 2 - new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_ #end if diff -r 3cc51ada0ffa -r 57dce001024c tool_dependencies.xml --- a/tool_dependencies.xml Wed Jan 20 03:41:48 2016 -0500 +++ b/tool_dependencies.xml Wed Feb 10 08:49:49 2016 -0500 @@ -6,7 +6,10 @@ - - + + + + +