Mercurial > repos > lecorguille > xcms_xcmsset

diff abims_xcms_xcmsSet.xml @ 38:e66eeca443e4 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
author lecorguille
date Wed, 05 Sep 2018 05:56:32 -0400
parents 9ada611dd63f
children e8d7395a70b2
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--- a/abims_xcms_xcmsSet.xml	Fri Aug 31 08:59:03 2018 -0400
+++ b/abims_xcms_xcmsSet.xml	Wed Sep 05 05:56:32 2018 -0400
@@ -408,24 +408,22 @@
 
 **Upstream tools**
 
-========================= ================= ============================== ==========
-Name                      output file       format                         parameter
-========================= ================= ============================== ==========
-MSnbase readMSData        raw.RData         rdata.msnbase.raw              RData file
-========================= ================= ============================== ==========
+========================= ================= ==============================
+Name                      Output file       Format
+========================= ================= ==============================
+MSnbase.readMSData        ``*``.raw.RData   rdata.msnbase.raw
+========================= ================= ==============================
 
 
 **Downstream tools**
 
-=========================== ==================== =================
-Name                        Output file          Format
-=========================== ==================== =================
-xcms.group                  xset.RData           rdata.xcms.raw
---------------------------- -------------------- -----------------
-PCA ellipsoid by factors    sampleMetadata.tsv   Tabular
---------------------------- -------------------- -----------------
-Anova                       sampleMetadata.tsv   Tabular
-=========================== ==================== =================
+==================================== ======================== =========================
+Name                                 Output file              Format
+==================================== ======================== =========================
+xcms.findChromPeaks Merger (single)  ``*``.raw.xset.RData     rdata.xcms.findchrompeaks
+------------------------------------ ------------------------ -------------------------
+xcms.groupChromPeaks (zip)           ``*``.raw.xset.RData     rdata.xcms.findchrompeaks
+==================================== ======================== =========================
 
 
 **Example of a metabolomic workflow**
@@ -474,14 +472,10 @@
 Output files
 ------------
 
-sampleMetadata.tsv
-
-    | Tabular file that contains for each sample, it's associated class and polarity (positive,negative and mixed).
-    | This file is necessary in the Anova and PCA step of the workflow.
-
 xset.RData: rdata.xcms.findchrompeaks format
 
-    | RData file that is necessary in the second step of the workflow "xcms.group".
+    | (single) RData files that is necessary in the second step of the workflow "xcms.groupChromPeaks" must to be merged using "xcms.findChromPeaks Merger"
+    | (zip) RData file that is necessary in the second step of the workflow "xcms.groupChromPeaks".
 
 ---------------------------------------------------