Mercurial > repos > lecorguille > xcms_retcor

diff abims_xcms_retcor.xml @ 37:35a20d7c9f33 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
author lecorguille
date Wed, 05 Sep 2018 05:59:21 -0400
parents 9714270678a7
children 67ee46ce9781
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line diff
--- a/abims_xcms_retcor.xml	Fri Aug 31 09:02:01 2018 -0400
+++ b/abims_xcms_retcor.xml	Wed Sep 05 05:59:21 2018 -0400
@@ -127,8 +127,8 @@
     </inputs>
 
     <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="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.adjustRtime.RData" from_work_dir="retcor.RData" />
+        <data name="rawVSadjustedPdf" format="pdf"  label="${image.name[:-6]}_rawVSadjusted.adjustRtime.Rplots.pdf" from_work_dir="raw_vs_adjusted_rt.pdf" />
     </outputs>
 
     <tests>
@@ -246,22 +246,22 @@
 
 **Upstream tools**
 
-========================= ================= ============================== ==========
-Name                      output file       format                         parameter
-========================= ================= ============================== ==========
-xcms.xcmsSet              xset.RData        rdata.xcms.findchrompeaks      RData file
-------------------------- ----------------- ------------------------------ ----------
-xcms.group                xset.group.RData  RData                          RData file
-========================= ================= ============================== ==========
+========================= ============================ ==============================
+Name                      Output file                  Format
+========================= ============================ ==============================
+xcms.findChromPeaks       raw.xset.RData               rdata.xcms.findchrompeaks
+------------------------- ---------------------------- ------------------------------
+xcms.groupChromPeaks      ``*``.groupChromPeaks.RData  rdata.xcms.group
+========================= ============================ ==============================
 
 
 **Downstream tools**
 
-=========================== ================== ========
-Name                        Output file        Format
-=========================== ================== ========
-xcms.group                  xset.retcor.RData  RData
-=========================== ================== ========
+=========================== ============================ ================
+Name                        Output file                  Format
+=========================== ============================ ================
+xcms.groupChromPeaks        ``*``.groupChromPeaks.RData  rdata.xcms.group
+=========================== ============================ ================
 
 
 **General schema of the metabolomic workflow**
@@ -296,9 +296,9 @@
 Output files
 ------------
 
-xset.group.retcor.RData: rdata.xcms.retcor format
+xset.groupChromPeaks.adjustRtime.RData: rdata.xcms.retcor format
 
-    | Rdata file that will be necessary in the **xcms.group** step of the workflow.
+    | Rdata file that will be necessary in the **xcms.groupChromPeaks** step of the workflow.
 
 
 ---------------------------------------------------