diff abims_xcms_retcor.xml @ 33:69b5a006fca1 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309

--- a/abims_xcms_retcor.xml	Tue Mar 06 04:03:16 2018 -0500
+++ b/abims_xcms_retcor.xml	Thu Mar 08 05:54:22 2018 -0500
@@ -43,7 +43,7 @@
     ]]></command>
 
     <inputs>
-        <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />
+        <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks, groupChromPeaks" />
         <conditional name="methods">
             <param name="method" type="select" label="Method to use for retention time correction" help="See the help section below" >
                 <option value="PeakGroups" selected="true">PeakGroups - retention time correction based on aligment of features (peak groups) present in most/all samples.</option>
@@ -128,8 +128,6 @@
     <outputs>
         <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.retcor.RData" from_work_dir="retcor.RData" />
         <data name="rawVSadjustedPdf" format="pdf"  label="${image.name[:-6]}_rawVSadjusted.retcor.Rplots.pdf" from_work_dir="raw_vs_adjusted_rt.pdf" />
-        <data name="ticsCorPdf"   format="pdf"  label="${image.name[:-6]}.retcor.TICs_adjusted.pdf" from_work_dir="TICs.pdf"/>
-        <data name="bpcsCorPdf"   format="pdf" label="${image.name[:-6]}.retcor.BPCs_adjusted.pdf" from_work_dir="BICs.pdf" />
     </outputs>
 
     <tests>
@@ -366,26 +364,37 @@
 Changelog/News
 --------------
 
-**Version 3.0.0.0 - 14/02/2018**
+**Version 3.0.0.0 - 08/03/2018**
+
+- UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed.
 
-- UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlining codes and methods
+- NEW: a bunch of new options: Obiwarp.(centerSample, response, distFun, gapInit, gapExtend, factorDiag, factorGap, localAlignment, initPenalty)
+
+- IMPROVEMENT: the advanced options are now in sections. It will allow you to access to all the parameters and to know their default values.
+
+- CHANGE: removing of the TIC and BPC plots. You can new use the dedicated tool "xcms plot chromatogram"
+
 
 **Version 2.1.1 - 29/11/2017**
 
 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
 
+
 **Version 2.1.0 - 03/02/2017**
 
 - IMPROVEMENT: xcms.retcor can deal with merged individual data
 
+
 **Version 2.0.8 - 22/12/2016**
 
 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph
 
+
 **Version 2.0.7 - 06/07/2016**
 
 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
 
+
 **Version 2.0.6 - 04/04/2016**
 
 - TEST: refactoring to pass planemo test using conda dependencies