Mercurial > repos > lecorguille > xcms_fillpeaks

diff abims_xcms_fillPeaks.xml @ 37:9eefb022a189 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
author lecorguille
date Wed, 05 Sep 2018 06:00:18 -0400
parents d8bac1291473
children a3e80894efd3
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--- a/abims_xcms_fillPeaks.xml	Fri Aug 31 09:02:49 2018 -0400
+++ b/abims_xcms_fillPeaks.xml	Wed Sep 05 06:00:18 2018 -0400
@@ -44,7 +44,7 @@
     </inputs>
 
     <outputs>
-        <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" from_work_dir="fillpeaks.RData" />
+        <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillChromPeaks.RData" from_work_dir="fillpeaks.RData" />
         <expand macro="output_peaklist" function="fillpeaks" />
     </outputs>
 
@@ -155,22 +155,22 @@
 
 **Upstream tools**
 
-========================= ================= ================== ==========
-Name                      output file       format             parameter
-========================= ================= ================== ==========
-xcms.group                xset.group.RData  rdata.xcms.group   RData file
-========================= ================= ================== ==========
+========================= ============================ ==================
+Name                      Output file                  Format
+========================= ============================ ==================
+xcms.groupChromPeaks      ``*``.groupChromPeaks.RData  rdata.xcms.group
+========================= ============================ ==================
 
 
 **Downstream tools**
 
-=========================== ================== =======================
-Name                        Output file        Format
-=========================== ================== =======================
-CAMERA.annotate             xset.retcor.RData  rdata.xcms.fillpeaks
---------------------------- ------------------ -----------------------
-xcms.summary                xset.retcor.RData  rdata.xcms.fillpeaks
-=========================== ================== =======================
+=========================== =========================== =======================
+Name                        Output file                 Format
+=========================== =========================== =======================
+CAMERA.annotate             ``*``.fillChromPeaks.RData  rdata.xcms.fillpeaks
+--------------------------- --------------------------- -----------------------
+xcms.process_history        ``*``.fillChromPeaks.RData  rdata.xcms.fillpeaks
+=========================== =========================== =======================
 
 
 **General schema of the metabolomic workflow**
@@ -197,7 +197,7 @@
 
 xset.fillPeaks.RData : rdata.xcms.fillpeaks format
 
-    | Rdata file that will be used in the **CAMERA.annotate** or **xcms.summary** step of the workflow.
+    | Rdata file that will be used in the **CAMERA.annotate** or **xcms.process_history** step of the workflow.
 
 @HELP_PEAKLIST_OUTPUT@