Mercurial > repos > lecorguille > xcms_group
diff abims_xcms_group.xml @ 35:aeba79c716b1 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
| author | lecorguille |
|---|---|
| date | Wed, 05 Sep 2018 05:58:38 -0400 |
| parents | 68282292acc4 |
| children | eddc995c6df1 |
line wrap: on
line diff
--- a/abims_xcms_group.xml Fri Aug 31 09:01:20 2018 -0400 +++ b/abims_xcms_group.xml Wed Sep 05 05:58:38 2018 -0400 @@ -79,8 +79,8 @@ </inputs> <outputs> - <data name="xsetRData" format="rdata.xcms.group" label="${image.name[:-6]}.group.RData" from_work_dir="group.RData"/> - <data name="plotChromPeakDensity" format="pdf" label="${image.name[:-6]}.group.plotChromPeakDensity.pdf" from_work_dir="plotChromPeakDensity.pdf"/> + <data name="xsetRData" format="rdata.xcms.group" label="${image.name[:-6]}.groupChromPeaks.RData" from_work_dir="group.RData"/> + <data name="plotChromPeakDensity" format="pdf" label="${image.name[:-6]}.groupChromPeaks.plotChromPeakDensity.pdf" from_work_dir="plotChromPeakDensity.pdf"/> <expand macro="output_peaklist" function="group"/> </outputs> @@ -276,26 +276,26 @@ **Upstream tools** -========================= ================= ============================== ========== -Name output file format parameter -========================= ================= ============================== ========== -xcms.xcmsSet xset.RData rdata.xcms.findchrompeaks RData file -------------------------- ----------------- ------------------------------ ---------- -xcms.xcmsSet Merger xset.RData rdata.xcms.findchrompeaks RData file -------------------------- ----------------- ------------------------------ ---------- -xcms.retcor xset.RData rdata.xcms.retcor RData file -========================= ================= ============================== ========== +==================================== ======================== ============================== +Name Output file Format +==================================== ======================== ============================== +xcms.findChromPeaks Merger (single) xset.merged.RData rdata.xcms.findchrompeaks +------------------------------------ ------------------------ ------------------------------ +xcms.findChromPeaks (zip) ``*``.raw.xset.RData rdata.xcms.findchrompeaks +------------------------------------ ------------------------ ------------------------------ +xcms.adjustRtime ``*``.adjustRtime.RData rdata.xcms.retcor +==================================== ======================== ============================== **Downstream tools** -=========================== ================= ==================== -Name Output file Format -=========================== ================= ==================== -xcms.retcor xset.RData rdata.xcms.group ---------------------------- ----------------- -------------------- -xcms.fillPeaks xset.RData rdata.xcms.group -=========================== ================= ==================== +=========================== =========================== ==================== +Name Output file Format +=========================== =========================== ==================== +xcms.adjustRtime ``*``.groupChromPeaks.RData rdata.xcms.group +--------------------------- --------------------------- -------------------- +xcms.fillChromPeaks ``*``.groupChromPeaks.RData rdata.xcms.group +=========================== =========================== ==================== **General schema of the metabolomic workflow** @@ -337,11 +337,11 @@ Output files ------------ -xset.group.RData: rdata.xcms.group format +xset.groupChromPeaks.RData: rdata.xcms.group format - | Rdata file that will be necessary in the third and fourth step of the workflow (xcms.retcor and xcms.fillpeaks). + | RData file that will be necessary in the third and fourth step of the workflow (xcms.adjustRtime and xcms.fillChromPeaks). -xset.group.plotChromPeakDensity.pdf +xset.groupChromPeaks.plotChromPeakDensity.pdf | Density plot